This is a list of selected publications by EVBC members. For all virus related publications published by members of the EVBC (from the time of being member) see our Google Scholar account. For a full list of publications from EVBC members, see PubMed.

Authors: Type:

2021

  • [DOI] M. Möckel, V. M. Corman, M. S. Stegemann, J. Hofmann, A. Stein, T. C. Jones, P. Gastmeier, J. Seybold, R. Offermann, U. Bachmann, T. Lindner, W. Bauer, C. Drosten, A. Rosen, and R. Somasundaram, “SARS-CoV-2 antigen rapid immunoassay for diagnosis of COVID-19 in the emergency department.,” Biomarkers, p. 1–13, 2021.
    [Bibtex]
    @Article{Moeckel:21,
    author = {Möckel, Martin and Corman, Victor M. and Stegemann, Miriam S. and Hofmann, Jörg and Stein, Angela and Jones, Terry C. and Gastmeier, Petra and Seybold, Joachim and Offermann, Ralf and Bachmann, Ulrike and Lindner, Tobias and Bauer, Wolfgang and Drosten, Christian and Rosen, Alexander and Somasundaram, Rajan},
    journal = {{Biomarkers}},
    title = {{SARS-CoV-2} Antigen Rapid Immunoassay for Diagnosis of {COVID-19} in the Emergency Department.},
    year = {2021},
    pages = {1--13},
    abstract = {In the emergency department (ED) setting, rapid testing for SARS-CoV-2 is likely associated with advantages to patients and healthcare workers, for example enabling early but rationale use of limited isolation resources. Most recently, several SARS-CoV-2 rapid point-of-care antigen tests (AGTEST) became available. There is a growing need for data regarding their clinical utility and performance in the diagnosis of SARS-CoV-2 infection in the real life setting of 5 EDs. We implemented AGTEST (here: Roche/SD Biosensor) in all four adult and the one pediatric EDs at Charité - Universitätsmedizin Berlin in our diagnostic testing strategy. Test indication was limited to symptomatic suspected COVID-19 patients. Detailed written instructions on who to test were distributed and testing personnel were trained in proper specimen collection and handling. In each suspected COVID-19 patient, two sequential deep oro-nasopharyngeal swabs were obtained for viral tests. The first swab was collected for nucleic acid testing through SARS-CoV-2 Real-Time Reverse Transcriptase (rt)-PCR diagnostic panel (PCRTEST) in the central laboratory. The second swab was collected to perform the AGTEST. Analysis of routine data was prospectively planned and data were retrieved from the medical records after the inclusion period in the adult or pediatric ED. Diagnostic performance was calculated using the PCRTEST as reference standard. False negative and false positive AGTEST results were analyzed individually and compared with viral concentrations derived from the calibrated PCRTEST. We included n = 483 patients including n= 202 from the pediatric ED. N = 10 patients had to be excluded due to missing data and finally n = 473 patients were analyzed. In the adult cohort, the sensitivity of the AGTEST was 75.3 (95%CI: 65.8/83.4)% and the specificity was 100 (95%CI: 98.4/100)% with a SARS-CoV-2 prevalence of 32.8%; the positive predictive value was 100 (95%CI: 95.7/100)% and the negative predictive value 89.2 (95%CI: 84.5/93.9)%. In the pediatric cohort the sensitivity was 72.0 (95%CI: 53.3/86.7)%, the specificity was 99.4 (95%CI:97.3/99.9)% with a prevalence of 12.4%; the positive predictive value was 94.7 (95%CI: 78.3/99.7)% and the negative predictive value was 96.2 (95%CI:92.7/98.3)%.Thus, n = 22 adult and n = 7 pediatric patients showed false negative AGTEST results and only one false positive AGTEST occurred, in the pediatric cohort. Calculated viral concentrations from the rt-PCR lay between 3.16 and 9.51 log10 RNA copies/mL buffer. All false negative patients in the adult ED cohort, who had confirmed symptom onset at least seven days earlier had less than 5x 10^5 RNA copies/mL buffer. We conclude that the use of AGTEST among symptomatic patients in the emergency setting is useful for the early identification of COVID-19, but patients who test negative require confirmation by PCRTEST and must stay isolated until this result becomes available. Adult patients with a false negative AGTEST and symptom onset at least one week earlier have typically a low SARS-CoV-2 RNA concentration and likely pass the infectious period.},
    doi = {10.1080/1354750X.2021.1876769},
    pmid = {33455451},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Osterman, H. Baldauf, M. Eletreby, J. M. Wettengel, S. Q. Afridi, T. Fuchs, E. Holzmann, A. Maier, J. Döring, N. Grzimek-Koschewa, M. Muenchhoff, U. Protzer, L. Kaderali, and O. T. Keppler, “Evaluation of two rapid antigen tests to detect SARS-CoV-2 in a hospital setting.,” Med Microbiol Immunol, 2021.
    [Bibtex]
    @Article{Osterman:21,
    author = {Osterman, Andreas and Baldauf, Hanna-Mari and Eletreby, Marwa and Wettengel, Jochen M. and Afridi, Suliman Q. and Fuchs, Thimo and Holzmann, Elena and Maier, Anton and Döring, Johanna and Grzimek-Koschewa, Natascha and Muenchhoff, Maximilian and Protzer, Ulrike and Kaderali, Lars and Keppler, Oliver T.},
    journal = {{Med Microbiol Immunol}},
    title = {Evaluation of two rapid antigen tests to detect {SARS-CoV-2} in a hospital setting.},
    year = {2021},
    abstract = {Successful containment strategies for the SARS-CoV-2 pandemic will depend on reliable diagnostic assays. Point-of-care antigen tests (POCT) may provide an alternative to time-consuming PCR tests to rapidly screen for acute infections on site. Here, we evaluated two SARS-CoV-2 antigen tests: the STANDARD™ F COVID-19 Ag FIA (FIA) and the SARS-CoV-2 Rapid Antigen Test (RAT). For diagnostic assessment, we used a large set of PCR-positive and PCR-negative respiratory swabs from asymptomatic and symptomatic patients and health care workers in the setting of two University Hospitals in Munich, Germany, i.e. emergency rooms, patient care units or employee test centers. For FIA, overall clinical sensitivity and specificity were 45.4% (n = 381) and 97.8% (n = 360), respectively, and for RAT, 50.3% (n = 445) and 97.7% (n = 386), respectively. For primary diagnosis of asymptomatic and symptomatic individuals, diagnostic sensitivities were 60.9% (FIA) (n = 189) and 64.5% (RAT) (n = 256). This questions these tests' utility for the reliable detection of acute SARS-CoV-2-infected individuals, in particular in high-risk settings. We support the proposal that convincing high-quality outcome data on the impact of false-negative and false-positive antigen test results need to be obtained in a POCT setting. Moreover, the efficacy of alternative testing strategies to complement PCR assays must be evaluated by independent laboratories, prior to widespread implementation in national and international test strategies.},
    doi = {10.1007/s00430-020-00698-8},
    keywords = {COVID-19 point-of-care; Diagnostic test; SARS-CoV-2 antigen test; Sensitivity; Specificity},
    pmid = {33452927},
    pubstate = {aheadofprint},
    }
  • [DOI] M. Bárcena, C. O. Barnes, M. Beck, P. J. Bjorkman, B. Canard, G. F. Gao, Y. Gao, R. Hilgenfeld, G. Hummer, A. Patwardhan, G. Santoni, E. O. Saphire, C. Schaffitzel, S. L. Schendel, J. L. Smith, A. Thorn, D. Veesler, P. Zhang, and Q. Zhou, “Structural biology in the fight against COVID-19.,” Nat Struct Mol Biol, vol. 28, p. 2–7, 2021.
    [Bibtex]
    @Article{Barcena:21,
    author = {Bárcena, Montserrat and Barnes, Christopher O. and Beck, Martin and Bjorkman, Pamela J. and Canard, Bruno and Gao, George F. and Gao, Yunyun and Hilgenfeld, Rolf and Hummer, Gerhard and Patwardhan, Ardan and Santoni, Gianluca and Saphire, Erica Ollmann and Schaffitzel, Christiane and Schendel, Sharon L. and Smith, Janet L. and Thorn, Andrea and Veesler, David and Zhang, Peijun and Zhou, Qiang},
    journal = {{Nat Struct Mol Biol}},
    title = {Structural biology in the fight against {COVID-19}.},
    year = {2021},
    pages = {2--7},
    volume = {28},
    doi = {10.1038/s41594-020-00544-8},
    issue = {1},
    keywords = {Computational Biology, methods; Cryoelectron Microscopy, methods; Databases, Protein; Epitopes, chemistry, immunology; Host-Pathogen Interactions; Humans; Linoleic Acid, chemistry, metabolism, pharmacology; Molecular Biology, methods; SARS-CoV-2, chemistry, genetics, pathogenicity; Spike Glycoprotein, Coronavirus, chemistry, metabolism; Viral Proteins, chemistry, metabolism; Viral Vaccines, immunology, pharmacology; Virus Replication, physiology},
    pmid = {33437043},
    pubstate = {ppublish},
    }
  • [DOI] D. A. Hofmaenner, P. D. Wendel Garcia, B. Duvnjak, B. Chakrakodi, J. D. Maier, M. Huber, J. Huder, A. Wolfensberger, P. W. Schreiber, R. A. Schuepbach, A. S. Zinkernagel, P. K. Buehler, S. D. Brugger, and COVID-19 ICU-Research Group Zurich, “Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients.,” Antimicrob Resist Infect Control, vol. 10, p. 11, 2021.
    [Bibtex]
    @Article{Hofmaenner:21,
    author = {Hofmaenner, Daniel A. and Wendel Garcia, Pedro David and Duvnjak, Branko and Chakrakodi, Bhavya and Maier, Julian D. and Huber, Michael and Huder, Jon and Wolfensberger, Aline and Schreiber, Peter W. and Schuepbach, Reto A. and Zinkernagel, Annelies S. and Buehler, Philipp K. and Brugger, Silvio D. and {COVID-19 ICU-Research Group Zurich}},
    journal = {{Antimicrob Resist Infect Control}},
    title = {Bacterial but no {SARS-CoV-2} contamination after terminal disinfection of tertiary care intensive care units treating {COVID-19} patients.},
    year = {2021},
    pages = {11},
    volume = {10},
    abstract = {In intensive care units (ICUs) treating patients with Coronavirus disease 2019 (COVID-19) invasive ventilation poses a high risk for aerosol and droplet formation. Surface contamination of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) or bacteria can result in nosocomial transmission. Two tertiary care COVID-19 intensive care units treating 53 patients for 870 patient days were sampled after terminal cleaning and preparation for regular use to treat non-COVID-19 patients. A total of 176 swabs were sampled of defined locations covering both ICUs. No SARS-CoV-2 ribonucleic acid (RNA) was detected. Gram-negative bacterial contamination was mainly linked to sinks and siphons. Skin flora was isolated from most swabbed areas and Enterococcus faecium was detected on two keyboards. After basic cleaning with standard disinfection measures no remaining SARS-CoV-2 RNA was detected. Bacterial contamination was low and mainly localised in sinks and siphons.},
    doi = {10.1186/s13756-021-00885-z},
    investigator = {Bartussek, Jan and Buehler, Phillip and Heuberger, Dorothea Monika and Hilty, Matthias Peter and Hofmänner, Daniel Andrea and Maibach, Martina and Andreas, Schuepbach Reto and Wendel Garcia, Pedro David},
    issue = {1},
    keywords = {Aerosols, analysis; Bacteria, classification, genetics, growth & development, isolation & purification; COVID-19, therapy, virology; Cross Infection, microbiology, prevention & control, virology; Disinfection, methods; Equipment Contamination, statistics & numerical data; Female; Humans; Intensive Care Units, statistics & numerical data; Male; Middle Aged; SARS-CoV-2, genetics, isolation & purification, physiology; Tertiary Healthcare, statistics & numerical data; Disinfection; Hospital epidemiology; Hydrogen peroxide nebulisation; ICU; Nosocomial infection; SARS-CoV-2},
    pmid = {33436105},
    pubstate = {epublish},
    }
  • [DOI] U. Teichgräber, A. Malouhi, M. Ingwersen, R. Neumann, M. Reljic, S. Deinhardt-Emmer, B. Löffler, W. Behringer, J. Lewejohann, A. Stallmach, and P. Reuken, “Ruling out COVID-19 by chest CT at emergency admission when prevalence is low: the prospective, observational SCOUT study.,” Respir Res, vol. 22, p. 13, 2021.
    [Bibtex]
    @Article{Teichgraeber:21,
    author = {Teichgräber, Ulf and Malouhi, Amer and Ingwersen, Maja and Neumann, Rotraud and Reljic, Marina and Deinhardt-Emmer, Stefanie and Löffler, Bettina and Behringer, Wilhelm and Lewejohann, Jan-Christoph and Stallmach, Andreas and Reuken, Philipp},
    journal = {{Respir Res}},
    title = {Ruling out {COVID-19} by chest {CT} at emergency admission when prevalence is low: the prospective, observational {SCOUT} study.},
    year = {2021},
    pages = {13},
    volume = {22},
    abstract = {It is essential to avoid admission of patients with undetected corona virus disease 2019 (COVID-19) to hospitals' general wards. Even repeated negative reverse transcription polymerase chain reaction (RT-PCR) results do not rule-out COVID-19 with certainty. The study aimed to evaluate a rule-out strategy for COVID-19 using chest computed tomography (CT) in adults being admitted to the emergency department and suspected of COVID-19. In this prospective, single centre, diagnostic accuracy cohort study, consecutive adults (≥ 18 years) presenting with symptoms consistent with COVID-19 or previous contact to infected individuals, admitted to the emergency department and supposed to be referred to general ward were included in March and April 2020. All participants underwent low-dose chest CT. RT-PCR- and specific antibody tests were used as reference standard. Main outcome measures were sensitivity and specificity of chest CT. Predictive values were calculated based on the theorem of Bayes using Fagan's nomogram. Of 165 participants (56.4% male, 71 ± 16 years) included in the study, the diagnosis of COVID-19 was confirmed with RT-PCR and AB tests in 13 participants (prevalence 7.9%). Sensitivity and specificity of chest CT were 84.6% (95% confidence interval [CI], 54.6-98.1) and 94.7% (95% CI, 89.9-97.7), respectively. Positive and negative likelihood ratio of chest CT were 16.1 (95% CI, 7.9-32.8) and 0.16 (95% CI, 0.05-0.58) and positive and negative predictive value were 57.9% (95% CI, 40.3-73.7) and 98.6% (95% CI, 95.3-99.6), respectively. At a low prevalence of COVID-19, chest CT could be used as a complement to repeated RT-PCR testing for early COVID-19 exclusion in adults with suspected infection before referral to hospital's general wards. Trial registration ClinicalTrials.gov: NCT04357938 April 22, 2020.},
    doi = {10.1186/s12931-020-01611-w},
    issue = {1},
    keywords = {Aged; Aged, 80 and over; COVID-19, blood, diagnostic imaging, epidemiology; Cohort Studies; Emergency Service, Hospital, trends; Female; Germany, epidemiology; Humans; Male; Middle Aged; Patient Admission, trends; Prevalence; Prospective Studies; Quarantine, methods, trends; Tomography, X-Ray Computed, methods, trends; COVID-19; Computed tomography; Prevalence; Reverse transcriptase polymerase chain reaction; Sensitivity and specificity; Severe acute respiratory syndrome coronavirus 2},
    pmid = {33435973},
    pubstate = {epublish},
    }
  • [DOI] I. P. Trougakos, K. Stamatelopoulos, E. Terpos, O. E. Tsitsilonis, E. Aivalioti, D. Paraskevis, E. Kastritis, G. N. Pavlakis, and M. A. Dimopoulos, “Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications.,” J Biomed Sci, vol. 28, p. 9, 2021.
    [Bibtex]
    @Article{Trougakos:21,
    author = {Trougakos, Ioannis P. and Stamatelopoulos, Kimon and Terpos, Evangelos and Tsitsilonis, Ourania E. and Aivalioti, Evmorfia and Paraskevis, Dimitrios and Kastritis, Efstathios and Pavlakis, George N. and Dimopoulos, Meletios A.},
    journal = {{J Biomed Sci}},
    title = {Insights to {SARS-CoV-2} life cycle, pathophysiology, and rationalized treatments that target {COVID-19} clinical complications.},
    year = {2021},
    pages = {9},
    volume = {28},
    abstract = {Gaining further insights into SARS-CoV-2 routes of infection and the underlying pathobiology of COVID-19 will support the design of rational treatments targeting the life cycle of the virus and/or the adverse effects (e.g., multi-organ collapse) that are triggered by COVID-19-mediated adult respiratory distress syndrome (ARDS) and/or other pathologies. COVID-19 is a two-phase disease being marked by (phase 1) increased virus transmission and infection rates due to the wide expression of the main infection-related ACE2, TMPRSS2 and CTSB/L human genes in tissues of the respiratory and gastrointestinal tract, as well as by (phase 2) host- and probably sex- and/or age-specific uncontrolled inflammatory immune responses which drive hyper-cytokinemia, aggressive inflammation and (due to broad organotropism of SARS-CoV-2) collateral tissue damage and systemic failure likely because of imbalanced ACE/ANGII/AT1R and ACE2/ANG(1-7)/MASR axes signaling. Here we discuss SARS-CoV-2 life cycle and a number of approaches aiming to suppress viral infection rates or propagation; increase virus antigen presentation in order to activate a robust and durable adaptive immune response from the host, and/or mitigate the ARDS-related "cytokine storm" and collateral tissue damage that triggers the severe life-threatening complications of COVID-19.},
    doi = {10.1186/s12929-020-00703-5},
    issue = {1},
    keywords = {COVID-19, complications, drug therapy, physiopathology, virology; Humans; Life Cycle Stages; SARS-CoV-2, isolation & purification, physiology; ACE2; ARDS; COVID-19; SARS-CoV-2; TMPRSS2},
    pmid = {33435929},
    pubstate = {epublish},
    }
  • [DOI] C. M. Crava, F. S. Varghese, E. Pischedda, R. Halbach, U. Palatini, M. Marconcini, L. Gasmi, S. Redmond, Y. Afrane, D. Ayala, C. Paupy, R. Carballar-Lejarazu, P. Miesen, R. P. van Rij, and M. Bonizzoni, “Population genomics in the arboviral vector aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.,” Mol Ecol, 2021.
    [Bibtex]
    @Article{Crava:21,
    author = {Crava, Cristina M. and Varghese, Finny S. and Pischedda, Elisa and Halbach, Rebecca and Palatini, Umberto and Marconcini, Michele and Gasmi, Leila and Redmond, Seth and Afrane, Yaw and Ayala, Diego and Paupy, Christophe and Carballar-Lejarazu, Rebeca and Miesen, Pascal and van Rij, Ronald P. and Bonizzoni, Mariangela},
    journal = {{Mol Ecol}},
    title = {Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.},
    year = {2021},
    abstract = {Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a non-retroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we intersect population genomics and evolutionary approaches to analyze the genomic architecture of nrEVEs in Ae. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of eighty individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex events with only few nrEVEs contributing to adaptive evolution in Ae. aegypti.},
    doi = {10.1111/mec.15798},
    keywords = {Aedes aegypti ; endogenous viral elements; mosquito genomes; piRNA cluster},
    pmid = {33432714},
    pubstate = {aheadofprint},
    }
  • [DOI] S. R. Vaidya, S. M. Kasibhatla, M. B. Kamble, A. Munivenkatappa, N. S. Kumbhar, M. M. Jayaswamy, M. R. Ramtirthkar, M. M. Kale, and U. Kulkarni-Kale, “Genetic and antigenic characterization of wild type rubella viruses isolated from India.,” Vaccine, 2021.
    [Bibtex]
    @Article{Vaidya21,
    author = {Vaidya, Sunil R. and Kasibhatla, Sunitha M. and Kamble, Madhukar B. and Munivenkatappa, Ashok and Kumbhar, Neelakshi S. and Jayaswamy, Manjunatha M. and Ramtirthkar, Mukund R. and Kale, Mohan M. and Kulkarni-Kale, Urmila},
    journal = {Vaccine},
    title = {Genetic and antigenic characterization of wild type rubella viruses isolated from {I}ndia.},
    year = {2021},
    abstract = {Rubella, is a contagious disease caused by Rubella virus (RuV) that manifests as fever with skin-rashes in children and adults along with complications in pregnant women. WHO-SEAR has set a target for Rubella elimination by 2023. This is the first report of antigenic characterization and genome sequencing of nine RuVs sampled during 1992, 2007-9, and 2015-17 from four Indian states. Comparative analysis of Indian RuVs (2B) with that of global isolates and vaccine strain RA 27/3 (1a) revealed that the observed mutations in structural proteins have no major impact on the 3D structure, function and antigenicity. Indian RuVs formed three major clusters (Pune-1992, Kannur-2009 and Chitradurg-2007) in genome-based phylogeny of global isolates. Neutralizing antibody titers in a panel of serum samples from measles negative cases were significantly higher to the vaccine strain compared to a wild-type 2B isolate (Kannur) with concordance of 91.9%, thereby substantiating the use of current vaccines.},
    doi = {10.1016/j.vaccine.2020.12.063},
    keywords = {Complete genome; Epitopes; Indian rubella virus isolates; Neutralization test; Rubella vaccine strain; Rubella virus bioinformatics},
    pmid = {33423836},
    pubstate = {aheadofprint},
    }
  • [DOI] C. Müller, W. Obermann, N. Karl, H. Wendel, G. Taroncher-Oldenburg, S. Pleschka, R. K. Hartmann, A. Grünweller, and J. Ziebuhr, “The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.,” Antiviral Res, vol. 186, p. 105012, 2021.
    [Bibtex]
    @Article{Mueller:21,
    author = {Müller, Christin and Obermann, Wiebke and Karl, Nadja and Wendel, Hans-Guido and Taroncher-Oldenburg, Gaspar and Pleschka, Stephan and Hartmann, Roland K. and Grünweller, Arnold and Ziebuhr, John},
    journal = {{Antiviral Res}},
    title = {The rocaglate {CR-31-B} (-) inhibits {SARS-CoV-2} replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.},
    year = {2021},
    pages = {105012},
    volume = {186},
    abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, a severe respiratory disease with varying clinical presentations and outcomes, and responsible for a major pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against multiple RNA viruses including coronaviruses. Specifically, rocaglates inhibit eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. Here, we assessed the antiviral activity of the synthetic rocaglate CR-31-B (-) against SARS-CoV-2 using both in vitro and ex vivo cell culture models. In Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC of ~1.8 nM. In primary human airway epithelial cells, CR-31-B (-) reduced viral titers to undetectable levels at a concentration of 100 nM. Reduced virus reproduction was accompanied by substantially reduced viral protein accumulation and replication/transcription complex formation. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.},
    doi = {10.1016/j.antiviral.2021.105012},
    keywords = {Antiviral activity; COVID-19; Rocaglate; SARS-CoV-2; Translation initiation; eIF4A},
    pmid = {33422611},
    pubstate = {aheadofprint},
    }
  • [DOI] E. Criscuolo, R. A. Diotti, R. Ferrarese, C. Alippi, G. Viscardi, C. Signorelli, N. Mancini, M. Clementi, and N. Clementi, “Fast inactivation of SARS-CoV-2 by UV-C and ozone exposure on different materials.,” Emerg Microbes Infect, p. 1–18, 2021.
    [Bibtex]
    @Article{Criscuolo:21,
    author = {Criscuolo, Elena and Diotti, Roberta A. and Ferrarese, Roberto and Alippi, Cesare and Viscardi, Gabriele and Signorelli, Carlo and Mancini, Nicasio and Clementi, Massimo and Clementi, Nicola},
    journal = {{Emerg Microbes Infect}},
    title = {Fast inactivation of {SARS-CoV-2} by {UV-C} and ozone exposure on different materials.},
    year = {2021},
    pages = {1--18},
    doi = {10.1080/22221751.2021.1872354},
    keywords = {SARS-CoV-2; UV-C; contact transmission; inactivation; ozone},
    pmid = {33399524},
    pubstate = {aheadofprint},
    }
  • [DOI] T. Tu, B. Zehnder, B. Qu, and S. Urban, “de novo synthesis of hepatitis B virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of cccdna,” JHEP Rep, vol. 3, p. 100195, 2021.
    [Bibtex]
    @Article{Tu21,
    author = {Tu, Thomas and Zehnder, Benno and Qu, Bingqian and Urban, Stephan},
    journal = {{JHEP Rep}},
    title = {De novo synthesis of hepatitis {B} virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of cccDNA},
    year = {2021},
    pages = {100195},
    volume = {3},
    abstract = {Chronic HBV infection cannot be cured by current therapeutics owing to their limited ability to reduce covalently closed circular (ccc)DNA levels in the livers of infected individuals. Therefore, greater understanding of the molecular determinants of cccDNA formation and persistence is required. One key issue is the extent to which nucleocapsid-mediated replenishment (reimport) contributes to cccDNA levels in an infected hepatocyte. We engineered an infectious HBV mutant with a genome encoding a stop codon at position T67 in the HBV core open reading frame (ΔHBc HBV). Importantly, ΔHBc HBV virions cannot initiate nucleocapsid synthesis upon infection. Long-term HBV infection markers were followed for up for 9 weeks in HepG2-NTCP cells (A3 clone) and HBV DNA was quantified using a newly-developed, highly-precise PCR assay (cccDNA inversion quantitative PCR). ΔHBc and wild-type (WT) HBV resulted in comparable expression of HBV surface antigen (HBsAg), which could be blocked using the entry inhibitor Myrcludex B, confirming infection via the receptor sodium taurocholate cotransporting polypeptide (NTCP). In primary human hepatocytes, Huh7-NTCP, HepG2-NTCP, and HepaRG-NTCP cells, comparable copy numbers of cccDNA were formed. cccDNA levels, transcription of viral RNA, and HBsAg secretion remained comparably stable in WT and ΔHBc HBV-infected cells for at least 9 weeks. Our results imply that synthesised HBc plays a minor role in transcriptional regulation of cccDNA. Importantly, we show that initially-formed cccDNA is stable in hepatocytes without requiring continuous replenishment in infection systems and contribution from DNA-containing nucleocapsids is not required. Thus, short-term therapeutic targeting of capsid-reimport is likely an inefficient strategy in eliminating cccDNA in chronically infected hepatocytes. The hepatitis B virus can maintain itself in the liver for a patient's lifetime, causing liver injury and cancer. We have clarified exactly how it maintains itself in an infected cell. This now means we have a better idea at how to target the virus and cure a chronic infection.},
    doi = {10.1016/j.jhepr.2020.100195},
    issue = {1},
    keywords = {ALT, alanine aminotransferase; Antivirals; Bulevirtide; CIs, capsid inhibitors; Capsid inhibitors; Core protein; Covalently closed circular DNA; DHBV, duck hepatitis B virus; HBV DNA integration; HBV persistence; HBV, hepatitis B virus; HBcAg; HBsAg, hepatitis B virus surface antigen; Hepcludex; Myrcludex B; NC, naked capsids; NTCP, sodium taurocholate cotransporting polypeptide; NUCs, nucleos(t)ide analogues; ORF, open reading frame; PEG, polyethylene glycol; PHH, primary human hepatocytes; SN, supernatant; VP, virions; WT, wild-type; cccDNA, covalently closed circular DNA; dpi, days post inoculation; mge, multiplicity of genomic equivalent; pgRNA, pregenomic RNA; rcDNA, relaxed circular DNA; vge, viral genome equivalents},
    pmid = {33385130},
    pubstate = {epublish},
    }
  • [DOI] T. Toptan, L. Eckermann, A. E. Pfeiffer, S. Hoehl, S. Ciesek, C. Drosten, and V. M. Corman, “Evaluation of a SARS-CoV-2 rapid antigen test: potential to help reduce community spread?,” J Clin Virol, vol. 135, p. 104713, 2021.
    [Bibtex]
    @Article{Toptan:21,
    author = {Tuna Toptan and Lisa Eckermann and Annika E. Pfeiffer and Sebastian Hoehl and Sandra Ciesek and Christian Drosten and Victor M. Corman},
    title = {Evaluation of a {SARS}-{CoV}-2 rapid antigen test: Potential to help reduce community spread?},
    journal = {{J Clin Virol}},
    year = {2021},
    volume = {135},
    pages = {104713},
    doi = {10.1016/j.jcv.2020.104713},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, I. Falcó, A. Allende, and G. Sánchez, “Comparing analytical methods to detect SARS-CoV-2 in wastewater,” Sci Total Environ, vol. 758, p. 143870, 2021.
    [Bibtex]
    @Article{Perez-Cataluna:21,
    author = {Alba P{\'{e}}rez-Catalu{\~{n}}a and Enric Cuevas-Ferrando and Walter Randazzo and Irene Falc{\'{o}} and Ana Allende and Gloria S{\'{a}}nchez},
    title = {Comparing analytical methods to detect {SARS}-{CoV}-2 in wastewater},
    journal = {{Sci Total Environ}},
    year = {2021},
    volume = {758},
    pages = {143870},
    doi = {10.1016/j.scitotenv.2020.143870},
    publisher = {Elsevier {BV}},
    }

2020

  • [DOI] D. Paraskevis, E. G. Kostaki, N. Alygizakis, N. S. Thomaidis, C. Cartalis, S. Tsiodras, and M. A. Dimopoulos, “A review of the impact of weather and climate variables to COVID-19: in the absence of public health measures high temperatures cannot probably mitigate outbreaks.,” Sci Total Environ, vol. 768, p. 144578, 2020.
    [Bibtex]
    @Article{Paraskevis:20a,
    author = {Paraskevis, Dimitrios and Kostaki, Evangelia Georgia and Alygizakis, Nikiforos and Thomaidis, Nikolaos S. and Cartalis, Constantinos and Tsiodras, Sotirios and Dimopoulos, Meletios Athanasios},
    journal = {{Sci Total Environ}},
    title = {A review of the impact of weather and climate variables to {COVID-19}: In the absence of public health measures high temperatures cannot probably mitigate outbreaks.},
    year = {2020},
    pages = {144578},
    volume = {768},
    abstract = {The new severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) pandemic was first recognized at the end of 2019 and has caused one of the most serious global public health crises in the last years. In this paper, we review current literature on the effect of weather (temperature, humidity, precipitation, wind, etc.) and climate (temperature as an essential climate variable, solar radiation in the ultraviolet, sunshine duration) variables on SARS-CoV-2 and discuss their impact to the COVID-19 pandemic; the review also refers to respective effect of urban parameters and air pollution. Most studies suggest that a negative correlation exists between ambient temperature and humidity on the one hand and the number of COVID-19 cases on the other, while there have been studies which support the absence of any correlation or even a positive one. The urban environment and specifically the air ventilation rate, as well as air pollution, can probably affect, also, the transmission dynamics and the case fatality rate of COVID-19. Due to the inherent limitations in previously published studies, it remains unclear if the magnitude of the effect of temperature or humidity on COVID-19 is confounded by the public health measures implemented widely during the first pandemic wave. The effect of weather and climate variables, as suggested previously for other viruses, cannot be excluded, however, under the conditions of the first pandemic wave, it might be difficult to be uncovered. The increase in the number of cases observed during summertime in the Northern hemisphere, and especially in countries with high average ambient temperatures, demonstrates that weather and climate variables, in the absence of public health interventions, cannot mitigate the resurgence of COVID-19 outbreaks.},
    doi = {10.1016/j.scitotenv.2020.144578},
    keywords = {Air pollution; Climate and weather variables; Outbreak; Pandemic; Public health interventions; SARS-CoV-2; Urban environment},
    pmid = {33450689},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, and G. Sánchez, “Bias of library preparation for virome characterization in untreated and treated wastewaters.,” The science of the total environment, vol. 767, p. 144589, 2020.
    [Bibtex]
    @Article{PerezCataluna20,
    author = {Pérez-Cataluña, Alba and Cuevas-Ferrando, Enric and Randazzo, Walter and Sánchez, Gloria},
    journal = {The Science of the total environment},
    title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.},
    year = {2020},
    pages = {144589},
    volume = {767},
    abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.},
    doi = {10.1016/j.scitotenv.2020.144589},
    keywords = {Enteric viruses; Metagenomics; Viability RT-qPCR; Wastewater},
    pmid = {33422963},
    pubstate = {aheadofprint},
    }
  • [DOI] A. A. Gulyaeva and A. E. Gorbalenya, “A nidovirus perspective on sars-cov-2.,” Biochem Biophys Res Commun, 2020.
    [Bibtex]
    @Article{Gulyaeva20a,
    author = {Gulyaeva, Anastasia A. and Gorbalenya, Alexander E.},
    journal = {{Biochem Biophys Res Commun}},
    title = {A nidovirus perspective on SARS-CoV-2.},
    year = {2020},
    abstract = {Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.},
    doi = {10.1016/j.bbrc.2020.11.015},
    keywords = {Comparative genomics; Coronaviruses; Evolution; Nidoviruses; Proteome},
    pmid = {33413979},
    pubstate = {aheadofprint},
    }
  • [DOI] O. M. Allicock, N. Sahadeo, P. Lemey, A. J. Auguste, M. A. Suchard, A. Rambaut, and C. V. F. Carrington, “Determinants of dengue virus dispersal in the Americas.,” Virus Evol, vol. 6, p. veaa074, 2020.
    [Bibtex]
    @Article{Allicock20,
    author = {Allicock, Orchid M. and Sahadeo, Nikita and Lemey, Philippe and Auguste, Albert J. and Suchard, Marc A. and Rambaut, Andrew and Carrington, Christine V. F.},
    journal = {{Virus Evol}},
    title = {Determinants of dengue virus dispersal in the {A}mericas.},
    year = {2020},
    pages = {veaa074},
    volume = {6},
    abstract = {Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments.},
    doi = {10.1093/ve/veaa074},
    issue = {2},
    keywords = {Bayesian phylogeography; dengue virus; hypothesis testing; spatial diffusion},
    pmid = {33408877},
    pubstate = {epublish},
    }
  • [DOI] A. Brinkmann, C. Kohl, A. Radonić, P. W. Dabrowski, K. Mühldorfer, A. Nitsche, G. Wibbelt, and A. Kurth, “First detection of bat-borne Issyk-Kul virus in Europe,” Sci Rep, vol. 10, iss. 1, 2020.
    [Bibtex]
    @Article{Brinkmann20a,
    author = {Annika Brinkmann and Claudia Kohl and Aleksandar Radoni{\'{c}} and Piotr Wojtek Dabrowski and Kristin Mühldorfer and Andreas Nitsche and Gudrun Wibbelt and Andreas Kurth},
    journal = {{Sci Rep}},
    title = {First detection of bat-borne {I}ssyk-{K}ul virus in {E}urope},
    year = {2020},
    number = {1},
    volume = {10},
    doi = {10.1038/s41598-020-79468-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. Blake, J. Corner, C. Cirelli, J. Hassard, L. Briggs, J. M. Daly, M. Bennett, J. G. Chappell, L. Fairclough, P. C. McClure, A. Tarr, P. Tighe, A. Favier, W. Irving, and J. Ball, “Perceptions and experiences of the University of Nottingham pilot SARS-CoV-2 asymptomatic testing service: a mixed-methods study.,” Int J Environ Res Public Health, vol. 18, 2020.
    [Bibtex]
    @Article{Blake20,
    author = {Blake, Holly and Corner, Jessica and Cirelli, Cecilia and Hassard, Juliet and Briggs, Lydia and Daly, Janet M. and Bennett, Malcolm and Chappell, Joseph G. and Fairclough, Lucy and McClure, C. Patrick and Tarr, Alexander and Tighe, Patrick and Favier, Alex and Irving, William and Ball, Jonathan},
    journal = {{Int J Environ Res Public Health}},
    title = {Perceptions and Experiences of the {U}niversity of {N}ottingham Pilot {SARS-CoV-2} Asymptomatic Testing Service: A Mixed-Methods Study.},
    year = {2020},
    volume = {18},
    abstract = {We aimed to explore student and staff perceptions and experiences of a pilot SARS-CoV-2 asymptomatic testing service (P-ATS) in a UK university campus setting. This was a mixed-method study comprised of an online survey, and thematic analysis of qualitative data from interviews and focus groups conducted at the mid-point and end of the 12-week P-ATS programme. Ninety-nine students (84.8% female, 70% first year; 93.9% P-ATS participants) completed an online survey, 41 individuals attended interviews or focus groups, including 31 students (21 first year; 10 final year) and 10 staff. All types of testing and logistics were highly acceptable ( : swab, saliva; : finger prick) and 94.9% would participate again. Reported adherence to weekly virus testing was high (92.4% completed ≥6 tests; 70.8% submitted all 10 swabs; 89.2% completed ≥1 saliva sample) and 76.9% submitted ≥3 blood samples. Students tested to "keep campus safe", "contribute to national efforts to control COVID-19", and "protect others". In total, 31.3% had high anxiety as measured by the Generalized Anxiety Disorder scale (GAD-7) (27.1% of first year). Students with lower levels of anxiety and greater satisfaction with university communications around P-ATS were more likely to adhere to virus and antibody tests. Increased adherence to testing was associated with higher perceived risk of COVID-19 to self and others. Qualitative findings revealed 5 themes and 13 sub-themes: "emotional responses to COVID-19", "university life during COVID-19", "influences on testing participation", "testing physical and logistical factors" and "testing effects on mental wellbeing". Asymptomatic COVID-19 testing (SARS-CoV-2 virus/antibodies) is highly acceptable to students and staff in a university campus setting. Clear communications and strategies to reduce anxiety are likely to be important for testing uptake and adherence. Strategies are needed to facilitate social connections and mitigate the mental health impacts of COVID-19 and self-isolation.},
    doi = {10.3390/ijerph18010188},
    issue = {1},
    keywords = {Asymptomatic Infections; COVID-19, diagnosis, psychology; COVID-19 Testing; Female; Humans; Male; Specimen Handling; Surveys and Questionnaires; United Kingdom; Universities; Young Adult; COVID-19; SARS-CoV-2; coronavirus; disease outbreaks; health promotion; students; virus; young people},
    pmid = {33383781},
    pubstate = {epublish},
    }
  • [DOI] S. Lequime, J. Dehecq, S. Matheus, F. de Laval, L. Almeras, S. Briolant, and A. Fontaine, “Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus,” PLoS Pathog, vol. 16, iss. 12, p. e1009068, 2020.
    [Bibtex]
    @Article{Lequime20a,
    author = {Sebastian Lequime and Jean-S{\'{e}}bastien Dehecq and S{\'{e}}verine Matheus and Franck de Laval and Lionel Almeras and S{\'{e}}bastien Briolant and Albin Fontaine},
    journal = {{PLoS Pathog}},
    title = {Modeling intra-mosquito dynamics of {Z}ika virus and its dose-dependence confirms the low epidemic potential of {A}edes albopictus},
    year = {2020},
    number = {12},
    pages = {e1009068},
    volume = {16},
    doi = {10.1371/journal.ppat.1009068},
    editor = {Elizabeth Ann McGraw},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Trump, S. Lukassen, M. S. Anker, R. L. Chua, J. Liebig, L. Thürmann, V. M. Corman, M. Binder, J. Loske, C. Klasa, T. Krieger, B. P. Hennig, M. Messingschlager, F. Pott, J. Kazmierski, S. Twardziok, J. P. Albrecht, J. Eils, S. Hadzibegovic, A. Lena, B. Heidecker, T. Bürgel, J. Steinfeldt, C. Goffinet, F. Kurth, M. Witzenrath, M. T. Völker, S. D. Müller, U. G. Liebert, N. Ishaque, L. Kaderali, L. Sander, C. Drosten, S. Laudi, R. Eils, C. Conrad, U. Landmesser, and I. Lehmann, “Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with covid-19.,” Nat Biotechnol, 2020.
    [Bibtex]
    @Article{Trump20,
    author = {Trump, Saskia and Lukassen, Soeren and Anker, Markus S. and Chua, Robert Lorenz and Liebig, Johannes and Thürmann, Loreen and Corman, Victor Max and Binder, Marco and Loske, Jennifer and Klasa, Christina and Krieger, Teresa and Hennig, Bianca P. and Messingschlager, Marey and Pott, Fabian and Kazmierski, Julia and Twardziok, Sven and Albrecht, Jan Philipp and Eils, Jürgen and Hadzibegovic, Sara and Lena, Alessia and Heidecker, Bettina and Bürgel, Thore and Steinfeldt, Jakob and Goffinet, Christine and Kurth, Florian and Witzenrath, Martin and Völker, Maria Theresa and Müller, Sarah Dorothea and Liebert, Uwe Gerd and Ishaque, Naveed and Kaderali, Lars and Sander, Leif-Erik and Drosten, Christian and Laudi, Sven and Eils, Roland and Conrad, Christian and Landmesser, Ulf and Lehmann, Irina},
    journal = {{Nat Biotechnol}},
    title = {Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19.},
    year = {2020},
    abstract = {In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.},
    doi = {10.1038/s41587-020-00796-1},
    pmid = {33361824},
    pubstate = {aheadofprint},
    }
  • [DOI] J. Nkengasong, A. Iwasaki, C. Victora, J. Oh, G. F. Gao, A. Agrawal, C. Drosten, C. Söderberg-Naucler, E. López-Collazo, A. M. Pollock, A. Viola, and M. Baker, “The global response to the COVID-19 pandemic.,” Med (NY), vol. 1, p. 3–8, 2020.
    [Bibtex]
    @Article{Nkengasong20,
    author = {Nkengasong, John and Iwasaki, Akiko and Victora, Cesar and Oh, Juhwan and Gao, George F. and Agrawal, Anurag and Drosten, Christian and Söderberg-Naucler, Cecilia and López-Collazo, Eduardo and Pollock, Allyson M. and Viola, Antonella and Baker, Michael},
    journal = {{Med (NY)}},
    title = {The Global Response to the {COVID-19} Pandemic.},
    year = {2020},
    pages = {3--8},
    volume = {1},
    abstract = {Global approaches towards pandemic control range from strict lockdowns to minimal restrictions. We asked experts worldwide about the lessons learned from their countries' response. Their voices converge on the importance of scientifically guided interventions to limit the spread of SARS-CoV-2 and its impact on human health.},
    doi = {10.1016/j.medj.2020.12.003},
    issue = {1},
    pmid = {33363282},
    pubstate = {ppublish},
    }
  • [DOI] S. Peter, P. Dittrich, and B. Ibrahim, “Structure and hierarchy of SARS-CoV-2 infection dynamics models revealed by reaction network analysis.,” Viruses, vol. 13, 2020.
    [Bibtex]
    @Article{Peter20,
    author = {Peter, Stephan and Dittrich, Peter and Ibrahim, Bashar},
    journal = {Viruses},
    title = {Structure and Hierarchy of {SARS-CoV-2} Infection Dynamics Models Revealed by Reaction Network Analysis.},
    year = {2020},
    volume = {13},
    abstract = {This work provides a mathematical technique for analyzing and comparing infection dynamics models with respect to their potential long-term behavior, resulting in a hierarchy integrating all models. We apply our technique to coupled ordinary and partial differential equation models of SARS-CoV-2 infection dynamics operating on different scales, that is, within a single organism and between several hosts. The structure of a model is assessed by the theory of chemical organizations, not requiring quantitative kinetic information. We present the Hasse diagrams of organizations for the twelve virus models analyzed within this study. For comparing models, each organization is characterized by the types of species it contains. For this, each species is mapped to one out of four types, representing uninfected, infected, immune system, and bacterial species, respectively. Subsequently, we can integrate these results with those of our former work on Influenza-A virus resulting in a single joint hierarchy of 24 models. It appears that the SARS-CoV-2 models are simpler with respect to their long term behavior and thus display a simpler hierarchy with little dependencies compared to the Influenza-A models. Our results can support further development towards more complex SARS-CoV-2 models targeting the higher levels of the hierarchy.},
    doi = {10.3390/v13010014},
    issue = {1},
    keywords = {COVID-19, virology; Host-Pathogen Interactions; Humans; Influenza A virus; Influenza, Human, virology; Models, Biological; Models, Theoretical; SARS-CoV-2; Covid-19; ODEs; PDEs; SARS-CoV-2; between hosts; chemical organization theory; corona; reaction networks analysis; virus dynamics modeling; within hosts},
    pmid = {33374824},
    pubstate = {epublish},
    }
  • [DOI] A. Strömer, R. Rose, M. Schäfer, F. Schön, A. Vollersen, T. Lorentz, H. Fickenscher, and A. Krumbholz, “Performance of a point-of-care test for the rapid detection of SARS-CoV-2 antigen.,” Microorganisms, vol. 9, 2020.
    [Bibtex]
    @Article{Stroemer20,
    author = {Strömer, Annabelle and Rose, Ruben and Schäfer, Miriam and Schön, Frieda and Vollersen, Anna and Lorentz, Thomas and Fickenscher, Helmut and Krumbholz, Andi},
    journal = {Microorganisms},
    title = {Performance of a Point-of-Care Test for the Rapid Detection of {SARS-CoV-2} Antigen.},
    year = {2020},
    volume = {9},
    abstract = {The rapid detection of infections caused by the (SARS-CoV-2) is necessary in the ongoing pandemic. Antigen-specific point-of-care tests (POCT) may be useful for this purpose. Here, such a POCT (SARS-CoV-2 NADAL COVID-19 Ag) was compared to a laboratory-developed triplex real-time polymerase chain reaction (RT-PCR) designed for the detection of viral nucleoprotein gene and two control targets. This RT-PCR served as a reference to investigate POCT sensitivity by re-testing upper respiratory tract (URT) samples ( = 124) exhibiting different SARS-CoV-2 loads in terms of RT-PCR threshold cycle (Ct) values. The optical intensities of the antigen bands were compared to the Ct values of the RT-PCR. The infectivity of various virus loads was estimated by inoculating Vero cells with URT samples ( = 64, Ct 17-34). POCT sensitivity varied from 100% (Ct < 25) to 73.1% (Ct ≤ 30); higher SARS-CoV-2 loads correlated with higher band intensities. All samples with a Ct > 30 were negative; among SARS-CoV-2 free samples ( = 10) no false-positives were detected. A head-to-head comparison with another POCT (Abbott, Panbio™ COVID-19 Ag Rapid Test) yielded similar results. Isolation of SARS-CoV-2 in cell-culture was successful up to a Ct value of 29. The POCT reliably detects high SARS-CoV-2 loads and rapidly identifies infectious individuals.},
    doi = {10.3390/microorganisms9010058},
    issue = {1},
    keywords = {COVID-19; PCR; POCT; antigen; comparison; diagnostic},
    pmid = {33379279},
    pubstate = {epublish},
    }
  • [DOI] B. Morel, P. Barbera, L. Czech, B. Bettisworth, L. Hübner, S. Lutteropp, D. Serdari, E. Kostaki, I. Mamais, A. M. Kozlov, P. Pavlidis, D. Paraskevis, and A. Stamatakis, “Phylogenetic analysis of SARS-CoV-2 data is difficult,” Mol Biol Evol, 2020.
    [Bibtex]
    @Article{Morel:20,
    author = {Benoit Morel and Pierre Barbera and Lucas Czech and Ben Bettisworth and Lukas Hübner and Sarah Lutteropp and Dora Serdari and Evangelia-Georgia Kostaki and Ioannis Mamais and Alexey M Kozlov and Pavlos Pavlidis and Dimitrios Paraskevis and Alexandros Stamatakis},
    title = {Phylogenetic analysis of {SARS}-{CoV}-2 data is difficult},
    journal = {{Mol Biol Evol}},
    year = {2020},
    doi = {10.1093/molbev/msaa314},
    editor = {Harmit Malik},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. P. Szillat, D. Höper, M. Beer, and P. König, “Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1),” Virus Evol, vol. 6, iss. 2, 2020.
    [Bibtex]
    @Article{Szillat:20,
    author = {Kevin P Szillat and Dirk Höper and Martin Beer and Patricia König},
    title = {Full-genome sequencing of {G}erman rabbit haemorrhagic disease virus uncovers recombination between {RHDV} ({GI}.2) and {EBHSV} ({GII}.1)},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa080},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. P. Shannon, T. M. Blimkie, R. Ben-Othman, N. Gladish, N. Amenyogbe, S. Drissler, R. D. Edgar, Q. Chan, M. Krajden, L. J. Foster, M. S. Kobor, W. W. Mohn, R. R. Brinkman, K. L. Cao, R. H. Scheuermann, S. J. Tebbutt, R. E. W. Hancock, W. C. Koff, T. R. Kollmann, M. Sadarangani, and A. H. Lee, “Multi-omic data integration allows baseline immune signatures to predict hepatitis B vaccine response in a small cohort,” Front Immunol, vol. 11, 2020.
    [Bibtex]
    @Article{Shannon:20b,
    author = {Casey P. Shannon and Travis M. Blimkie and Rym Ben-Othman and Nicole Gladish and Nelly Amenyogbe and Sibyl Drissler and Rachel D. Edgar and Queenie Chan and Mel Krajden and Leonard J. Foster and Michael S. Kobor and William W. Mohn and Ryan R. Brinkman and Kim-Anh Le Cao and Richard H. Scheuermann and Scott J. Tebbutt and Robert E.W. Hancock and Wayne C. Koff and Tobias R. Kollmann and Manish Sadarangani and Amy Huei-Yi Lee},
    title = {Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis {B} Vaccine Response in a Small Cohort},
    journal = {{Front Immunol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.578801},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] P. Simmonds, S. Williams, and H. Harvala, “Understanding the outcomes of COVID-19 – does the current model of an acute respiratory infection really fit?,” J Gen Virol, 2020.
    [Bibtex]
    @Article{Simmonds:20,
    author = {Peter Simmonds and Sarah Williams and Heli Harvala},
    title = {Understanding the outcomes of {COVID}-19 {\textendash} does the current model of an acute respiratory infection really fit?},
    journal = {{J Gen Virol}},
    year = {2020},
    doi = {10.1099/jgv.0.001545},
    publisher = {Microbiology Society},
    }
  • [DOI] J. Wolff, S. A. E. Rahman, J. King, M. El-Beskawy, A. Pohlmann, M. Beer, and B. Hoffmann, “Establishment of a challenge model for sheeppox virus infection,” Microorganisms, vol. 8, iss. 12, p. 2001, 2020.
    [Bibtex]
    @Article{Wolff:20,
    author = {Janika Wolff and Sahar Abd El Rahman and Jacqueline King and Mohamed El-Beskawy and Anne Pohlmann and Martin Beer and Bernd Hoffmann},
    title = {Establishment of a Challenge Model for Sheeppox Virus Infection},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {2001},
    doi = {10.3390/microorganisms8122001},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. S. da Filipe, J. G. Shepherd, T. Williams, J. Hughes, E. Aranday-Cortes, P. Asamaphan, S. Ashraf, C. Balcazar, K. Brunker, A. Campbell, S. Carmichael, C. Davis, R. Dewar, M. D. Gallagher, R. Gunson, V. Hill, A. Ho, B. Jackson, E. James, N. Jesudason, N. Johnson, C. M. E. Leitch, K. Li, A. MacLean, D. Mair, D. A. McAllister, J. T. McCrone, S. E. McDonald, M. P. McHugh, K. A. Morris, J. Nichols, M. Niebel, K. Nomikou, R. J. Orton, Á. O’Toole, M. Palmarini, B. J. Parcell, Y. A. Parr, A. Rambaut, S. Rooke, S. Shaaban, R. Shah, J. B. Singer, K. Smollett, I. Starinskij, L. Tong, V. B. Sreenu, E. Wastnedge, M. T. G. Holden, D. L. Robertson, K. Templeton, and E. C. Thomson, “Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland,” Nat Microbiol, vol. 6, iss. 1, p. 112–122, 2020.
    [Bibtex]
    @Article{SilvaFilipe:20,
    author = {Ana da Silva Filipe and James G. Shepherd and Thomas Williams and Joseph Hughes and Elihu Aranday-Cortes and Patawee Asamaphan and Shirin Ashraf and Carlos Balcazar and Kirstyn Brunker and Alasdair Campbell and Stephen Carmichael and Chris Davis and Rebecca Dewar and Michael D. Gallagher and Rory Gunson and Verity Hill and Antonia Ho and Ben Jackson and Edward James and Natasha Jesudason and Natasha Johnson and E. Carol McWilliam Leitch and Kathy Li and Alasdair MacLean and Daniel Mair and David A. McAllister and John T. McCrone and Sarah E. McDonald and Martin P. McHugh and A. Keith Morris and Jenna Nichols and Marc Niebel and Kyriaki Nomikou and Richard J. Orton and {\'{A}}ine O'Toole and Massimo Palmarini and Benjamin J. Parcell and Yasmin A. Parr and Andrew Rambaut and Stefan Rooke and Sharif Shaaban and Rajiv Shah and Joshua B. Singer and Katherine Smollett and Igor Starinskij and Lily Tong and Vattipally B. Sreenu and Elizabeth Wastnedge and Matthew T. G. Holden and David L. Robertson and Kate Templeton and Emma C. Thomson},
    title = {Genomic epidemiology reveals multiple introductions of {SARS}-{CoV}-2 from mainland {E}urope into {S}cotland},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {112--122},
    doi = {10.1038/s41564-020-00838-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] N. Schmidt, C. A. Lareau, H. Keshishian, S. Ganskih, C. Schneider, T. Hennig, R. Melanson, S. Werner, Y. Wei, M. Zimmer, J. Ade, L. Kirschner, S. Zielinski, L. Dölken, E. S. Lander, N. Caliskan, U. Fischer, J. Vogel, S. A. Carr, J. Bodem, and M. Munschauer, “The SARS-CoV-2 RNA–protein interactome in infected human cells,” Nat Microbiol, 2020.
    [Bibtex]
    @Article{Schmidt:20,
    author = {Nora Schmidt and Caleb A. Lareau and Hasmik Keshishian and Sabina Ganskih and Cornelius Schneider and Thomas Hennig and Randy Melanson and Simone Werner and Yuanjie Wei and Matthias Zimmer and Jens Ade and Luisa Kirschner and Sebastian Zielinski and Lars Dölken and Eric S. Lander and Neva Caliskan and Utz Fischer and Jörg Vogel and Steven A. Carr and Jochen Bodem and Mathias Munschauer},
    title = {The {SARS}-{CoV}-2 {RNA}{\textendash}protein interactome in infected human cells},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-00846-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Michelitsch, D. Hoffmann, K. Wernike, and M. Beer, “Occurrence of antibodies against SARS-CoV-2 in the domestic cat population of germany,” Vaccines, vol. 8, iss. 4, p. 772, 2020.
    [Bibtex]
    @Article{Michelitsch:20,
    author = {Anna Michelitsch and Donata Hoffmann and Kerstin Wernike and Martin Beer},
    title = {Occurrence of Antibodies against {SARS}-{CoV}-2 in the Domestic Cat Population of Germany},
    journal = {Vaccines},
    year = {2020},
    volume = {8},
    number = {4},
    pages = {772},
    doi = {10.3390/vaccines8040772},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladimirova, J. Kazmierski, F. Pott, K. Dietert, M. Mülleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Höfler, B. Sawitzki, C. Drosten, L. E. Sander, N. Suttorp, M. Ralser, D. Beule, A. D. Gruber, C. Goffinet, M. Landthaler, J. Trimpert, and M. Witzenrath, “Longitudinal omics in syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2,” bioRxiv, 2020.
    [Bibtex]
    @Article{Nouailles:20,
    author = {Geraldine Nouailles and Emanuel Wyler and Peter Pennitz and Dylan Postmus and Daria Vladimirova and Julia Kazmierski and Fabian Pott and Kristina Dietert and Michael Mülleder and Vadim Farztdinov and Benedikt Obermayer and Sandra-Maria Wienhold and Sandro Andreotti and Thomas Höfler and Birgit Sawitzki and Christian Drosten and Leif Erik Sander and Norbert Suttorp and Markus Ralser and Dieter Beule and Achim Dieter Gruber and Christine Goffinet and Markus Landthaler and Jakob Trimpert and Martin Witzenrath},
    title = {Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.18.423524},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Rüeger, C. Hammer, A. Loetscher, P. J. McLaren, D. Lawless, O. Naret, D. P. Depledge, S. Morfopoulou, J. Breuer, E. Zdobnov, and J. F. and, “The influence of human genetic variation on Epstein-Barr virus sequence diversity,” medRxiv, 2020.
    [Bibtex]
    @Article{Rüeger:20,
    author = {Sina Rüeger and Christian Hammer and Alexis Loetscher and Paul J McLaren and Dylan Lawless and Olivier Naret and Daniel P. Depledge and Sofia Morfopoulou and Judith Breuer and Evgeny Zdobnov and Jacques Fellay and},
    title = {The influence of human genetic variation on {E}pstein-{B}arr virus sequence diversity},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.02.20242370},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] F. S. Varghese, E. van Woudenbergh, G. J. Overheul, M. J. Eleveld, L. Kurver, N. van Heerbeek, A. van Laarhoven, P. Miesen, G. den Hartog, M. I. de Jonge, and R. P. van Rij, “Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro,” bioRxiv, 2020.
    [Bibtex]
    @Article{Varghese:20,
    author = {Finny S. Varghese and Esther van Woudenbergh and Gijs J. Overheul and Marc J. Eleveld and Lisa Kurver and Niels van Heerbeek and Arjan van Laarhoven and Pascal Miesen and Gerco den Hartog and Marien I. de Jonge and Ronald P. van Rij},
    title = {Berberine and obatoclax inhibit {SARS}-{CoV}-2 replication in primary human nasal epithelial cells in vitro},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.23.424189},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Weersma, R. Gacesa, A. Kurilshikov, A. V. Vila, T. Sinha, M. Klaassen, L. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. Dekens, V. Lenters, J. Björk, C. J. Swarte, M. Swertz, B. H. Jansen, J. Gelderloos-Arends, M. Hofker, R. Vermeuelen, S. Sanna, H. Harmsen, C. Wijmenga, J. Fu, and A. Zhernakova, “The Dutch Microbiome Project defines factors that shape the healthy gut microbiome,” Research Square, 2020.
    [Bibtex]
    @Article{Weersma:20,
    author = {Rinse Weersma and Ranko Gacesa and Alexander Kurilshikov and Arnau Vich Vila and Trishla Sinha and Marjolein Klaassen and Laura Bolte and Sergio Andreu-Sanchez and Lianmin Chen and Valerie Collij and Shixian Hu and Jackie Dekens and Virissa Lenters and Johannes Björk and J. Casper Swarte and Morris Swertz and B. H. Jansen and Jody Gelderloos-Arends and Marten Hofker and Roel Vermeuelen and Serena Sanna and Hermie Harmsen and Cisca Wijmenga and Jingyuan Fu and Alexandra Zhernakova},
    title = {The {D}utch {M}icrobiome {P}roject defines factors that shape the healthy gut microbiome},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-117376/v1},
    publisher = {Research Square},
    }
  • [DOI] M. Kohls, M. Kircher, J. Krepel, P. Liebig, and K. Jung, “Estimating the distribution of viral taxa in next-generation sequencing data using artificial neural networks,” Research Square, 2020.
    [Bibtex]
    @Article{Kohls:20,
    author = {Moritz Kohls and Magdalena Kircher and Jessica Krepel and Pamela Liebig and Klaus Jung},
    title = {Estimating the Distribution of Viral Taxa in Next-generation Sequencing data using Artificial Neural Networks},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-127809/v1},
    publisher = {Research Square},
    }
  • [DOI] E. G. Kostaki, S. Limnaios, S. Roussos, M. Psichogiou, G. K. Nikolopoulos, S. R. Friedman, A. Antoniadou, M. Chini, A. Hatzakis, V. Sypsa, G. Magiorkinis, C. Seguin-Devaux, and D. Paraskevis, “Validation of molecular clock inferred HIV infection ages: evidence for accurate estimation of infection dates,” medRxiv, 2020.
    [Bibtex]
    @Article{Kostaki:20,
    author = {Evangelia Georgia Kostaki and Stefanos Limnaios and Sotirios Roussos and Mina Psichogiou and Georgios K. Nikolopoulos and Samuel R. Friedman and Anastasia Antoniadou and Maria Chini and Angelos Hatzakis and Vana Sypsa and Gkikas Magiorkinis and Carole Seguin-Devaux and Dimitrios Paraskevis},
    title = {Validation of molecular clock inferred {HIV} infection ages: evidence for accurate estimation of infection dates},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.11.20247601},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. Karakike, E. J. Giamarellos-Bourboulis, M. Kyprianou, C. Fleischmann-Struzek, M. W. Pletz, M. G. Netea, K. Reinhart, and E. Kyriazopoulou, “COVID-19 as cause of viral sepsis: a systematic review and meta-analysis,” medRxiv, 2020.
    [Bibtex]
    @Article{Karakike:20,
    author = {Eleni Karakike and Evangelos J. Giamarellos-Bourboulis and Miltiades Kyprianou and Carolin Fleischmann-Struzek and Mathias W. Pletz and Mihai G. Netea and Konrad Reinhart and Evdoxia Kyriazopoulou},
    title = {{COVID}-19 as cause of viral sepsis: A Systematic Review and Meta-Analysis},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.02.20242354},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Zafferani, C. Haddad, L. Luo, J. Davila-Calderon, L. Yuan-Chiu, C. S. Mugisha, A. G. Monaghan, A. A. Kennedy, J. D. Yesselman, R. R. Gifford, A. W. Tai, S. B. Kutluay, M. Li, G. Brewer, B. S. Tolbert, and A. E. Hargrove, “Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures,” bioRxiv, 2020.
    [Bibtex]
    @Article{Zafferani:20,
    author = {Martina Zafferani and Christina Haddad and Le Luo and Jesse Davila-Calderon and Liang Yuan-Chiu and Christian Shema Mugisha and Adeline G. Monaghan and Andrew A. Kennedy and Joseph D. Yesselman and Robert R. Gifford and Andrew W. Tai and Sebla B. Kutluay and Mei-Ling Li and Gary Brewer and Blanton S. Tolbert and Amanda E. Hargrove},
    title = {Amilorides inhibit {SARS}-{CoV}-2 replication in vitro by targeting {RNA} structures},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.05.409821},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Huber, P. W. Schreiber, T. Scheier, A. Audigé, R. Buonomano, A. Rudiger, D. L. Braun, G. Eich, D. Keller, B. Hasse, C. Berger, A. Manrique, H. F. Günthard, J. Böni, and A. Trkola, “Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for SARS-CoV-2 detection by RT-PCR,” medRxiv, 2020.
    [Bibtex]
    @Article{Huber:20,
    author = {Michael Huber and Peter W. Schreiber and Thomas Scheier and Annette Audig{\'{e}} and Roberto Buonomano and Alain Rudiger and Dominique L. Braun and Gerhard Eich and Dagmar Keller and Barbara Hasse and Christoph Berger and Amapola Manrique and Huldrych F. Günthard and Jürg Böni and Alexandra Trkola},
    title = {Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for {SARS}-{CoV}-2 detection by {RT}-{PCR}},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.01.20241778},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] I. Jungreis, C. W. Nelson, Z. Ardern, Y. Finkel, N. J. Krogan, K. Sato, J. Ziebuhr, N. Stern-Ginossar, A. Pavesi, A. E. Firth, A. E. Gorbalenya, and M. Kellis, “Conflicting and ambiguous names of overlapping ORFs in SARS-CoV-2: a homology-based resolution,” Preprints, 2020.
    [Bibtex]
    @Article{Jungreis:20,
    author = {Irwin Jungreis and Chase W. Nelson and Zachary Ardern and Yaara Finkel and Nevan J. Krogan and Kei Sato and John Ziebuhr and Noam Stern-Ginossar and Angelo Pavesi and Andrew E. Firth and Alexander E. Gorbalenya and Manolis Kellis},
    title = {Conflicting and Ambiguous Names of Overlapping {ORFs} in {SARS}-{CoV}-2: A Homology-Based Resolution},
    journal = {{Preprints}},
    year = {2020},
    doi = {10.20944/preprints202012.0048.v1},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Bartolini, M. Rueca, C. E. M. Gruber, F. Messina, E. Giombini, G. Ippolito, M. R. Capobianchi, and A. D. Caro, “The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy,” medRxiv, 2020.
    [Bibtex]
    @Article{Bartolini:20a,
    author = {Barbara Bartolini and Martina Rueca and Cesare Ernesto Maria Gruber and Francesco Messina and Emanuela Giombini and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro},
    title = {The newly introduced {SARS}-{CoV}-2 variant {A222V} is rapidly spreading in {L}azio region, {I}taly},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.28.20237016},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. S. Huisman, J. Scire, D. C. Angst, R. A. Neher, S. Bonhoeffer, and T. Stadler, “Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2,” medRxiv, 2020.
    [Bibtex]
    @Article{Huisman:20,
    author = {Jana S. Huisman and J{\'{e}}r{\'{e}}mie Scire and Daniel C. Angst and Richard A. Neher and Sebastian Bonhoeffer and Tanja Stadler},
    title = {Estimation and worldwide monitoring of the effective reproductive number of {SARS}-{CoV}-2},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.26.20239368},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. J. D. Ouwendijk, D. P. Depledge, L. Rajbhandari, T. L. Rovis, S. Jonjic, J. Breuer, A. Venkatesan, G. M. G. M. Verjans, and T. Sadaoka, “Varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency,” Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Ouwendijk:20,
    author = {Werner J. D. Ouwendijk and Daniel P. Depledge and Labchan Rajbhandari and Tihana Lenac Rovis and Stipan Jonjic and Judith Breuer and Arun Venkatesan and Georges M. G. M. Verjans and Tomohiko Sadaoka},
    title = {Varicella-zoster virus {VLT}-{ORF}63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-20031-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. K. Lindner, O. Nikolai, F. Kausch, M. Wintel, F. Hommes, M. Gertler, L. J. Krüger, M. Gaeddert, F. Tobian, F. Lainati, L. Köppel, J. Seybold, V. M. Corman, C. Drosten, J. Hofmann, J. A. Sacks, F. P. Mockenhaupt, and C. M. Denkinger, “Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.,” Eur Respir J, 2020.
    [Bibtex]
    @Article{Lindner:20,
    author = {Lindner, Andreas K and Nikolai, Olga and Kausch, Franka and Wintel, Mia and Hommes, Franziska and Gertler, Maximilian and Krüger, Lisa J and Gaeddert, Mary and Tobian, Frank and Lainati, Federica and Köppel, Lisa and Seybold, Joachim and Corman, Victor M and Drosten, Christian and Hofmann, Jörg and Sacks, Jilian A and Mockenhaupt, Frank P and Denkinger, Claudia M},
    title = {Head-to-head comparison of {SARS-CoV-2} antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.},
    journal = {{Eur Respir J}},
    year = {2020},
    doi = {10.1183/13993003.03961-2020},
    pmid = {33303544},
    }
  • [DOI] X. Chen and D. Li, “Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data,” Genomics, 2020.
    [Bibtex]
    @Article{Chen:20,
    author = {Xun Chen and Dawei Li},
    title = {Sequencing facility and {DNA} source associated patterns of virus-mappable reads in whole-genome sequencing data},
    journal = {Genomics},
    year = {2020},
    doi = {10.1016/j.ygeno.2020.12.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. I. Andersson, C. V. Arancibia-Carcamo, K. Auckland, K. J. Baillie, E. Barnes, T. Beneke, S. Bibi, T. Brooks, M. Carroll, D. Crook, K. Dingle, C. Dold, L. O. Downs, L. Dunn, D. W. Eyre, J. G. Jaramillo, H. Harvala, S. Hoosdally, S. Ijaz, T. James, W. James, K. Jeffery, A. Justice, P. Klenerman, J. C. Knight, M. Knight, X. Liu, S. F. Lumley, P. C. Matthews, A. L. McNaughton, A. J. Mentzer, J. Mongkolsapaya, S. Oakley, M. S. Oliveira, T. Peto, R. J. Ploeg, J. Ratcliff, M. J. Robbins, D. J. Roberts, J. Rudkin, R. A. Russell, G. Screaton, M. G. Semple, D. Skelly, P. Simmonds, N. Stoesser, L. Turtle, S. Wareing, and M. Zambon, “SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus,” Wellcome Open Res, vol. 5, p. 181, 2020.
    [Bibtex]
    @Article{Andersson:20,
    author = {Monique I. Andersson and Carolina V. Arancibia-Carcamo and Kathryn Auckland and J. Kenneth Baillie and Eleanor Barnes and Tom Beneke and Sagida Bibi and Tim Brooks and Miles Carroll and Derrick Crook and Kate Dingle and Christina Dold and Louise O. Downs and Laura Dunn and David W. Eyre and Javier Gilbert Jaramillo and Heli Harvala and Sarah Hoosdally and Samreen Ijaz and Tim James and William James and Katie Jeffery and Anita Justice and Paul Klenerman and Julian C. Knight and Michael Knight and Xu Liu and Sheila F. Lumley and Philippa C. Matthews and Anna L. McNaughton and Alexander J. Mentzer and Juthathip Mongkolsapaya and Sarah Oakley and Marta S. Oliveira and Timothy Peto and Rutger J. Ploeg and Jeremy Ratcliff and Melanie J. Robbins and David J. Roberts and Justine Rudkin and Rebecca A. Russell and Gavin Screaton and Malcolm G. Semple and Donal Skelly and Peter Simmonds and Nicole Stoesser and Lance Turtle and Susan Wareing and Maria Zambon},
    title = {{SARS}-{CoV}-2 {RNA} detected in blood products from patients with {COVID}-19 is not associated with infectious virus},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {181},
    doi = {10.12688/wellcomeopenres.16002.2},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] F. Hufsky, N. Beerenwinkel, I. M. Meyer, S. Roux, G. M. Cook, C. M. Kinsella, K. Lamkiewicz, M. Marquet, D. F. Nieuwenhuijse, I. Olendraite, S. Paraskevopoulou, F. Young, R. Dijkman, B. Ibrahim, J. Kelly, P. Le Mercier, M. Marz, A. Ramette, and V. Thiel, “The international virus bioinformatics meeting 2020.,” Viruses, vol. 12, 2020.
    [Bibtex]
    @Article{Hufsky:20a,
    author = {Hufsky, Franziska and Beerenwinkel, Niko and Meyer, Irmtraud M and Roux, Simon and Cook, Georgia May and Kinsella, Cormac M and Lamkiewicz, Kevin and Marquet, Mike and Nieuwenhuijse, David F and Olendraite, Ingrida and Paraskevopoulou, Sofia and Young, Francesca and Dijkman, Ronald and Ibrahim, Bashar and Kelly, Jenna and Le Mercier, Philippe and Marz, Manja and Ramette, Alban and Thiel, Volker},
    title = {The International Virus Bioinformatics Meeting 2020.},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    abstract = {The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.},
    doi = {10.3390/v12121398},
    issue = {12},
    keywords = {COVID-19; genome evolution; identification; metagenomics; software; viral diversity; viral taxonomy; virology; virome; virus bioinformatics},
    pmid = {33291220},
    }
  • [DOI] A. Bahai, E. Asgari, M. R. K. Mofrad, A. Kloetgen, and A. C. McHardy, “EpitopeVec: linear epitope prediction using deep protein sequence embeddings,” bioRxiv, 2020.
    [Bibtex]
    @Article{Bahai:20,
    author = {Akash Bahai and Ehsaneddin Asgari and Mohammad R.K. Mofrad and Andreas Kloetgen and Alice C. McHardy},
    title = {{EpitopeVec}: Linear Epitope Prediction Using Deep Protein Sequence Embeddings},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.26.395830},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] G. Cantelli, G. Cochrane, C. Brooksbank, E. McDonagh, P. Flicek, J. McEntyre, E. Birney, and R. Apweiler, “The European Bioinformatics Institute: empowering cooperation in response to a global health crisis,” Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Cantelli:20,
    author = {Gaia Cantelli and Guy Cochrane and Cath Brooksbank and Ellen McDonagh and Paul Flicek and Johanna McEntyre and Ewan Birney and Rolf Apweiler},
    title = {The {E}uropean {B}ioinformatics {I}nstitute: empowering cooperation in response to a global health crisis},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1077},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. M. Price, K. E. Hayer, A. B. R. McIntyre, N. S. Gokhale, J. S. Abebe, A. D. N. Fera, C. E. Mason, S. M. Horner, A. C. Wilson, D. P. Depledge, and M. D. Weitzman, “Direct RNA sequencing reveals m6a modifications on adenovirus RNA are necessary for efficient splicing,” Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Price:20,
    author = {Alexander M. Price and Katharina E. Hayer and Alexa B. R. McIntyre and Nandan S. Gokhale and Jonathan S. Abebe and Ashley N. Della Fera and Christopher E. Mason and Stacy M. Horner and Angus C. Wilson and Daniel P. Depledge and Matthew D. Weitzman},
    title = {Direct {RNA} sequencing reveals m6A modifications on adenovirus {RNA} are necessary for efficient splicing},
    journal = {{Nat Commun}},
    year = {2020},
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    }
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    [Bibtex]
    @Article{Santos-Hövener:20,
    author = {Claudia Santos-Hövener and Hannelore K Neuhauser and Angelika Schaffrath Rosario and Markus Busch and Martin Schlaud and Robert Hoffmann and Antje Gö{\ss}wald and Carmen Koschollek and Jens Hoebel and Jennifer Allen and Antje Haack-Erdmann and Stefan Brockmann and Thomas Ziese and Andreas Nitsche and Janine Michel and Sebastian Haller and Hendrik Wilking and Osamah Hamouda and Victor M Corman and Christian Drosten and Lars Schaade and Lothar H Wieler and Thomas Lampert and},
    title = {Serology- and {PCR}-based cumulative incidence of {SARS}-{CoV}-2 infection in adults in a successfully contained early hotspot ({CoMoLo} study), {G}ermany, {M}ay to {J}une 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {47},
    doi = {10.2807/1560-7917.es.2020.25.47.2001752},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
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    @Article{Husain-Syed:20,
    author = {Faeq Husain-Syed and Istv{\'{a}}n Vad{\'{a}}sz and Jochen Wilhelm and Hans-Dieter Walmrath and Werner Seeger and Horst-Walter Birk and Birgit Jennert and Hartmut Dietrich and Susanne Herold and Janina Trauth and Khodr Tello and Michael Sander and Rory E. Morty and Heiko Slanina and Christian G. Schüttler and John Ziebuhr and Shadi Kassoumeh and Claudio Ronco and Fiorenza Ferrari and Klaus Warnatz and Klaus Stahl and Benjamin Seeliger and Marius M. Hoeper and Tobias Welte and Sascha David},
    title = {Immunoglobulin Deficiency as an Indicator of Disease Severity in Patients with {COVID}-19},
    journal = {{Am J Physiol Lung Cell Mol Physiol}},
    year = {2020},
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    publisher = {American Physiological Society},
    }
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    [Bibtex]
    @Article{Duchene:20,
    author = {Sebastian Duchene and Leo Featherstone and Melina Haritopoulou-Sinanidou and Andrew Rambaut and Philippe Lemey and Guy Baele},
    title = {Temporal signal and the phylodynamic threshold of {SARS}-{CoV}-2},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa061},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Alygizakis:20,
    author = {Nikiforos Alygizakis and Athina N. Markou and Nikolaos I. Rousis and Aikaterini Galani and Margaritis Avgeris and Panagiotis G. Adamopoulos and Andreas Scorilas and Evi S. Lianidou and Dimitrios Paraskevis and Sotirios Tsiodras and Athanassios Tsakris and Meletios-Athanasios Dimopoulos and Nikolaos S. Thomaidis},
    title = {Analytical methodologies for the detection of {SARS}-{CoV}-2 in wastewater: Protocols and future perspectives},
    journal = {{Trends Analyt Chem}},
    year = {2020},
    pages = {116125},
    doi = {10.1016/j.trac.2020.116125},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Schlesinger:20,
    author = {Tobias Schlesinger and Benedikt Wei{\ss}brich and Florian Wedekink and Quirin Notz and Johannes Herrmann and Manuel Krone and Magdalena Sitter and Benedikt Schmid and Markus Kredel and Jan Stumpner and Lars Dölken and Jörg Wischhusen and Peter Kranke and Patrick Meybohm and Christopher Lotz},
    title = {Biodistribution and serologic response in {SARS}-{CoV}-2 induced {ARDS}: A cohort study},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {11},
    pages = {e0242917},
    doi = {10.1371/journal.pone.0242917},
    editor = {Francesco Di Gennaro},
    publisher = {Public Library of Science ({PLoS})},
    }
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    @Article{Gryseels:20a,
    author = {Sophie Gryseels and Luc De Bruyn and Ralf Gyselings and S{\'{e}}bastien Calvignac-Spencer and Fabian H. Leendertz and Herwig Leirs},
    title = {Risk of human-to-wildlife transmission of {SARS}-{CoV}-2},
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    publisher = {Wiley},
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    [Bibtex]
    @Article{Popa:20,
    author = {Alexandra Popa and Jakob-Wendelin Genger and Michael D. Nicholson and Thomas Penz and Daniela Schmid and Stephan W. Aberle and Benedikt Agerer and Alexander Lercher and Lukas Endler and Henrique Cola{\c{c}}o and Mark Smyth and Michael Schuster and Miguel L. Grau and Francisco Mart{\'{\i}}nez-Jim{\'{e}}nez and Oriol Pich and Wegene Borena and Erich Pawelka and Zsofia Keszei and Martin Senekowitsch and Jan Laine and Judith H. Aberle and Monika Redlberger-Fritz and Mario Karolyi and Alexander Zoufaly and Sabine Maritschnik and Martin Borkovec and Peter Hufnagl and Manfred Nairz and Günter Weiss and Michael T. Wolfinger and Dorothee von Laer and Giulio Superti-Furga and Nuria Lopez-Bigas and Elisabeth Puchhammer-Stöckl and Franz Allerberger and Franziska Michor and Christoph Bock and Andreas Bergthaler},
    title = {Genomic epidemiology of superspreading events in {A}ustria reveals mutational dynamics and transmission properties of {SARS}-{CoV}-2},
    journal = {{Sci Transl Med}},
    year = {2020},
    pages = {eabe2555},
    doi = {10.1126/scitranslmed.abe2555},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
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    [Bibtex]
    @Article{Feuillet:20,
    author = {Vincent Feuillet and Bruno Canard and Alain Trautmann},
    title = {Combining Antivirals and Immunomodulators to Fight {COVID}-19},
    journal = {{Trends Immunol}},
    year = {2020},
    doi = {10.1016/j.it.2020.11.003},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Lopez-Labrador:20,
    author = {F. Xavier L{\'{o}}pez-Labrador and Julianne R. Brown and Nicole Fischer and Heli Harvala and Sander Van Boheemen and Ondrej Cinek and Arzu Sayiner and Tina Vasehus Madsen and Eeva Auvinen and Verena Kufner and Michael Huber and Christophe Rodriguez and Marcel Jonges and Mario Hönemann and Petri Susi and Hugo Sousa and Paul E. Klapper and Alba P{\'{e}}rez-Catalu{\v{n}}a and Marta Hernandez and Richard Molenkamp and Lia van der Hoek and Rob Schuurman and Natacha Couto and Karoline Leuzinger and Peter Simmonds and Martin Beer and Dirk Höper and Sergio Kamminga and Mariet C.W. Feltkamp and Jes{\'{u}}s Rodr{\'{\i}}guez-D{\'{\i}}az and Els Keyaerts and Xiaohui Chen Nielsen and Elisabeth Puchhammer-Stöckl and Aloys C.M. Kroes and Javier Buesa and Judy Breuer and Eric C.J. Claas and Jutte J.C. de Vries},
    title = {Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part {I}: Wet lab procedure},
    journal = {{J Clin Virol}},
    year = {2020},
    volume = {134},
    pages = {104691},
    doi = {10.1016/j.jcv.2020.104691},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Brinkmann:20,
    author = {Annika Brinkmann and Aline R. V. Souza and Jos{\'{e}} Esparza and Andreas Nitsche and Clarissa R. Damaso},
    title = {Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the {USA}},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02202-0},
    publisher = {Springer Science and Business Media {LLC}},
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    [Bibtex]
    @Article{Volz:20,
    author = {Erik Volz and Verity Hill and John T. McCrone and Anna Price and David Jorgensen and {\'{A}}ine O'Toole and Joel Southgate and Robert Johnson and Ben Jackson and Fabricia F. Nascimento and Sara M. Rey and Samuel M. Nicholls and Rachel M. Colquhoun and Ana da Silva Filipe and James Shepherd and David J. Pascall and Rajiv Shah and Natasha Jesudason and Kathy Li and Ruth Jarrett and Nicole Pacchiarini and Matthew Bull and Lily Geidelberg and Igor Siveroni and Ian Goodfellow and Nicholas J. Loman and Oliver G. Pybus and David L. Robertson and Emma C. Thomson and Andrew Rambaut and Thomas R. Connor and Cherian Koshy and Emma Wise and Nick Cortes and Jessica Lynch and Stephen Kidd and Matilde Mori and Derek J. Fairley and Tanya Curran and James P. McKenna and Helen Adams and Christophe Fraser and Tanya Golubchik and David Bonsall and Catrin Moore and Sarah L. Caddy and Fahad A. Khokhar and Michelle Wantoch and Nicola Reynolds and Ben Warne and Joshua Maksimovic and Karla Spellman and Kathryn McCluggage and Michaela John and Robert Beer and Safiah Afifi and Sian Morgan and Angela Marchbank and Anna Price and Christine Kitchen and Huw Gulliver and Ian Merrick and Joel Southgate and Martyn Guest and Robert Munn and Trudy Workman and Thomas R. Connor and William Fuller and Catherine Bresner and Luke B. Snell and Themoula Charalampous and Gaia Nebbia and Rahul Batra and Jonathan Edgeworth and Samuel C. Robson and Angela Beckett and Katie F. Loveson and David M. Aanensen and Anthony P. Underwood and Corin A. Yeats and Khalil Abudahab and Ben E.W. Taylor and Mirko Menegazzo and Gemma Clark and Wendy Smith and Manjinder Khakh and Vicki M. Fleming and Michelle M. Lister and Hannah C. 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Fisher and Ali R. Awan and John Boyes and Judith Breuer and Kathryn Ann Harris and Julianne Rose Brown and Divya Shah and Laura Atkinson and Jack C.D. Lee and Adela Alcolea-Medina and Nathan Moore and Nicholas Cortes and Rebecca Williams and Michael R. Chapman and Lisa J. Levett and Judith Heaney and Darren L. Smith and Matthew Bashton and Gregory R. Young and John Allan and Joshua Loh and Paul A. Randell and Alison Cox and Pinglawathee Madona and Alison Holmes and Frances Bolt and James Price and Siddharth Mookerjee and Aileen Rowan and Graham P. Taylor and Manon Ragonnet-Cronin and Fabricia F. Nascimento and David Jorgensen and Igor Siveroni and Rob Johnson and Olivia Boyd and Lily Geidelberg and Erik M. Volz and Kirstyn Brunker and Katherine L. Smollett and Nicholas J. Loman and Joshua Quick and Claire McMurray and Joanne Stockton and Sam Nicholls and Will Rowe and Radoslaw Poplawski and Rocio T. Martinez-Nunez and Jenifer Mason and Trevor I. 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Curran and Surendra Parmar and Angie Lackenby and Tamyo Mbisa and Steven Platt and Shahjahan Miah and David Bibby and Carmen Manso and Jonathan Hubb and Meera Chand and Gavin Dabrera and Mary Ramsay and Daniel Bradshaw and Alicia Thornton and Richard Myers and Ulf Schaefer and Natalie Groves and Eileen Gallagher and David Lee and David Williams and Nicholas Ellaby and Ian Harrison and Hassan Hartman and Nikos Manesis and Vineet Patel and Chloe Bishop and Vicki Chalker and Husam Osman and Andrew Bosworth and Esther Robinson and Matthew T.G. Holden and Sharif Shaaban and Alec Birchley and Alexander Adams and Alisha Davies and Amy Gaskin and Amy Plimmer and Bree Gatica-Wilcox and Caoimhe McKerr and Catherine Moore and Chris Williams and David Heyburn and Elen De Lacy and Ember Hilvers and Fatima Downing and Giri Shankar and Hannah Jones and Hibo Asad and Jason Coombes and Joanne Watkins and Johnathan M. Evans and Laia Fina and Laura Gifford and Lauren Gilbert and Lee Graham and Malorie Perry and Mari Morgan and Matthew Bull and Michelle Cronin and Nicole Pacchiarini and Noel Craine and Rachel Jones and Robin Howe and Sally Corden and Sara Rey and Sara Kumziene-Summerhayes and Sarah Taylor and Simon Cottrell and Sophie Jones and Sue Edwards and Justin O'Grady and Andrew J. Page and John Wain and Mark A. Webber and Alison E. Mather and David J. Baker and Steven Rudder and Muhammad Yasir and Nicholas M. Thomson and Alp Aydin and Ana P. Tedim and Gemma L. Kay and Alexander J. Trotter and Rachel A.J. Gilroy and Nabil-Fareed Alikhan and Leonardo de Oliveira Martins and Thanh Le-Viet and Lizzie Meadows and Anastasia Kolyva and Maria Diaz and Andrew Bell and Ana Victoria Gutierrez and Ian G. Charles and Evelien M. Adriaenssens and Robert A. Kingsley and Anna Casey and David A. Simpson and Zoltan Molnar and Thomas Thompson and Erwan Acheson and Jane A.H. Masoli and Bridget A. Knight and Andrew Hattersley and Sian Ellard and Cressida Auckland and Tabitha W. Mahungu and Dianne Irish-Tavares and Tanzina Haque and Yann Bourgeois and Garry P. Scarlett and David G. Partridge and Mohammad Raza and Cariad Evans and Kate Johnson and Steven Liggett and Paul Baker and Sarah Essex and Ronan A. Lyons and Laura G. Caller and Sergi Castellano and Rachel J. Williams and Mark Kristiansen and Sunando Roy and Charlotte A. Williams and Patricia L. Dyal and Helena J. Tutill and Yasmin N. Panchbhaya and Leysa M. Forrest and Paola Niola and Jacqueline Findlay and Tony T. Brooks and Artemis Gavriil and Lamia Mestek-Boukhibar and Sam Weeks and Sarojini Pandey and Lisa Berry and Katie Jones and Alex Richter and Andrew Beggs and Colin P. Smith and Giselda Bucca and Andrew R. Hesketh and Ewan M. Harrison and Sharon J. Peacock and Sophie Palmer and Carol M. Churcher and Katherine L. Bellis and Sophia T. Girgis and Plamena Naydenova and Beth Blane and Sushmita Sridhar and Chris Ruis and Sally Forrest and Claire Cormie and Harmeet K. Gill and Joana Dias and Ellen E. Higginson and Mailis Maes and Jamie Young and Leanne M. Kermack and Nazreen F. Hadjirin and Dinesh Aggarwal and Luke Griffith and Tracey Swingler and Rose K. Davidson and Andrew Rambaut and Thomas Williams and Carlos E. Balcazar and Michael D. Gallagher and {\'{A}}ine O{\textquotesingle}Toole and Stefan Rooke and Ben Jackson and Rachel Colquhoun and Jordan Ashworth and Verity Hill and J.T. McCrone and Emily Scher and Xiaoyu Yu and Kathleen A. Williamson and Thomas D. Stanton and Stephen L. Michell and Claire M. Bewshea and Ben Temperton and Michelle L. Michelsen and Joanna Warwick-Dugdale and Robin Manley and Audrey Farbos and James W. Harrison and Christine M. Sambles and David J. Studholme and Aaron R. Jeffries and Alistair C. Darby and Julian A. Hiscox and Steve Paterson and Miren Iturriza-Gomara and Kathryn A. Jackson and Anita O. Lucaci and Edith E. Vamos and Margaret Hughes and Lucille Rainbow and Richard Eccles and Charlotte Nelson and Mark Whitehead and Lance Turtle and Sam T. Haldenby and Richard Gregory and Matthew Gemmell and Dominic Kwiatkowski and Thushan I. de Silva and Nikki Smith and Adrienn Angyal and Benjamin B. Lindsey and Danielle C. Groves and Luke R. Green and Dennis Wang and Timothy M. Freeman and Matthew D. Parker and Alexander J. Keeley and Paul J. Parsons and Rachel M. Tucker and Rebecca Brown and Matthew Wyles and Chrystala Constantinidou and Meera Unnikrishnan and Sascha Ott and Jeffrey K.J. Cheng and Hannah E. Bridgewater and Lucy R. Frost and Grace Taylor-Joyce and Richard Stark and Laura Baxter and Mohammad T. Alam and Paul E. Brown and Patrick C. McClure and Joseph G. Chappell and Theocharis Tsoleridis and Jonathan Ball and Dimitris Gramatopoulos and David Buck and John A. 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Berger and Gaurang Patel and Maria V. Garcia-Casado and Thomas Dibling and Samantha McGuigan and Hazel A. Rogers and Adam D. Hunter and Emily Souster and Alexandra S. Neaverson},
    title = {Evaluating the Effects of {SARS}-{CoV}-2 Spike Mutation {D614G} on Transmissibility and Pathogenicity},
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    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Trimpert:20,
    author = {Jakob Trimpert and Daria Vladimirova and Kristina Dietert and Azza Abdelgawad and Dusan Kunec and Simon Dökel and Anne Voss and Achim D. Gruber and Luca D. Bertzbach and Nikolaus Osterrieder},
    title = {The {R}oborovski Dwarf Hamster Is A Highly Susceptible Model for a Rapid and Fatal Course of {SARS}-{CoV}-2 Infection},
    journal = {{Cell Rep}},
    year = {2020},
    pages = {108488},
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    publisher = {Elsevier {BV}},
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    [Bibtex]
    @Article{Cuevas-Ferrando:20,
    author = {Enric Cuevas-Ferrando and Alba P{\'{e}}rez-Catalu{\~{n}}a and Ana Allende and Susana Guix and Walter Randazzo and Gloria S{\'{a}}nchez},
    title = {Recovering coronavirus from large volumes of water},
    journal = {{Sci Total Environ}},
    year = {2020},
    pages = {143101},
    doi = {10.1016/j.scitotenv.2020.143101},
    publisher = {Elsevier {BV}},
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    @Article{Weissberg:20,
    author = {Dana Weissberg and Jürg Böni and Silvana K. Rampini and Verena Kufner and Maryam Zaheri and Peter W. Schreiber and Irene A. Abela and Michael Huber and Hugo Sax and Aline Wolfensberger},
    title = {Does respiratory co-infection facilitate dispersal of {SARS}-{CoV}-2? {I}nvestigation of a super-spreading event in an open-space office},
    journal = {{Antimicrob Resist Infect Control}},
    year = {2020},
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    @Article{Psichogiou:20,
    author = {Mina Psichogiou and Andreas Karabinis and Ioanna D. Pavlopoulou and Dimitrios Basoulis and Konstantinos Petsios and Sotirios Roussos and Maria Pratikaki and Edison Jahaj and Konstantinos Protopapas and Konstantinos Leontis and Vasiliki Rapti and Anastasia Kotanidou and Anastasia Antoniadou and Garyphallia Poulakou and Dimitrios Paraskevis and Vana Sypsa and Angelos Hatzakis},
    title = {Antibodies against {SARS}-{CoV}-2 among health care workers in a country with low burden of {COVID}-19},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {12},
    pages = {e0243025},
    doi = {10.1371/journal.pone.0243025},
    editor = {Ronald Dijkman},
    publisher = {Public Library of Science ({PLoS})},
    }
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    [Bibtex]
    @Article{Gasbarri:20,
    author = {Matteo Gasbarri and Philip V'kovski and Giulia Torriani and Volker Thiel and Francesco Stellacci and Caroline Tapparel and Valeria Cagno},
    title = {{SARS}-{CoV}-2 Inhibition by Sulfonated Compounds},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
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    doi = {10.3390/microorganisms8121894},
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    @Article{Rastogi:20,
    author = {Meghana Rastogi and Neha Pandey and Astha Shukla and Sunit K. Singh},
    title = {{SARS} coronavirus 2: from genome to infectome},
    journal = {{Respir Res}},
    year = {2020},
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    [Bibtex]
    @Article{Sanchez-Felipe:20,
    author = {Lorena Sanchez-Felipe and Thomas Vercruysse and Sapna Sharma and Ji Ma and Viktor Lemmens and Dominique Van Looveren and Mahadesh Prasad Arkalagud Javarappa and Robbert Boudewijns and Bert Malengier-Devlies and Laurens Liesenborghs and Suzanne J. F. Kaptein and Carolien De Keyzer and Lindsey Bervoets and Sarah Debaveye and Madina Rasulova and Laura Seldeslachts and Li-Hsin Li and Sander Jansen and Michael Bright Yakass and Babs E. Verstrepen and Kinga P. Böszörm{\'{e}}nyi and Gwendoline Kiemenyi-Kayere and Nikki van Driel and Osbourne Quaye and Xin Zhang and Sebastiaan ter Horst and Niraj Mishra and Ward Deboutte and Jelle Matthijnssens and Lotte Coelmont and Corinne Vandermeulen and Elisabeth Heylen and Valentijn Vergote and Dominique Schols and Zhongde Wang and Willy Bogers and Thijs Kuiken and Ernst Verschoor and Christopher Cawthorne and Koen Van Laere and Ghislain Opdenakker and Greetje Vande Velde and Birgit Weynand and Dirk E. Teuwen and Patrick Matthys and Johan Neyts and Hendrik Jan Thibaut and Kai Dallmeier},
    title = {A single-dose live-attenuated {YF}17D-vectored {SARS}-{CoV}-2 vaccine candidate},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-3035-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    @Article{Ziv:20,
    author = {Omer Ziv and Jonathan Price and Lyudmila Shalamova and Tsveta Kamenova and Ian Goodfellow and Friedemann Weber and Eric A. Miska},
    title = {The Short- and Long-Range {RNA}-{RNA} Interactome of {SARS}-{CoV}-2},
    journal = {{Mol Cell}},
    year = {2020},
    doi = {10.1016/j.molcel.2020.11.004},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Meinhardt:20,
    author = {Jenny Meinhardt and Josefine Radke and Carsten Dittmayer and Jonas Franz and Carolina Thomas and Ronja Mothes and Michael Laue and Julia Schneider and Sebastian Brünink and Selina Greuel and Malte Lehmann and Olga Hassan and Tom Aschman and Elisa Schumann and Robert Lorenz Chua and Christian Conrad and Roland Eils and Werner Stenzel and Marc Windgassen and Larissa Rö{\ss}ler and Hans-Hilmar Goebel and Hans R. Gelderblom and Hubert Martin and Andreas Nitsche and Walter J. Schulz-Schaeffer and Samy Hakroush and Martin S. Winkler and Björn Tampe and Franziska Scheibe and P{\'{e}}ter Körtv{\'{e}}lyessy and Dirk Reinhold and Britta Siegmund and Anja A. Kühl and Sefer Elezkurtaj and David Horst and Lars Oesterhelweg and Michael Tsokos and Barbara Ingold-Heppner and Christine Stadelmann and Christian Drosten and Victor Max Corman and Helena Radbruch and Frank L. Heppner},
    title = {Olfactory transmucosal {SARS}-{CoV}-2 invasion as a port of central nervous system entry in individuals with {COVID}-19},
    journal = {{Nat Neurosci}},
    year = {2020},
    doi = {10.1038/s41593-020-00758-5},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Hawman:20,
    author = {David W. Hawman and Gustaf Ahl{\'{e}}n and K. Sofia Appelberg and Kimberly Meade-White and Patrick W. Hanley and Dana Scott and Vanessa Monteil and Stephanie Devignot and Atsushi Okumura and Friedemann Weber and Heinz Feldmann and Matti Sällberg and Ali Mirazimi},
    title = {A {DNA}-based vaccine protects against {C}rimean-{C}ongo haemorrhagic fever virus disease in a {C}ynomolgus macaque model},
    journal = {{Nat Microbiol}},
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    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Hörner:20,
    author = {Cindy Hörner and Christoph Schürmann and Arne Auste and Aileen Ebenig and Samada Muraleedharan and Kenneth H. Dinnon and Tatjana Scholz and Maike Herrmann and Barbara S. Schnierle and Ralph S. Baric and Michael D. Mühlebach},
    title = {A highly immunogenic and effective measles virus-based {T}h1-biased {COVID}-19 vaccine},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202014468},
    doi = {10.1073/pnas.2014468117},
    publisher = {Proceedings of the National Academy of Sciences},
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    [Bibtex]
    @Article{Holwerda:20,
    author = {Melle Holwerda and Philip V'kovski and Manon Wider and Volker Thiel and Ronald Dijkman},
    title = {Identification of an Antiviral Compound from the Pandemic Response Box that Efficiently Inhibits {SARS}-{CoV}-2 Infection In Vitro},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1872},
    doi = {10.3390/microorganisms8121872},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Brown:20,
    author = {David M. Brown and Yun Zhang and Richard H. Scheuermann},
    title = {Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1856},
    doi = {10.3390/microorganisms8121856},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Ben-Othman:20,
    author = {Rym Ben-Othman and Bing Cai and Aaron C. Liu and Natallia Varankovich and Daniel He and Travis M. Blimkie and Amy H. Lee and Erin E. Gill and Mark Novotny and Brian Aevermann and Sibyl Drissler and Casey P. Shannon and Sarah McCann and Kim Marty and Gordean Bjornson and Rachel D. Edgar and David Tse Shen Lin and Nicole Gladish and Julia Maclsaac and Nelly Amenyogbe and Queenie Chan and Alba Llibre and Joyce Collin and Elise Landais and Khoa Le and Samantha M. Reiss and Wayne C. Koff and Colin Havenar-Daughton and Manraj Heran and Bippan Sangha and David Walt and Mel Krajden and Shane Crotty and Devin Sok and Bryan Briney and Dennis R. Burton and Darragh Duffy and Leonard J. Foster and William W. Mohn and Michael S. Kobor and Scott J. Tebbutt and Ryan R. Brinkman and Richard H. Scheuermann and Robert E. W. Hancock and Tobias R. Kollmann and Manish Sadarangani},
    title = {Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults},
    journal = {Frontiers in Immunology},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.580373},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] F. L. Nobrega, H. Walinga, B. E. Dutilh, and S. J. J. Brouns, “Prophages are associated with extensive CRISPR–cas auto-immunity,” Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Nobrega:20,
    author = {Franklin L Nobrega and Hielke Walinga and Bas E Dutilh and Stan J J Brouns},
    title = {Prophages are associated with extensive {CRISPR}{\textendash}Cas auto-immunity},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1071},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Weis, A. Scherag, M. Baier, M. Kiehntopf, T. Kamradt, S. Kolanos, J. Ankert, S. Glöckner, O. Makarewicz, S. Hagel, C. Bahrs, A. Kimmig, H. Proquitté, J. Guerra, D. Rimek, B. Löffler, M. W. Pletz, T. Hotz, P. Enders, R. Koch, S. Mai, M. Ullrich, C. Richert, C. Eibner, B. Meinung, K. Stötzer, J. Köhler, H. Cipowicz, C. Pinkwart, M. Bauer, P. Dickmann, A. Licht, J. Scholz, W. Wetzker, A. Hartung, D. Weiss, L. Thieme, G. Hanf, C. Schnizer, J. Müller, J. Kosenkow, F. Röstel, N. Andreas, R. Marquardt, S. Deinhardt-Emmer, and S. Kuhn, “Antibody response using six different serological assays in a completely PCR-tested community after a COVID-19 outbreak – the CoNAN study,” Clin Microbiol Infect, 2020.
    [Bibtex]
    @Article{Weis:20,
    author = {Sebastian Weis and Andr{\'{e}} Scherag and Michael Baier and Michael Kiehntopf and Thomas Kamradt and Steffi Kolanos and Juliane Ankert and Stefan Glöckner and Oliwia Makarewicz and Stefan Hagel and Christina Bahrs and Aurelia Kimmig and Hans Proquitt{\'{e}} and Joel Guerra and Dagmar Rimek and Bettina Löffler and Mathias W. Pletz and Thomas Hotz and Petra Enders and Renate Koch and Steffen Mai and Matthias Ullrich and Cora Richert and Cornelius Eibner and Bettina Meinung and Kay Stötzer and Julia Köhler and Hans Cipowicz and Christine Pinkwart and Michael Bauer and Petra Dickmann and Annika Licht and Juliane Scholz and Wibke Wetzker and Anita Hartung and Daniel Weiss and Lara Thieme and Gabi Hanf and Clara Schnizer and Jasmin Müller and Jennifer Kosenkow and Franziska Röstel and Nico Andreas and Raphaela Marquardt and Stefanie Deinhardt-Emmer and Sebastian Kuhn},
    title = {Antibody response using six different serological assays in a completely {PCR}-tested community after a {COVID}-19 outbreak - The {CoNAN} study},
    journal = {{Clin Microbiol Infect}},
    year = {2020},
    doi = {10.1016/j.cmi.2020.11.009},
    publisher = {Elsevier {BV}},
    }
  • [DOI] I. Kalvari, E. P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S. R. Eddy, R. Finn, A. Bateman, and A. I. Petrov, “Rfam 14: expanded coverage of metagenomic, viral and microRNA families,” Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Kalvari:20,
    author = {Ioanna Kalvari and Eric P Nawrocki and Nancy Ontiveros-Palacios and Joanna Argasinska and Kevin Lamkiewicz and Manja Marz and Sam Griffiths-Jones and Claire Toffano-Nioche and Daniel Gautheret and Zasha Weinberg and Elena Rivas and Sean R Eddy and Robert~D Finn and Alex Bateman and Anton I Petrov},
    title = {Rfam 14: expanded coverage of metagenomic, viral and {microRNA} families},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1047},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] L. Novelli, F. Motta, A. Ceribelli, G. M. Guidelli, N. Luciano, N. Isailovic, M. Vecellio, M. Caprioli, N. Clementi, M. Clementi, N. Mancini, C. Selmi, and M. D. Santis, “A case of psoriatic arthritis triggered by SARS-CoV-2 infection,” Rheumatology, 2020.
    [Bibtex]
    @Article{Novelli:20,
    author = {Lucia Novelli and Francesca Motta and Angela Ceribelli and Giacomo M Guidelli and Nicoletta Luciano and Natasa Isailovic and Matteo Vecellio and Marta Caprioli and Nicola Clementi and Massimo Clementi and Nicasio Mancini and Carlo Selmi and Maria De Santis},
    title = {A case of psoriatic arthritis triggered by {SARS}-{CoV}-2 infection},
    journal = {Rheumatology},
    year = {2020},
    doi = {10.1093/rheumatology/keaa691},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] P. A. Reuken, M. Wüst, B. Löffler, M. Bauer, and A. Stallmach, “Letter: SARS-CoV-2-induced gastrointestinal inflammation.,” Aliment Pharmacol Ther, vol. 52, p. 1748–1749, 2020.
    [Bibtex]
    @Article{Reuken:20,
    author = {Reuken, Philipp A and Wüst, Michaela and Löffler, Bettina and Bauer, Michael and Stallmach, Andreas},
    title = {Letter: {SARS-CoV-2}-induced gastrointestinal inflammation.},
    journal = {{Aliment Pharmacol Ther}},
    year = {2020},
    volume = {52},
    pages = {1748--1749},
    doi = {10.1111/apt.16087},
    issue = {11-12},
    pmid = {33205881},
    }
  • [DOI] R. Boudewijns, H. J. Thibaut, S. J. F. Kaptein, R. Li, V. Vergote, L. Seldeslachts, J. Van Weyenbergh, C. De Keyzer, L. Bervoets, S. Sharma, L. Liesenborghs, J. Ma, S. Jansen, D. Van Looveren, T. Vercruysse, X. Wang, D. Jochmans, E. Martens, K. Roose, D. De Vlieger, B. Schepens, T. Van Buyten, S. Jacobs, Y. Liu, J. Martí-Carreras, B. Vanmechelen, T. Wawina-Bokalanga, L. Delang, J. Rocha-Pereira, L. Coelmont, W. Chiu, P. Leyssen, E. Heylen, D. Schols, L. Wang, L. Close, J. Matthijnssens, M. Van Ranst, V. Compernolle, G. Schramm, K. Van Laere, X. Saelens, N. Callewaert, G. Opdenakker, P. Maes, B. Weynand, C. Cawthorne, G. Vande Velde, Z. Wang, J. Neyts, and K. Dallmeier, “STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters.,” Nat Commun, vol. 11, p. 5838, 2020.
    [Bibtex]
    @Article{Boudewijns:20,
    author = {Boudewijns, Robbert and Thibaut, Hendrik Jan and Kaptein, Suzanne J F and Li, Rong and Vergote, Valentijn and Seldeslachts, Laura and Van Weyenbergh, Johan and De Keyzer, Carolien and Bervoets, Lindsey and Sharma, Sapna and Liesenborghs, Laurens and Ma, Ji and Jansen, Sander and Van Looveren, Dominique and Vercruysse, Thomas and Wang, Xinyu and Jochmans, Dirk and Martens, Erik and Roose, Kenny and De Vlieger, Dorien and Schepens, Bert and Van Buyten, Tina and Jacobs, Sofie and Liu, Yanan and Martí-Carreras, Joan and Vanmechelen, Bert and Wawina-Bokalanga, Tony and Delang, Leen and Rocha-Pereira, Joana and Coelmont, Lotte and Chiu, Winston and Leyssen, Pieter and Heylen, Elisabeth and Schols, Dominique and Wang, Lanjiao and Close, Lila and Matthijnssens, Jelle and Van Ranst, Marc and Compernolle, Veerle and Schramm, Georg and Van Laere, Koen and Saelens, Xavier and Callewaert, Nico and Opdenakker, Ghislain and Maes, Piet and Weynand, Birgit and Cawthorne, Christopher and Vande Velde, Greetje and Wang, Zhongde and Neyts, Johan and Dallmeier, Kai},
    title = {{STAT2} signaling restricts viral dissemination but drives severe pneumonia in {SARS-CoV-2} infected hamsters.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {5838},
    abstract = {Emergence of SARS-CoV-2 causing COVID-19 has resulted in hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that Syrian hamsters, in contrast to mice, are highly permissive to SARS-CoV-2 and develop bronchopneumonia and strong inflammatory responses in the lungs with neutrophil infiltration and edema, further confirmed as consolidations visualized by micro-CT alike in clinical practice. Moreover, we identify an exuberant innate immune response as key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.},
    doi = {10.1038/s41467-020-19684-y},
    issue = {1},
    pmid = {33203860},
    }
  • [DOI] K. Wernike, A. Aebischer, A. Michelitsch, D. Hoffmann, C. Freuling, A. Balkema-Buschmann, A. Graaf, T. Müller, N. Osterrieder, M. Rissmann, D. Rubbenstroth, J. Schön, C. Schulz, J. Trimpert, L. Ulrich, A. Volz, T. Mettenleiter, and M. Beer, “Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals,” Transbound Emerg Dis, 2020.
    [Bibtex]
    @Article{Wernike:20b,
    author = {Kerstin Wernike and Andrea Aebischer and Anna Michelitsch and Donata Hoffmann and Conrad Freuling and Anne Balkema-Buschmann and Annika Graaf and Thomas Müller and Nikolaus Osterrieder and Melanie Rissmann and Dennis Rubbenstroth and Jacob Schön and Claudia Schulz and Jakob Trimpert and Lorenz Ulrich and Asisa Volz and Thomas Mettenleiter and Martin Beer},
    title = {Multi-species {ELISA} for the detection of antibodies against {SARS}-{CoV}-2 in animals},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
    doi = {10.1111/tbed.13926},
    publisher = {Wiley},
    }
  • [DOI] B. Zhou, T. T. N. Thao, D. Hoffmann, A. Taddeo, N. Ebert, F. Labroussaa, A. Pohlmann, J. King, J. Portmann, N. J. Halwe, L. Ulrich, B. S. Trüeb, J. N. Kelly, X. Fan, B. Hoffmann, S. Steiner, L. Wang, L. Thomann, X. Lin, H. Stalder, B. Pozzi, S. de Brot, N. Jiang, D. Cui, J. Hossain, M. Wilson, M. Keller, T. J. Stark, J. R. Barnes, R. Dijkman, J. Jores, C. Benarafa, D. E. Wentworth, V. Thiel, and M. Beer, “SARS-CoV-2 spike d614g variant confers enhanced replication and transmissibility,” bioRxiv, 2020.
    [Bibtex]
    @Article{Zhou:20,
    author = {Bin Zhou and Tran Thi Nhu Thao and Donata Hoffmann and Adriano Taddeo and Nadine Ebert and Fabien Labroussaa and Anne Pohlmann and Jacqueline King and Jasmine Portmann and Nico Joel Halwe and Lorenz Ulrich and Bettina Salome Trüeb and Jenna N. Kelly and Xiaoyu Fan and Bernd Hoffmann and Silvio Steiner and Li Wang and Lisa Thomann and Xudong Lin and Hanspeter Stalder and Berta Pozzi and Simone de Brot and Nannan Jiang and Dan Cui and Jaber Hossain and Malania Wilson and Matthew Keller and Thomas J. Stark and John R. Barnes and Ronald Dijkman and Joerg Jores and Charaf Benarafa and David E. Wentworth and Volker Thiel and Martin Beer},
    title = {{SARS}-{CoV}-2 spike D614G variant confers enhanced replication and transmissibility},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.27.357558},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] V. M. Corman, V. C. Haage, T. Bleicker, M. L. Schmidt, B. Mühlemann, M. Zuchowski, W. K. Jó. Lei, P. Tscheak, E. Möncke-Buchner, M. A. Müller, A. Krumbholz, J. F. Drexler, and C. Drosten, “Comparison of seven commercial SARS-CoV-2 rapid point-of-care antigen tests,” medRxiv, 2020.
    [Bibtex]
    @Article{Corman:20b,
    author = {Victor M. Corman and Verena Claudia Haage and Tobias Bleicker and Marie Luisa Schmidt and Barbara Mühlemann and Marta Zuchowski and Wendy Karen J{\'{o}} Lei and Patricia Tscheak and Elisabeth Möncke-Buchner and Marcel A. Müller and Andi Krumbholz and Jan Felix Drexler and Christian Drosten},
    title = {Comparison of seven commercial {SARS}-{CoV}-2 rapid Point-of-Care Antigen tests},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.12.20230292},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lytras, G. Arriagada, and R. J. Gifford, “Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes,” bioRxiv, 2020.
    [Bibtex]
    @Article{Lytras:20a,
    author = {Spyros Lytras and Gloria Arriagada and Robert J. Gifford},
    title = {Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.02.364562},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. C. Thomson, L. E. Rosen, J. G. Shepherd, R. Spreafico, A. S. da Filipe, J. A. Wojcechowskyj, C. Davis, L. Piccoli, D. J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, A. D. Marco, K. Li, J. Bassi, A. O’Toole, D. Pinto, R. M. Colquhoun, K. Culap, B. Jackson, F. Zatta, A. Rambaut, S. Jaconi, V. B. Sreenu, J. Nix, R. F. Jarrett, M. Beltramello, K. Nomikou, M. Pizzuto, L. Tong, E. Cameroni, N. Johnson, A. Wickenhagen, A. Ceschi, D. Mair, P. Ferrari, K. Smollett, F. Sallusto, S. Carmichael, C. Garzoni, J. Nichols, M. Galli, J. Hughes, A. Riva, A. Ho, M. G. Semple, P. J. M. Openshaw, K. J. Baillie, S. J. Rihn, S. J. Lycett, H. W. Virgin, A. Telenti, D. Corti, D. L. Robertson, G. Snell, and and, “The circulating SARS-CoV-2 spike variant n439k maintains fitness while evading antibody-mediated immunity,” bioRxiv, 2020.
    [Bibtex]
    @Article{Thomson:20,
    author = {Emma C. Thomson and Laura E. Rosen and James G. Shepherd and Roberto Spreafico and Ana da Silva Filipe and Jason A. Wojcechowskyj and Chris Davis and Luca Piccoli and David J. Pascall and Josh Dillen and Spyros Lytras and Nadine Czudnochowski and Rajiv Shah and Marcel Meury and Natasha Jesudason and Anna De Marco and Kathy Li and Jessica Bassi and Aine O'Toole and Dora Pinto and Rachel M. Colquhoun and Katja Culap and Ben Jackson and Fabrizia Zatta and Andrew Rambaut and Stefano Jaconi and Vattipally B. Sreenu and Jay Nix and Ruth F. Jarrett and Martina Beltramello and Kyriaki Nomikou and Matteo Pizzuto and Lily Tong and Elisabetta Cameroni and Natasha Johnson and Arthur Wickenhagen and Alessandro Ceschi and Daniel Mair and Paolo Ferrari and Katherine Smollett and Federica Sallusto and Stephen Carmichael and Christian Garzoni and Jenna Nichols and Massimo Galli and Joseph Hughes and Agostino Riva and Antonia Ho and Malcolm G. Semple and Peter J.M. Openshaw and J. Kenneth Baillie and Suzannah J. Rihn and Samantha J. Lycett and Herbert W. Virgin and Amalio Telenti and Davide Corti and David L. Robertson and Gyorgy Snell and and},
    title = {The circulating {SARS}-{CoV}-2 spike variant N439K maintains fitness while evading antibody-mediated immunity},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.04.355842},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. V. der Toorn, D. Oh, D. Bourquain, J. Michel, E. Krause, A. Nitsche, and M. V. K. and, “COVIDStrategyCalculator: a standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation,” medRxiv, 2020.
    [Bibtex]
    @Article{Toorn:20,
    author = {Wiep Van der Toorn and Djin-Ye Oh and Daniel Bourquain and Janine Michel and Eva Krause and Andreas Nitsche and Max Von Kleist and},
    title = {{COVIDStrategyCalculator}: A standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.18.20233825},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • O. Zablocki, M. Michelsen, M. Burris, N. Solonenko, J. Warwick-Dugdale, R. Ghosh, J. Pett-Ridge, M. B. Sullivan, and B. Temperton, “VirION2: a short-and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature,” bioRxiv, 2020.
    [Bibtex]
    @Article{Zablocki:20,
    author = {Zablocki, Olivier and Michelsen, Michelle and Burris, Marie and Solonenko, Natalie and Warwick-Dugdale, Joanna and Ghosh, Romik and Pett-Ridge, Jennifer and Sullivan, Matthew B and Temperton, Ben},
    title = {{VirION2}: a short-and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature},
    journal = {{bioRxiv}},
    year = {2020},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. C. Gregory, K. Gerhardt, Z. Zhong, B. Bolduc, B. Temperton, K. T. Konstantinidis, and M. B. Sullivan, “MetaPop: a pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations,” bioRxiv, 2020.
    [Bibtex]
    @Article{Gregory:20,
    author = {Ann C. Gregory and Kenji Gerhardt and Zhi-Ping Zhong and Benjamin Bolduc and Ben Temperton and Konstantinos T. Konstantinidis and Matthew B. Sullivan},
    title = {{MetaPop}: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.01.363960},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Vetter, C. S. Eberhardt, B. Meyer, P. A. M. Murillo, G. Torriani, F. Pigny, S. Lemeille, S. Cordey, F. Laubscher, D. Vu, A. Calame, M. Schibler, F. Jacquerioz, G. Blanchard-Rohner, C. Siegrist, L. Kaiser, A. M. Didierlaurent, and I. Eckerle, “Daily viral kinetics and innate and adaptive immune response assessment in COVID-19: a case series,” mSphere, vol. 5, iss. 6, 2020.
    [Bibtex]
    @Article{Vetter:20,
    author = {Pauline Vetter and Christiane S. Eberhardt and Benjamin Meyer and Paola Andrea Martinez Murillo and Giulia Torriani and Fiona Pigny and Sylvain Lemeille and Samuel Cordey and Florian Laubscher and Diem-Lan Vu and Adrien Calame and Manuel Schibler and Frederique Jacquerioz and G{\'{e}}raldine Blanchard-Rohner and Claire-Anne Siegrist and Laurent Kaiser and Arnaud M. Didierlaurent and Isabella Eckerle},
    title = {Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in {COVID}-19: a Case Series},
    journal = {{mSphere}},
    year = {2020},
    volume = {5},
    number = {6},
    doi = {10.1128/msphere.00827-20},
    editor = {Christina F. Spiropoulou},
    publisher = {American Society for Microbiology},
    }
  • [DOI] B. O. B. Munnink, R. S. Sikkema, D. F. Nieuwenhuijse, R. J. Molenaar, E. Munger, R. Molenkamp, A. van der Spek, P. Tolsma, A. Rietveld, M. Brouwer, N. Bouwmeester-Vincken, F. Harders, R. H. der Honing, M. C. A. Wegdam-Blans, R. J. Bouwstra, C. GeurtsvanKessel, A. A. van der Eijk, F. C. Velkers, L. A. M. Smit, A. Stegeman, W. H. M. van der Poel, and M. P. G. Koopmans, “Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans,” Science, p. eabe5901, 2020.
    [Bibtex]
    @Article{Munnink:20,
    author = {Bas B. Oude Munnink and Reina S. Sikkema and David F. Nieuwenhuijse and Robert Jan Molenaar and Emmanuelle Munger and Richard Molenkamp and Arco van der Spek and Paulien Tolsma and Ariene Rietveld and Miranda Brouwer and Noortje Bouwmeester-Vincken and Frank Harders and Renate Hakze-van der Honing and Marjolein C. A. Wegdam-Blans and Ruth J. Bouwstra and Corine GeurtsvanKessel and Annemiek A. van der Eijk and Francisca C. Velkers and Lidwien A. M. Smit and Arjan Stegeman and Wim H. M. van der Poel and Marion P. G. Koopmans},
    title = {Transmission of {SARS}-{CoV}-2 on mink farms between humans and mink and back to humans},
    journal = {Science},
    year = {2020},
    pages = {eabe5901},
    doi = {10.1126/science.abe5901},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. K. Mirzaei and L. Deng, “Sustainable microbiome: a symphony orchestrated by synthetic phages,” Microb Biotechnol, 2020.
    [Bibtex]
    @Article{Mirzaei:20b,
    author = {Mohammadali Khan Mirzaei and Li Deng},
    title = {Sustainable Microbiome: a symphony orchestrated by synthetic phages},
    journal = {{Microb Biotechnol}},
    year = {2020},
    doi = {10.1111/1751-7915.13697},
    publisher = {Wiley},
    }
  • [DOI] I. Manfredonia, C. Nithin, A. Ponce-Salvatierra, P. Ghosh, T. K. Wirecki, T. Marinus, N. S. Ogando, E. Snijder, M. J. van~Hemert, J. M. Bujnicki, and D. Incarnato, “Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements,” Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Manfredonia:20,
    author = {Ilaria Manfredonia and Chandran Nithin and Almudena Ponce-Salvatierra and Pritha Ghosh and Tomasz K Wirecki and Tycho Marinus and Natacha S Ogando and Eric~J Snijder and Martijn J van~Hemert and Janusz M Bujnicki and Danny Incarnato},
    title = {Genome-wide mapping of {SARS}-{CoV}-2 {RNA} structures identifies therapeutically-relevant elements},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1053},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] D. Glebe, N. Goldmann, C. Lauber, and S. Seitz, “HBV evolution and genetic variability: impact on prevention, treatment and development of antivirals,” Antiviral Res, p. 104973, 2020.
    [Bibtex]
    @Article{Glebe:20,
    author = {Dieter Glebe and Nora Goldmann and Chris Lauber and Stefan Seitz},
    title = {{HBV} evolution and genetic variability: impact on prevention, treatment and development of antivirals},
    journal = {{Antiviral Res}},
    year = {2020},
    pages = {104973},
    doi = {10.1016/j.antiviral.2020.104973},
    publisher = {Elsevier {BV}},
    }
  • [DOI] B. Saremi, M. Kohls, P. Liebig, U. Siebert, and K. Jung, “Measuring reproducibility of virus meta-genomics analyses using bootstrap samples from FASTQ-files,” Bioinformatics, 2020.
    [Bibtex]
    @Article{Saremi:20,
    author = {Babak Saremi and Moritz Kohls and Pamela Liebig and Ursula Siebert and Klaus Jung},
    title = {Measuring reproducibility of virus Meta-Genomics analyses using bootstrap samples from {FASTQ}-Files},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa926},
    editor = {Lenore Cowen},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Bai:20,
    author = {Chunxue Bai and Sanjay H. Chotirmall and Jordi Rello and George A. Alba and Leo C. Ginns and Jerry A. Krishnan and Robert Rogers and Elisabeth Bendstrup and Pierre-Regis Burgel and James D. Chalmers and Abigail Chua and Kristina A. Crothers and Abhijit Duggal and Yeon Wook Kim and John G. Laffey and Carlos M. Luna and Michael S. Niederman and Ganesh Raghu and Julio A. Ramirez and Jordi Riera and Oriol Roca and Maximiliano Tamae-Kakazu and Antoni Torres and Richard R. Watkins and Miriam Barrecheguren and Mirko Belliato and Hassan A. Chami and Rongchang Chen and Gustavo A. Cortes-Puentes and Charles Delacruz and Margaret M. Hayes and Leo M.A. Heunks and Steven R. Holets and Catherine L. Hough and Sugeet Jagpal and Kyeongman Jeon and Takeshi Johkoh and May M. Lee and Janice Liebler and Gerry N. McElvaney and Ari Moskowitz and Richard A. Oeckler and I{\~{n}}igo Ojanguren and Anthony O{\textquotesingle}Regan and Mathias W. Pletz and Chin Kook Rhee and Marcus J. Schultz and Enrico Storti and Charlie Strange and Carey C. Thomson and Francesca J. Torriani and Xun Wang and Wim Wuyts and Tao Xu and Dawei Yang and Ziqiang Zhang and Kevin C. Wilson},
    title = {Updated guidance on the management of {COVID}-19: from an {A}merican {T}horacic {S}ociety/{E}uropean {R}espiratory {S}ociety coordinated {I}nternational {T}ask {F}orce (29 {J}uly 2020)},
    journal = {{Eur Respir Rev}},
    year = {2020},
    volume = {29},
    number = {157},
    pages = {200287},
    doi = {10.1183/16000617.0287-2020},
    publisher = {European Respiratory Society ({ERS})},
    }
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    @Article{Ciminski:20a,
    author = {Kevin Ciminski and Geoffrey P. Chase and Martin Beer and Martin Schwemmle},
    title = {Influenza {A} Viruses: Understanding Human Host Determinants},
    journal = {{Trends Mol Med}},
    year = {2020},
    doi = {10.1016/j.molmed.2020.09.014},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Pallerla:20,
    author = {Srinivas Reddy Pallerla and Dominik Harms and Reimar Johne and Daniel Todt and Eike Steinmann and Mathias Schemmerer and Jürgen J. Wenzel and Jörg Hofmann and James Wai Kuo Shih and Heiner Wedemeyer and C.-Thomas Bock and Thirumalaisamy P. Velavan},
    title = {Hepatitis {E} Virus Infection: Circulation, Molecular Epidemiology, and Impact on Global Health},
    journal = {Pathogens},
    year = {2020},
    volume = {9},
    number = {10},
    pages = {856},
    doi = {10.3390/pathogens9100856},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Deckert:20,
    author = {Volker Deckert and Tanja Deckert-Gaudig and Dana Cialla-May and Jürgen Popp and Roland Zell and Stefanie Deinhard-Emmer and Alexei V. Sokolov and Zhenhuan Yi and Marlan O. Scully},
    title = {Laser spectroscopic technique for direct identification of a single virus I: {FASTER} {CARS}},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202013169},
    doi = {10.1073/pnas.2013169117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
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    [Bibtex]
    @Article{Grossegesse:20,
    author = {Marica Grossegesse and Felix Hartkopf and Andreas Nitsche and Lars Schaade and Joerg Doellinger and Thilo Muth},
    title = {Perspective on Proteomics for Virus Detection in Clinical Samples},
    journal = {Journal of Proteome Research},
    year = {2020},
    doi = {10.1021/acs.jproteome.0c00674},
    publisher = {American Chemical Society ({ACS})},
    }
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    [Bibtex]
    @Article{Freuling:20,
    author = {Conrad M. Freuling and Angele Breithaupt and Thomas Müller and Julia Sehl and Anne Balkema-Buschmann and Melanie Rissmann and Antonia Klein and Claudia Wylezich and Dirk Höper and Kerstin Wernike and Andrea Aebischer and Donata Hoffmann and Virginia Friedrichs and Anca Dorhoi and Martin H. Groschup and Martin Beer and Thomas C. Mettenleiter},
    title = {Susceptibility of Raccoon Dogs for Experimental {SARS}-{CoV}-2 Infection},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {12},
    doi = {10.3201/eid2612.203733},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
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    [Bibtex]
    @Article{Conzelmann:20,
    author = {Carina Conzelmann and Rüdiger Gro{\ss} and Toni Luise Meister and Daniel Todt and Adalbert Krawczyk and Ulf Dittmer and Steffen Stenger and Jan Münch and Eike Steinmann and Janis A Müller and Stephanie Pfaender},
    title = {Pasteurization Inactivates {SARS}-{CoV}-2 Spiked Breast Milk},
    journal = {Pediatrics},
    year = {2020},
    pages = {e2020031690},
    doi = {10.1542/peds.2020-031690},
    publisher = {American Academy of Pediatrics ({AAP})},
    }
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    [Bibtex]
    @Article{Flageul:20,
    author = {Alexandre Flageul and Pierrick Lucas and Edouard Hirchaud and Fabrice Touzain and Yannick Blanchard and Nicolas Eterradossi and Paul Brown and B{\'{e}}atrice Grasland},
    title = {Viral variant visualizer ({VVV}): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity},
    journal = {{Virus Res}},
    year = {2020},
    volume = {291},
    pages = {198201},
    doi = {10.1016/j.virusres.2020.198201},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Page:20,
    author = {Andrew J Page and Alison E Mather and Thanh Le Viet and Emma J Meader and Nabil-Fareed J Alikhan and Gemma L Kay and Leonardo de Oliveira Martins and Alp Aydin and David J Baker and Alexander J. Trotter and Steven Rudder and Ana P Tedim and Anastasia Kolyva and Rachael Stanley and Maria Diaz and Will Potter and Claire Stuart and Lizzie Meadows and Andrew Bell and Ana Victoria Gutierrez and Nicholas M Thomson and Evelien M Adriaenssens and Tracey Swingler and Rachel AJ Gilroy and Luke Griffith and Dheeraj K Sethi and Rose K Davidson and Robert A Kingsley and Luke Bedford and Lindsay J Coupland and Ian G Charles and Ngozi Elumogo and John Wain and Reenesh Prakash and Mark A Webber and SJ Louise Smith and Meera Chand and Samir Dervisevic and Justin O{\textquotesingle}Grady and {The COVID-19 Genomics UK (COG-UK) consortium}},
    title = {Large scale sequencing of {SARS}-{CoV}-2 genomes from one region allows detailed epidemiology and enables local outbreak management},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.28.20201475},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Kuipers:20,
    author = {Jack Kuipers and Aashil A Batavia and Kim Philipp Jablonski and Fritz Bayer and Nico Borgsmüller and Arthur Dondi and Monica-Andreea Dr{\u{a}}gan and Pedro Ferreira and Katharina Jahn and Lisa Lamberti and Martin Pirkl and Susana Posada-C{\'{e}}spedes and Ivan Topolsky and Ina Nissen and Natascha Santacroce and Elodie Burcklen and Tobias Schär and Vincenzo Capece and Christiane Beckmann and Olivier Kobel and Christoph Noppen and Maurice Redondo and Sarah Nadeau and Sophie Seidel and Noemie Santamaria de Souza and Christian Beisel and Tanja Stadler and Niko Beerenwinkel},
    title = {Within-patient genetic diversity of {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.12.335919},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Zaeck:20,
    author = {Luca M. Zaeck and David Scheibner and Julia Sehl and Martin Müller and Donata Hoffmann and Martin Beer and Elsayed M. Abdelwhab and Thomas C. Mettenleiter and Angele Breithaupt and Stefan Finke},
    title = {3D reconstruction of {SARS}-{CoV}-2 infection in ferrets emphasizes focal infection pattern in the upper respiratory tract},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.17.339051},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Pohl:20,
    author = {Marie O. Pohl and Idoia Busnadiego and Verena Kufner and Stefan Schmutz and Maryam Zaheri and Irene Abela and Alexandra Trkola and Michael Huber and Silke Stertz and Benjamin G. Hale},
    title = {Distinct Phenotypes of {SARS}-{CoV}-2 Isolates Reveal Viral Traits Critical for Replication in Primary Human Respiratory Cells},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.22.350207},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Cotten:20,
    author = {Matthew Cotten and Dan Lule Bugembe and Pontiano Kaleebu and My V.T. Phan},
    title = {Alternate primers for whole-genome {SARS}-{CoV}-2 sequencing},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.12.335513},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Bhatt:20,
    author = {Pramod R. Bhatt and Alain Scaiola and Gary Loughran and Marc Leibundgut and Annika Kratzel and Angus E. McMillan and Kate M. O{\textquotesingle}Connor and Jeffrey W. Bode and Volker Thiel and John F. Atkins and Nenad Ban},
    title = {Structural basis of ribosomal frameshifting during translation of the {SARS}-{CoV}-2 {RNA} genome},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.26.355099},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Byrd:20,
    author = {Kevin M Byrd and Ni Huang and Paola Perez and Takafumi Kato and Yu Mikami and Kenichi Okuda and Rodney C. Gilmore and Cecilia Dominguez Conde and Billel Gasmi and Sydney Stein and Margaret Beach and Eileen Pelayo and Jose Maldonado-Ortiz and Bernard LaFont and Ricardo Padilla and Valerie Murrah and Robert Maile and Will Lovell and Shannon Wallet and Natalie M Bowman and Suzanne L Meinig and Matthew C Wolfgang and Saibyasachi N. Choudhury and Mark Novotny and Brian D Aevermann and Richard Scheuermann and Gabrielle Cannon and Carlton Anderson and Julie Marchesan and Mandy Bush and Marcelo Freire and Adam Kimple and Daniel L Herr and Joseph Rabin and Alison Grazioli and Benjamin N. French and Thomas JF Pranzatelli and John A. Chiorini and David E. Kleiner and Stefania Pittaluga and Stephen Hewitt and Peter D. Burbelo and Daniel Chertow and Karen M Frank and Janice Lee and Richard C. Boucher C. Boucher and Sarah A. Teichmann and Blake M Warner and and},
    title = {Integrated Single-Cell Atlases Reveal an Oral {SARS}-{CoV}-2 Infection and Transmission Axis},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.26.20219089},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Schulte-Schrepping:20,
    author = {Jonas Schulte-Schrepping and Nico Reusch and Daniela Paclik and Kevin Ba{\ss}ler and Stephan Schlickeiser and Bowen Zhang and Benjamin Krämer and Tobias Krammer and Sophia Brumhard and Lorenzo Bonaguro and Elena De Domenico and Daniel Wendisch and Martin Grasshoff and Theodore S. Kapellos and Michael Beckstette and Tal Pecht and Adem Saglam and Oliver Dietrich and Henrik E. Mei and Axel R. Schulz and Claudia Conrad and D{\'{e}}sir{\'{e}}e Kunkel and Ehsan Vafadarnejad and Cheng-Jian Xu and Arik Horne and Miriam Herbert and Anna Drews and Charlotte Thibeault and Moritz Pfeiffer and Stefan Hippenstiel and Andreas Hocke and Holger Müller-Redetzky and Katrin-Moira Heim and Felix Machleidt and Alexander Uhrig and Laure Bosquillon de Jarcy and Linda Jürgens and Miriam Stegemann and Christoph R. Glösenkamp and Hans-Dieter Volk and Christine Goffinet and Markus Landthaler and Emanuel Wyler and Philipp Georg and Maria Schneider and Chantip Dang-Heine and Nick Neuwinger and Kai Kappert and Rudolf Tauber and Victor Corman and Jan Raabe and Kim Melanie Kaiser and Michael To Vinh and Gereon Rieke and Christian Meisel and Thomas Ulas and Matthias Becker and Robert Geffers and Martin Witzenrath and Christian Drosten and Norbert Suttorp and Christof von Kalle and Florian Kurth and Kristian Händler and Joachim L. Schultze and Anna C. Aschenbrenner and Yang Li and Jacob Nattermann and Birgit Sawitzki and Antoine-Emmanuel Saliba and Leif Erik Sander and Angel Angelov and Robert Bals and Alexander Bartholomäus and Anke Becker and Daniela Bezdan and Ezio Bonifacio and Peer Bork and Thomas Clavel and Maria Colome-Tatche and Andreas Diefenbach and Alexander Dilthey and Nicole Fischer and Konrad Förstner and Julia-Stefanie Frick and Julien Gagneur and Alexander Goesmann and Torsten Hain and Michael Hummel and Stefan Janssen and Jörn Kalinowski and Ren{\'{e}} Kallies and Birte Kehr and Andreas Keller and Sarah Kim-Hellmuth and Christoph Klein and Oliver Kohlbacher and Jan O. Korbel and Ingo Kurth and Markus Landthaler and Yang Li and Kerstin Ludwig and Oliwia Makarewicz and Manja Marz and Alice McHardy and Christian Mertes and Markus Nöthen and Peter Nürnberg and Uwe Ohler and Stephan Ossowski and Jörg Overmann and Silke Peter and Klaus Pfeffer and Anna R. Poetsch and Alfred Pühler and Nikolaus Rajewsky and Markus Ralser and Olaf Rie{\ss} and Stephan Ripke and Ulisses Nunes da Rocha and Philip Rosenstiel and Antoine-Emmanuel Saliba and Leif Erik Sander and Birgit Sawitzki and Philipp Schiffer and Eva-Christina Schulte and Joachim L. Schultze and Alexander Sczyrba and Oliver Stegle and Jens Stoye and Fabian Theis and Janne Vehreschild and Jörg Vogel and Max von Kleist and Andreas Walker and Jörn Walter and Dagmar Wieczorek and John Ziebuhr},
    title = {Severe {COVID}-19 Is Marked by a Dysregulated Myeloid Cell Compartment},
    journal = {Cell},
    year = {2020},
    doi = {10.1016/j.cell.2020.08.001},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. J. Walker, S. G. Siddell, E. J. Lefkowitz, A. R. Mushegian, E. M. Adriaenssens, D. M. Dempsey, B. E. Dutilh, B. Harrach, R. L. Harrison, C. R. Hendrickson, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, R. J. Orton, L. Rubino, S. Sabanadzovic, P. Simmonds, D. B. Smith, A. Varsani, F. M. Zerbini, and A. J. Davison, “Changes to virus taxonomy and the statutes ratified by the International Committee on Taxonomy of Viruses (2020),” Arch Virol, 2020.
    [Bibtex]
    @Article{Walker:20,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Evelien M. Adriaenssens and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Richard J. Orton and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Donald B. Smith and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the Statutes ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2020)},
    journal = {{Arch Virol}},
    year = {2020},
    doi = {10.1007/s00705-020-04752-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Jordan-Paiz:20,
    author = {Ana Jordan-Paiz and Maria Nevot and Kevin Lamkiewicz and Marie Lataretu and Sandra Franco and Manja Marz and Miguel Angel Martinez},
    title = {{HIV}-1 lethality and loss of {E}nv protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer},
    journal = {{J Virol}},
    year = {2020},
    doi = {10.1128/jvi.01108-20},
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    @Article{MacLean:20a,
    author = {Oscar A MacLean and Richard J Orton and Joshua B Singer and David L Robertson},
    title = {No evidence for distinct types in the evolution of {SARS}-{CoV}-2},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    doi = {10.1093/ve/veaa034},
    publisher = {Oxford University Press ({OUP})},
    }
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    @Article{Jonge:20,
    author = {Patrick A. de Jonge and F.A. Bastiaan von Meijenfeldt and Ana Rita Costa and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts},
    journal = {{iScience}},
    year = {2020},
    volume = {23},
    number = {9},
    pages = {101439},
    doi = {10.1016/j.isci.2020.101439},
    publisher = {Elsevier {BV}},
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    @Article{Cacciabue:20,
    author = {Marco Cacciabue and Pablo Aguilera and Mar{\'{\i}}a In{\'{e}}s Gismondi and Oscar Taboga},
    title = {Covidex: an ultrafast and accurate tool for virus subtyping},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Han:20,
    author = {Namshik Han and Woochang Hwang and Kostas Tzelepis and Patrick Schmerer and Eliza Yankova and Meabh MacMahon and Winnie Lei and Nicholas M Katritsis and Anika Liu and Alison Schuldt and Rebecca Harris and Kathryn Chapman and Frank McCaughan and Friedemann Weber and Tony Kouzarides},
    title = {Identification of {SARS}-{CoV}-2 induced pathways reveal drug repurposing strategies},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.24.265496},
    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Rueca:20,
    author = {Martina Rueca and Barbara Bartolini and Cesare Ernesto Maria Gruber and Antonio Piralla and Fausto Baldanti and Emanuela Giombini and Francesco Messina and Luisa Marchioni and Giuseppe Ippolito and Antonino Di Caro and Maria Rosaria Capobianchi},
    title = {Compartmentalized Replication of {SARS}-{C}ov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {9},
    pages = {1302},
    doi = {10.3390/microorganisms8091302},
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    @Article{Zanella:20,
    author = {Marie-C{\'{e}}line Zanella and Samuel Cordey and Laurent Kaiser},
    title = {Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients},
    journal = {{Clin Microbiol Rev}},
    year = {2020},
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    @Article{Palatini:20,
    author = {Umberto Palatini and Reem A. Masri and Luciano V. Cosme and Sergey Koren and Fran{\c{c}}oise Thibaud-Nissen and James K. Biedler and Flavia Krsticevic and J. Spencer Johnston and Rebecca Halbach and Jacob E. Crawford and Igor Antoshechkin and Anna-Bella Failloux and Elisa Pischedda and Michele Marconcini and Jay Ghurye and Arang Rhie and Atashi Sharma and Dmitry A. Karagodin and Jeremy Jenrette and Stephanie Gamez and Pascal Miesen and Patrick Masterson and Adalgisa Caccone and Maria V. Sharakhova and Zhijian Tu and Philippos A. Papathanos and Ronald P. Van Rij and Omar S. Akbari and Jeffrey Powell and Adam M. Phillippy and Mariangela Bonizzoni},
    title = {Improved reference genome of the arboviral vector Aedes albopictus},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02141-w},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Schlottau:20,
    author = {Kore Schlottau and Melanie Rissmann and Annika Graaf and Jacob Schön and Julia Sehl and Claudia Wylezich and Dirk Höper and Thomas C Mettenleiter and Anne Balkema-Buschmann and Timm Harder and Christian Grund and Donata Hoffmann and Angele Breithaupt and Martin Beer},
    title = {{SARS}-{CoV}-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study},
    journal = {{Lancet Microbe}},
    year = {2020},
    volume = {1},
    number = {5},
    pages = {e218--e225},
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    @Article{Decock:20,
    author = {Kristof Decock and Koenraad Debackere and Anne- Mieke Vandamme and Bart Van Looy},
    title = {Scenario-driven forecasting: modeling peaks and paths. Insights from the {COVID}-19 pandemic in {B}elgium},
    journal = {Scientometrics},
    year = {2020},
    volume = {124},
    number = {3},
    pages = {2703--2715},
    doi = {10.1007/s11192-020-03591-6},
    publisher = {Springer Science and Business Media {LLC}},
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    @InCollection{Vkovski:20a,
    author = {Philip V'kovski and Silvio Steiner and Volker Thiel},
    title = {Proximity Labeling for the Identification of {C}oronavirus-Host Protein Interactions},
    booktitle = {Coronaviruses},
    publisher = {Springer {US}},
    year = {2020},
    pages = {187--204},
    doi = {10.1007/978-1-0716-0900-2_14},
    }
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    [Bibtex]
    @InCollection{Thao:20a,
    author = {Tran Thi Nhu Thao and Fabien Labroussaa and Nadine Ebert and Joerg Jores and Volker Thiel},
    title = {In-Yeast Assembly of Coronavirus Infectious {cDNA} Clones Using a Synthetic Genomics Pipeline},
    booktitle = {Coronaviruses},
    publisher = {Springer {US}},
    year = {2020},
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    @Article{Hoste:20,
    author = {Alexis C.R. Hoste and Angel Venteo and Alba Fresco-Taboada and Istar Tapia and Alejandro Monedero and Lissette L{\'{o}}pez and Maarten F. Jebbink and Elisa P{\'{e}}rez-Ram{\'{\i}}rez and Miguel Angel Jimenez-Clavero and Mercedes Almonacid and Patricia Mu{\~{n}}oz and Jesus Guinea and Carmen Vela and Lia van der Hoek and Paloma Rueda and Patricia Sastre},
    title = {Two serological approaches for detection of antibodies to {SARS}-{CoV}-2 in different scenarios: a screening tool and a point-of-care test},
    journal = {{Diagn Microbiol Infect Dis}},
    year = {2020},
    volume = {98},
    number = {4},
    pages = {115167},
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    publisher = {Elsevier {BV}},
    }
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    title = {The use of germicidal ultraviolet light, vaporized hydrogen peroxide and dry heat to decontaminate face masks and filtering respirators contaminated with a {SARS}-{CoV}-2 surrogate virus},
    journal = {{J Hosp Infect}},
    year = {2020},
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    author = {Jacqueline King and Timm Harder and Martin Beer and Anne Pohlmann},
    title = {Rapid multiplex {MinION} nanopore sequencing workflow for Influenza {A} viruses},
    journal = {{BMC Infect Dis}},
    year = {2020},
    volume = {20},
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    doi = {10.1186/s12879-020-05367-y},
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    @Article{Bach:20,
    author = {Simone Bach and Jana-Christin Demper and Nadine Biedenkopf and Stephan Becker and Roland K. Hartmann},
    title = {{RNA} secondary structure at the transcription start site influences {EBOV} transcription initiation and replication in a length- and stability-dependent manner},
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    @Article{Abrantes:20,
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    title = {Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/{GI}.2},
    journal = {Scientific Reports},
    year = {2020},
    volume = {10},
    number = {1},
    doi = {10.1038/s41598-020-71303-4},
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  • A. Tehel, T. Streicher, S. Tragust, and R. J. Paxton, “Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts,” R Soc Open Sci, vol. 7, iss. 7, p. 200480, 2020.
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    @Article{Tehel:20,
    author = {Tehel, Anja and Streicher, Tabea and Tragust, Simon and Paxton, Robert J},
    title = {Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts},
    journal = {{R Soc Open Sci}},
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    author = {Marleen Balvert and Xiao Luo and Ernestina Hauptfeld and Alexander Schönhuth and Bas E Dutilh},
    title = {{OGRE}: {O}verlap {G}raph-based metagenomic {R}ead clust{E}ring},
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    @Article{Mecate-Zambrano:20,
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    title = {Discrete spatio-temporal regulation of tyrosine phosphorylation directs influenza {A} virus {M1} protein towards its function in virion assembly},
    journal = {{PLoS Pathog}},
    year = {2020},
    volume = {16},
    number = {8},
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    doi = {10.1371/journal.ppat.1008775},
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    }
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    @Article{Schubert:20,
    author = {Schubert, Katharina and Karousis, Evangelos D and Jomaa, Ahmad and Scaiola, Alain and Echeverria, Blanca and Gurzeler, Lukas-Adrian and Leibundgut, Marc and Thiel, Volker and M{\"u}hlemann, Oliver and Ban, Nenad},
    title = {{SARS}-{CoV}-2 {Nsp1} binds the ribosomal {mRNA} channel to inhibit translation},
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    @Article{Rahman:20,
    author = {Sahar Abd El Rahman and Bernd Hoffmann and Reham Karam and Mohamed El-Beskawy and Mohammed F. Hamed and Leonie F. Forth and Dirk Höper and Michael Eschbaumer},
    title = {Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus},
    journal = {Viruses},
    year = {2020},
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    title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations},
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    @Article{Shannon:20a,
    author = {Ashleigh Shannon and Barbara Selisko and Nhung-Thi-Tuyet Le and Johanna Huchting and Franck Touret and G{\'{e}}raldine Piorkowski and V{\'{e}}ronique Fattorini and Fran{\c{c}}ois Ferron and Etienne Decroly and Chris Meier and Bruno Coutard and Olve Peersen and Bruno Canard},
    title = {Rapid incorporation of {F}avipiravir by the fast and permissive viral {RNA} polymerase complex results in {SARS}-{CoV}-2 lethal mutagenesis},
    journal = {{Nat Commun}},
    year = {2020},
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    @Article{Polo:20,
    author = {David Polo and Marcos Quintela-Baluja and Alexander Corbishley and Davey L. Jones and Andrew C. Singer and David W. Graham and Jes{\'{u}}s L. Romalde},
    title = {Making waves: Wastewater-based epidemiology for {COVID}-19 -- approaches and challenges for surveillance and prediction},
    journal = {{Water Res}},
    year = {2020},
    volume = {186},
    pages = {116404},
    doi = {10.1016/j.watres.2020.116404},
    publisher = {Elsevier {BV}},
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    @Article{Konno:20,
    author = {Yoriyuki Konno and Izumi Kimura and Keiya Uriu and Masaya Fukushi and Takashi Irie and Yoshio Koyanagi and Daniel Sauter and Robert J. Gifford and So Nakagawa and Kei Sato},
    title = {{SARS}-{CoV}-2 {ORF}3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant},
    journal = {{Cell Rep}},
    year = {2020},
    volume = {32},
    number = {12},
    pages = {108185},
    doi = {10.1016/j.celrep.2020.108185},
    publisher = {Elsevier {BV}},
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    @Article{Kinsella:20,
    author = {Cormac M. Kinsella and Aldert Bart and Martin Deijs and Patricia Broekhuizen and Joanna Kaczorowska and Maarten F. Jebbink and Tom van Gool and Matthew Cotten and Lia van der Hoek},
    title = {{E}ntamoeba and {G}iardia parasites implicated as hosts of {CRESS} viruses},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
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    doi = {10.1038/s41467-020-18474-w},
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    @Article{Welker:20,
    author = {Armin Welker and Christian Kersten and Christin Müller and Ramakanth Madhugiri and Collin Zimmer and Patrick Müller and Robert Alexander Zimmermann and Stefan Hammerschmidt and Hannah Maus and John Ziebuhr and Christoph Sotriffer and Tanja Schirmeister},
    title = {{SAR} of novel benzamides and isoindolines, designed as {SARS}-{CoV} protease inhibitors {\textendash} effective against {SARS}-{CoV}-2},
    journal = {{ChemMedChem}},
    year = {2020},
    doi = {10.1002/cmdc.202000548},
    publisher = {Wiley},
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    @Article{Edridge:20,
    author = {Arthur W. D. Edridge and Joanna Kaczorowska and Alexis C. R. Hoste and Margreet Bakker and Michelle Klein and Katherine Loens and Maarten F. Jebbink and Amy Matser and Cormac M. Kinsella and Paloma Rueda and Margareta Ieven and Herman Goossens and Maria Prins and Patricia Sastre and Martin Deijs and Lia van der Hoek},
    title = {Seasonal coronavirus protective immunity is short-lasting},
    journal = {{Nat Med}},
    year = {2020},
    doi = {10.1038/s41591-020-1083-1},
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    author = {Eleanor M. L. Scerri and Denise Kühnert and James Blinkhorn and Huw S. Groucutt and Patrick Roberts and Kathleen Nicoll and Andrea Zerboni and Emuobosa Akpo Orijemie and Huw Barton and Ian Candy and Steven T. Goldstein and John Hawks and Khady Niang and Didier N'Dah and Michael D. Petraglia and Nicholas C. Vella},
    title = {Field-based sciences must transform in response to {COVID}-19},
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    @Article{Baele:20,
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    journal = {{Wellcome Open Res}},
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    @Article{Almansour:20,
    author = {Iman Almansour},
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    @Article{MunozFontela:20,
    author = {C{\'{e}}sar Mu{\~{n}}oz-Fontela and William E. Dowling and Simon G. P. Funnell and Pierre-S. Gsell and Ximena Riveros Balta and Randy A. Albrecht and Hanne Andersen and Ralph S. Baric and Miles W. Carroll and Marco Cavaleri and Chuan Qin and Ian Crozier and Kai Dallmeier and Leon de Waal and Emmie de Wit and Leen Delang and Erik Dohm and W. Paul Duprex and Darryl Falzarano and Courtney L. Finch and Matthew B. Frieman and Barney S. Graham and Lisa Gralinski and Kate Guilfoyle and Bart L. Haagmans and Geraldine A. Hamilton and Amy L. Hartman and Sander Herfst and Suzanne J. F. Kaptein and William Klimstra and Ivana Knezevic and Philip R. Krause and Jens H. Kuhn and Roger Le Grand and Mark Lewis and Wen-Chun Liu and Pauline Maisonnasse and Anita K. McElroy and Vincent Munster and Nadia Oreshkova and Angela L. Rasmussen and Joana Rocha-Pereira and Barry Rockx and Estefan{\'{\i}}a Rodr{\'{\i}}guez and Thomas Rogers and Francisco J. Salguero and Michael Schotsaert and Koert J. Stittelaar and Hendrik Jan Thibaut and Chien-Te Tseng and J{\'{u}}lia Vergara-Alert and Martin Beer and Trevor Brasel and Jasper F. W. Chan and Adolfo Garc{\'{\i}}a-Sastre and Johan Neyts and Stanley Perlman and Douglas S. Reed and Juergen A. Richt and Chad J. Roy and Joaquim Segal{\'{e}}s and Seshadri S. Vasan and Ana Mar{\'{\i}}a Henao-Restrepo and Dan H. Barouch},
    title = {Animal models for {COVID}-19},
    journal = {Nature},
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    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Rossi:20,
    author = {Alessandro Rossi and Laura Treu and Stefano Toppo and Henrike Zschach and Stefano Campanaro and Bas E. Dutilh},
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    journal = {Viruses},
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    @Article{Stefaniak:20,
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    title = {{AnnapuRNA}: a scoring function for predicting {RNA}-small molecule interactions},
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    title = {{CIAlign} - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments},
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    @Article{Aubry:20,
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    @Article{Seifert:20,
    author = {Mona Seifert and Subhas Chandra Bera and Pauline van Nies and Robert N. Kirchdoerfer and Ashleigh Shannon and Thi-Tuyet-Nhung Le and Tyler L. Grove and Fl{\'{a}}via S. Papini and Jamie J. Arnold and Steven C. Almo and Bruno Canard and Martin Depken and Craig E. Cameron and David Dulin},
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    @Article{Simsek:20,
    author = {Ceren Simsek and Victor Max Corman and Hermann Ulrich Everling and Alexander N. Lukashev and Andrea Rasche and Gael Darren Maganga and Tabea Binger and Daan Jansen and Leen Beller and Ward Deboutte and Florian Gloza-Rausch and Antje Seebens-Hoyer and Stoian Yordanov and Augustina Sylverken and Samuel Oppong and Yaw Adu Sarkodie and Peter Vallo and Eric M. Leroy and Mathieu Bourgarel and Kwe Claude Yinda and Marc Van Ranst and Christian Drosten and Jan Felix Drexler and Jelle Matthijnssens},
    title = {At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions},
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    @Article{Kreye:20,
    author = {Jakob Kreye and S Momsen Reincke and Hans-Christian Kornau and Elisa S{\'{a}}nchez-Sendin and Victor Max Corman and Hejun Liu and Meng Yuan and Nicholas C. Wu and Xueyong Zhu and Chang-Chun D. Lee and Jakob Trimpert and Markus Höltje and Kristina Dietert and Laura Stöffler and Niels von Wardenburg and Scott van Hoof and Marie A Homeyer and Julius Hoffmann and Azza Abdelgawad and Achim D Gruber and Luca D Bertzbach and Daria Vladimirova and Lucie Y Li and Paula Charlotte Barthel and Karl Skriner and Andreas C Hocke and Stefan Hippenstiel and Martin Witzenrath and Norbert Suttorp and Florian Kurth and Christiana Franke and Matthias Endres and Dietmar Schmitz and Lara Maria Jeworowski and Anja Richter and Marie Luisa Schmidt and Tatjana Schwarz and Marcel Alexander Müller and Christian Drosten and Daniel Wendisch and Leif E Sander and Nikolaus Osterrieder and Ian A Wilson and Harald Prüss},
    title = {A {SARS}-{CoV}-2 neutralizing antibody protects from lung pathology in a {COVID}-19 hamster model},
    journal = {{bioRxiv}},
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    @Article{Gilroy:20,
    author = {Rachel Gilroy and Anuradha Ravi and Maria Getino and Isabella Pursley and Daniel Horton and Nabil-Fareed Alikhan and David Baker and Karim Gharbi and Neil Hall and Mick Watson and Evelien M. Adriaenssens and Ebenezer Foster-Nyarko and Sheikh Jarju and Arss Secka and Martin Antonio and Aharon Oren and Roy Chaudhuri and Falk Hildebrand and Mark Pallen},
    title = {A Genomic Blueprint of the Chicken Gut Microbiome},
    journal = {{Research Square}},
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    @Article{Meyer:20,
    author = {Fernando Meyer and Till-Robin Lesker and David Koslicki and Adrian Fritz and Alexey Gurevich and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {Tutorial: Assessing metagenomics software with the {CAMI} benchmarking toolkit},
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    @Article{Hölzer:20,
    author = {Martin Hölzer and Manja Marz},
    title = {{PoSeiDon}: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection},
    journal = {Bioinformatics},
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    @Article{Braun:20a,
    author = {Julian Braun and Lucie Loyal and Marco Frentsch and Daniel Wendisch and Philipp Georg and Florian Kurth and Stefan Hippenstiel and Manuela Dingeldey and Beate Kruse and Florent Fauchere and Emre Baysal and Maike Mangold and Larissa Henze and Roland Lauster and Marcus A. Mall and Kirsten Beyer and Jobst Röhmel and Sebastian Voigt and Jürgen Schmitz and Stefan Miltenyi and Ilja Demuth and Marcel A. Müller and Andreas Hocke and Martin Witzenrath and Norbert Suttorp and Florian Kern and Ulf Reimer and Holger Wenschuh and Christian Drosten and Victor M. Corman and Claudia Giesecke-Thiel and Leif Erik Sander and Andreas Thiel},
    title = {{SARS}-{CoV}-2-reactive T cells in healthy donors and patients with {COVID}-19},
    journal = {Nature},
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    @Article{Meister:20,
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    title = {Virucidal efficacy of different oral rinses against {SARS}-{CoV}-2},
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    @Article{Boni:20,
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    @Article{Lai:20,
    author = {Alessia Lai and Annalisa Bergna and Sara Caucci and Nicola Clementi and Ilaria Vicenti and Filippo Dragoni and Anna Maria Cattelan and Stefano Menzo and Angelo Pan and Annapaola Callegaro and Adriano Tagliabracci and Arnaldo Caruso and Francesca Caccuri and Silvia Ronchiadin and Claudia Balotta and Maurizio Zazzi and Emanuela Vaccher and Massimo Clementi and Massimo Galli and Gianguglielmo Zehender},
    title = {Molecular Tracing of {SARS}-{CoV}-2 in Italy in the First Three Months of the Epidemic},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {8},
    pages = {798},
    doi = {10.3390/v12080798},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. Henritzi, P. P. Petric, N. S. Lewis, A. Graaf, A. Pessia, E. Starick, A. Breithaupt, G. Strebelow, C. Luttermann, L. M. K. Parker, C. Schröder, B. Hammerschmidt, G. Herrler, E. große Beilage, D. Stadlbauer, V. Simon, F. Krammer, S. Wacheck, S. Pesch, M. Schwemmle, M. Beer, and T. C. Harder, “Surveillance of european domestic pig populations identifies an emerging reservoir of potentially zoonotic swine influenza A viruses,” Cell Host Microbe, 2020.
    [Bibtex]
    @Article{Henritzi:20,
    author = {Dinah Henritzi and Philipp Peter Petric and Nicola Sarah Lewis and Annika Graaf and Alberto Pessia and Elke Starick and Angele Breithaupt and Günter Strebelow and Christine Luttermann and Larissa Mareike Kristin Parker and Charlotte Schröder and Bärbel Hammerschmidt and Georg Herrler and Elisabeth gro{\ss}e Beilage and Daniel Stadlbauer and Viviana Simon and Florian Krammer and Silke Wacheck and Stefan Pesch and Martin Schwemmle and Martin Beer and Timm Clemens Harder},
    title = {Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza {A} Viruses},
    journal = {{Cell Host Microbe}},
    year = {2020},
    doi = {10.1016/j.chom.2020.07.006},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @InCollection{Leonetti:20,
    author = {Paola Leonetti and Pascal Miesen and Ronald P. van Rij and Vitantonio Pantaleo},
    title = {Viral and subviral derived small {RNAs} as pathogenic determinants in plants and insects},
    booktitle = {{Adv Virus Res}},
    publisher = {Elsevier},
    year = {2020},
    pages = {1--36},
    doi = {10.1016/bs.aivir.2020.04.001},
    }
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    [Bibtex]
    @Article{Papageorgiou:20,
    author = {Nicolas Papageorgiou and Maria Spiliopoulou and Thi-Hong Van Nguyen and Afroditi Vaitsopoulou and Elsie Yekwa Laban and Karine Alvarez and Irene Margiolaki and Bruno Canard and Fran{\c{c}}ois Ferron},
    title = {Brothers in Arms: Structure, Assembly and Function of Arenaviridae Nucleoprotein},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {7},
    pages = {772},
    doi = {10.3390/v12070772},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Zuckerman:20,
    author = {Neta S. Zuckerman and Rakefet Pando and Efrat Bucris and Yaron Drori and Yaniv Lustig and Oran Erster and Orna Mor and Ella Mendelson and Michal Mandelboim},
    title = {Comprehensive Analyses of {SARS}-{CoV}-2 Transmission in a Public Health Virology Laboratory},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {8},
    pages = {854},
    doi = {10.3390/v12080854},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Overholt:20,
    author = {Will A. Overholt and Martin Hölzer and Patricia Geesink and Celia Diezel and Manja Marz and Kirsten Küsel},
    title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system},
    journal = {{Environ Microbiol}},
    year = {2020},
    doi = {10.1111/1462-2920.15186},
    publisher = {Wiley},
    }
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    [Bibtex]
    @Article{Blome:20,
    author = {Sandra Blome and Kati Franzke and Martin Beer},
    title = {African swine fever -- A review of current knowledge},
    journal = {{Virus Res}},
    year = {2020},
    volume = {287},
    pages = {198099},
    doi = {10.1016/j.virusres.2020.198099},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Clementi:20,
    author = {Nicola Clementi and Elena Criscuolo and Roberta Antonia Diotti and Roberto Ferrarese and Matteo Castelli and Lorenzo Dagna and Roberto Burioni and Massimo Clementi and Nicasio Mancini},
    title = {Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-{SARS}-{CoV}-2 Effects in vitro},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fmicb.2020.01704},
    publisher = {Frontiers Media {SA}},
    }
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    [Bibtex]
    @Article{McLaughlin:20,
    author = {Katie-May McLaughlin and Marco Bechtel and Denisa Bojkova and Christian Münch and Sandra Ciesek and Mark N. Wass and Martin Michaelis and Jindrich Cinatl},
    title = {{COVID}-19-Related Coagulopathy{\textemdash}Is Transferrin a Missing Link?},
    journal = {Diagnostics},
    year = {2020},
    volume = {10},
    number = {8},
    pages = {539},
    doi = {10.3390/diagnostics10080539},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Valle:20,
    author = {Coralie Valle and Baptiste Martin and Franck Touret and Ashleigh Shannon and Bruno Canard and Jean-Claude Guillemot and Bruno Coutard and Etienne Decroly},
    title = {Drugs against {SARS}-{CoV} -2: What do we know about their mode of action?},
    journal = {{Rev Med Virol}},
    year = {2020},
    doi = {10.1002/rmv.2143},
    publisher = {Wiley},
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    [Bibtex]
    @Article{Mock:20,
    author = {Florian Mock and Adrian Viehweger and Emanuel Barth and Manja Marz},
    title = {{VIDHOP}, viral host prediction with Deep Learning},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa705},
    editor = {Jinbo Xu},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Lycett:20,
    author = {Samantha J. Lycett and Anne Pohlmann and Christoph Staubach and Valentina Caliendo and Mark Woolhouse and Martin Beer and Thijs Kuiken and},
    title = {Genesis and spread of multiple reassortants during the 2016/2017 {H5} avian influenza epidemic in {E}urasia},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202001813},
    doi = {10.1073/pnas.2001813117},
    publisher = {Proceedings of the National Academy of Sciences},
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    [Bibtex]
    @Article{Hofmänner:20,
    author = {Daniel A Hofmänner and Pedro D Wendel Garcia and Branko Duvnjak and Bhavya Chakrakodi and Julian D Maier and Michael Huber and Jon Huder and Aline Wolfensberger and Peter W Schreiber and Reto A. Schüpbach and Annelies S Zinkernagel and Philipp K Bühler and Silvio D Brugger},
    title = {Bacterial but no {SARS}-{CoV}-2 contamination after terminal disinfection of tertiary care intensive care units treating {COVID}-19 patients},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-47872/v1},
    publisher = {Research Square},
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    [Bibtex]
    @Article{Ferrarini:20,
    author = {Mariana G. Ferrarini and Avantika Lal and Rita Rebollo and Andreas Gruber and Andrea Guarracino and Itziar Martinez Gonzalez and Taylor Floyd and Daniel Siqueira de Oliveira and Justin Shanklin and Ethan Beausoleil and Taneli Pusa and Brett E. Pickett and Vanessa Aguiar-Pulido},
    title = {Genome-wide bioinformatic analyses predict key host and viral factors in {SARS}-{CoV}-2 pathogenesis},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.07.28.225581},
    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Loessner:20,
    author = {Holger Loessner and Insea Schlattmeier and Marie Anders-Maurer and Isabelle Bekeredjian-Ding and Christine Rohde and Johannes Wittmann and Cornelia Pokalyuk and Oleg Krut and Christel Kamp},
    title = {Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy},
    journal = {Antibiotics},
    year = {2020},
    volume = {9},
    number = {7},
    pages = {408},
    doi = {10.3390/antibiotics9070408},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Folegatti:20a,
    author = {Pedro M Folegatti and Katie J Ewer and Parvinder K Aley and Brian Angus and Stephan Becker and Sandra Belij-Rammerstorfer and Duncan Bellamy and Sagida Bibi and Mustapha Bittaye and Elizabeth A Clutterbuck and Christina Dold and Saul N Faust and Adam Finn and Amy L Flaxman and Bassam Hallis and Paul Heath and Daniel Jenkin and Rajeka Lazarus and Rebecca Makinson and Angela M Minassian and Katrina M Pollock and Maheshi Ramasamy and Hannah Robinson and Matthew Snape and Richard Tarrant and Merryn Voysey and Catherine Green and Alexander D Douglas and Adrian V S Hill and Teresa Lambe and Sarah C Gilbert and Andrew J Pollard and Jeremy Aboagye and Kelly Adams and Aabidah Ali and Elizabeth Allen and Jennifer L. Allison and Rachel Anslow and Edward H. Arbe-Barnes and Gavin Babbage and Kenneth Baillie and Megan Baker and Philip Baker and Ioana Baleanu and Juliana Ballaminut and Eleanor Barnes and Jordan Barrett and Louise Bates and Alexander Batten and Kirsten Beadon and Rebecca Beckley and Eleanor Berrie and Lisa Berry and Amy Beveridge and Kevin R. Bewley and Else Margreet Bijker and Tracey Bingham and Luke Blackwell and Caitlin L. Blundell and Emma Bolam and Elena Boland and Nicola Borthwick and Thomas Bower and Amy Boyd and Tanja Brenner and Philip D. Bright and Charlie Brown-O{\textquotesingle}Sullivan and Emily Brunt and Jamie Burbage and Sharon Burge and Karen R. Buttigieg and Nicholas Byard and Ingrid Cabera Puig and Anna Calvert and Susana Camara and Michelangelo Cao and Federica Cappuccini and Melanie Carr and Miles W. Carroll and Victoria Carter and Katrina Cathie and Ruth J. Challis and Irina Chelysheva and Jee-Sun Cho and Paola Cicconi and Liliana Cifuentes and Helen Clark and Elizabeth Clark and Tom Cole and Rachel Colin-Jones and Christopher P. Conlon and Aislinn Cook and Naomi S. Coombes and Rachel Cooper and Catherine A. Cosgrove and Karen Coy and Wendy E.M. Crocker and Christina J. Cunningham and Brad E. Damratoski and Lynne Dando and Mehreen S. Datoo and Hannah Davies and Hans De Graaf and Tesfaye Demissie and Claudio Di Maso and Isabelle Dietrich and Tao Dong and Francesca R. Donnellan and Naomi Douglas and Charlotte Downing and Jonathan Drake and Rachael Drake-Brockman and Ruth Elizabeth Drury and Susanna Jane Dunachie and Nick J. Edwards and Frances D.L. Edwards and Chris J. Edwards and Sean C. Elias and Michael J. Elmore and Katherine R.W. Emary and Marcus Rex English and Susanne Fagerbrink and Sally Felle and Shuo Feng and Samantha Field and Carine Fixmer and Clare Fletcher and Karen J. Ford and Jamie Fowler and Polly Fox and Emma Francis and John Frater and Julie Furze and Michelle Fuskova and Eva Galiza and Diane Gbesemete and Ciaran Gilbride and Giacomo Gorini and Lyndsey Goulston and Caroline Grabau and Lara Gracie and Zoe Gray and Lucy Belle Guthrie and Mark Hackett and Sandro Halwe and Elizabeth Hamilton and Joseph Hamlyn and Brama Hanumunthadu and Irasha Harding and Stephanie A. Harris and Andrew Harris and Daisy Harrison and Clare Harrison and Thomas C. Hart and Louise Haskell and Sophia Hawkins and Ian Head and John Aaron Henry and Jennifer Hill and Susanne H.C. Hodgson and Mimi M. Hou and Elizabeth Howe and Nicola Howell and Cecilia Hutlin and Sabina Ikram and Catherine Isitt and Poppy Iveson and Susan Jackson and Frederic Jackson and Sir William James and Megan Jenkins and Elizabeth Jones and Kathryn Jones and Christine E. Jones and Bryony Jones and Reshma Kailath and Konstantinos Karampatsas and Jade Keen and Sarah Kelly and Dearbhla Kelly and David Kerr and Simon Kerridge and Liaquat Khan and Uzma Khan and Annabel Killen and Jasmin Kinch and Thomas B. King and Lloyd King and Jade King and Lucy Kingham-Page and Paul Klenerman and Francesca Knapper and Julian C. Knight and Stanislava Koleva and Alexandra Kupke and Colin W. Larkworthy and Jessica P.J. Larwood and Anna Laskey and Alison M. Lawrie and Arlene Lee and Kim Yee Ngan Lee and Emily A. Lee and Helen Legge and Alice Lelliott and Nana-Marie Lemm and Amelia M. Lias and Aline Linder and Samuel Lipworth and Xinxue Liu and Shuchang Liu and Raquel Lopez Ramon and May Lwin and Francesca Mabesa and Meera Madhavan and Gary Mallett and Kushal Mansatta and In{\={e}}s Marcal and Spyridoula Marinou and Emma Marlow and Julia L. Marshall and Jane Martin and Joanne McEwan and Gretchen Meddaugh and Alexander J. Mentzer and Neginsadat Mirtorabi and Maria Moore and Edward Moran and Ella Morey and Victoria Morgan and Susan Jane Morris and Hazel Morrison and Gertraud Morshead and Richard Morter and Yama F. Mujadidi and Jilly Muller and Tatiana Munera-Huertas and Claire Munro and Alasdair Munro and Sarah Murphy and Vincent J. Muster and Philomena Mweu and Andr{\'{e}}s No{\'{e}} and Fay L. Nugent and Elizabeth Nugent and Katie O{\textquotesingle}Brien and Daniel O{\textquotesingle}Connor and Blanch{\'{e}} Oguti and Jennifer L. Oliver and Catarina Oliveira and Peter John O{\textquotesingle}Reilly and Mairead Osborn and Piper Osborne and Cathy Owen and Daniel Owens and Nelly Owino and Mihaela Pacurar and Kaye Parker and Helena Parracho and Maia Patrick-Smith and Victoria Payne and Jennifer Pearce and Yanchun Peng and Marco Polo Peralta Alvarez and James Perring and Katja Pfafferott and Dimitra Pipini and Emma Plested and Helen Pluess-Hall and Katrina Pollock and Ian Poulton and Laura Presland and Samuel Provstgaard-Morys and David Pulido and Kajal Radia and Fernando Ramos Lopez and Jade Rand and Helen Ratcliffe and Thomas Rawlinson and Sarah Rhead and Amy Riddell and Adam John Ritchie and Hannah Roberts and Joanna Robson and Sophie Roche and Cornelius Rohde and Christine S. Rollier and Rosanna Romani and Indra Rudiansyah and Stephen Saich and Sara Sajjad and Stephannie Salvador and Lidia Sanchez Riera and Helen Sanders and Katherine Sanders and Shari Sapaun and Chloe Sayce and Ella Schofield and Gavin Screaton and Beatrice Selby and Calum Semple and Hannah R. Sharpe and Adam Shea and Holly Shelton and Sarah Silk and Laura Silva-Reyes and Donal T. Skelly and Heather Smee and Catherine C. Smith and David J. Smith and Rinn Song and Alexandra J. Spencer and Elizabeth Stafford and Amy Steele and Elena Stefanova and Lisa Stockdale and Anna Szigeti and Abdessamad Tahiri-Alaoui and Moira Tait and Helen Talbot and Rachel Tanner and Iona Jennifer Taylor and Victoria Taylor and Rebecca Te Water Naude and Nazia Thakur and Yrene Themistocleous and Andreas Themistocleous and Merin Thomas and Tonia M. Thomas and Amber Thompson and Samantha Thomson-Hill and Jennifer Tomlins and Susan Tonks and James Towner and Nguyen Tran and Julia A. Tree and Adam Truby and Kate Turkentine and Cheryl Turner and Nicola Turner and Sally Turner and Toby Tuthill and Marta Ulaszewska and Rachel Varughese and Neeltje Van Doremalen and Kristin Veighey and Marije K. Verheul and Iason Vichos and Elia Vitale and Laura Walker and Marion E.E. Watson and Benjamin Welham and Julie Wheat and Caroline White and Rachel White and Andrew T. Worth and Danny Wright and Suzie Wright and Xin Li Yao and Yasmine Yau},
    title = {Safety and immunogenicity of the {ChAdOx}1 {nCoV}-19 vaccine against {SARS}-{CoV}-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial},
    journal = {Lancet},
    year = {2020},
    doi = {10.1016/s0140-6736(20)31604-4},
    publisher = {Elsevier {BV}},
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    @Article{Osterrieder:20,
    author = {Nikolaus Osterrieder and Luca D. Bertzbach and Kristina Dietert and Azza Abdelgawad and Daria Vladimirova and Dusan Kunec and Donata Hoffmann and Martin Beer and Achim D. Gruber and Jakob Trimpert},
    title = {Age-Dependent Progression of {SARS}-{CoV}-2 Infection in Syrian Hamsters},
    journal = {Viruses},
    year = {2020},
    volume = {12},
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    pages = {779},
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    publisher = {{MDPI} {AG}},
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    author = {Markus Hoffmann and Kirstin Mösbauer and Heike Hofmann-Winkler and Artur Kaul and Hannah Kleine-Weber and Nadine Krüger and Nils C. Gassen and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {Chloroquine does not inhibit infection of human lung cells with {SARS}-{CoV}-2},
    journal = {Nature},
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    title = {Relaxed Random Walks at Scale},
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    title = {What the {P}hage: A scalable workflow for the identification and analysis of phage sequences},
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    title = {Probability of aerosol transmission of {SARS}-{CoV}-2},
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    author = {Ferdinand Zettl and Toni Luise Meister and Tanja Vollmer and Bastian Fischer and Jörg Steinmann and Adalbert Krawczyk and Philip V'kovski and Daniel Todt and Eike Steinmann and Stephanie Pfaender and Gert Zimmer},
    title = {Rapid Quantification of {SARS}-{CoV}-2-Neutralizing Antibodies Using Propagation-Defective Vesicular Stomatitis Virus Pseudotypes},
    journal = {Vaccines},
    year = {2020},
    volume = {8},
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    author = {Bas B. {Oude Munnink} and and David F. Nieuwenhuijse and Mart Stein and {\'{A}}ine O'Toole and Manon Haverkate and Madelief Mollers and Sandra K. Kamga and Claudia Schapendonk and Mark Pronk and Pascal Lexmond and Anne van der Linden and Theo Bestebroer and Irina Chestakova and Ronald J. Overmars and Stefan van Nieuwkoop and Richard Molenkamp and Annemiek A. van der Eijk and Corine GeurtsvanKessel and Harry Vennema and Adam Meijer and Andrew Rambaut and Jaap van Dissel and Reina S. Sikkema and Aura Timen and Marion Koopmans},
    title = {Rapid {SARS}-{CoV}-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands},
    journal = {{Nat Med}},
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    doi = {10.1038/s41591-020-0997-y},
    publisher = {Springer Science and Business Media {LLC}},
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    author = {Christoph Kreer and Matthias Zehner and Timm Weber and Meryem S. Ercanoglu and Lutz Gieselmann and Cornelius Rohde and Sandro Halwe and Michael Korenkov and Philipp Schommers and Kanika Vanshylla and Veronica Di Cristanziano and Hanna Janicki and Reinhild Brinker and Artem Ashurov and Verena Krähling and Alexandra Kupke and Hadas Cohen-Dvashi and Manuel Koch and Jan Mathis Eckert and Simone Lederer and Nico Pfeifer and Timo Wolf and Maria J.G.T. Vehreschild and Clemens Wendtner and Ron Diskin and Henning Gruell and Stephan Becker and Florian Klein},
    title = {Longitudinal Isolation of Potent Near-Germline {SARS}-{CoV}-2-Neutralizing Antibodies from {COVID}-19 Patients},
    journal = {Cell},
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    title = {International external quality assessment for {SARS}-{CoV}-2 molecular detection and survey on clinical laboratory preparedness during the {COVID}-19 pandemic, {A}pril/{M}ay 2020},
    journal = {{Euro Surveill}},
    year = {2020},
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    doi = {10.2807/1560-7917.es.2020.25.27.2001223},
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    author = {Andrew E. Firth},
    title = {A putative new {SARS}-{CoV} protein, 3c, encoded in an {ORF} overlapping {ORF}3a},
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    author = {Valeria Caputo and Roberta Antonia Diotti and Enzo Boeri and Hamid Hasson and Michela Sampaolo and Elena Criscuolo and Sabrina Bagaglio and Emanuela Messina and Caterina Uberti-Foppa and Matteo Castelli and Roberto Burioni and Nicasio Mancini and Massimo Clementi and Nicola Clementi},
    title = {Detection of low-level {HCV} variants in {DAA} treated patients: comparison amongst three different {NGS} data analysis protocols},
    journal = {{Virol J}},
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    title = {Viral {CpG} deficiency provides no evidence that dogs were intermediate hosts for {SARS}-{CoV}-2},
    journal = {{Mol Biol Evol}},
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    author = {Yasutsugu Suzuki and Artem Baidaliuk and Pascal Miesen and Lionel Frangeul and Anna B. Crist and Sarah H. Merkling and Albin Fontaine and Sebastian Lequime and Isabelle Moltini-Conclois and Herv{\'{e}} Blanc and Ronald P. van Rij and Louis Lambrechts and Maria-Carla Saleh},
    title = {Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in {Aedes} aegypti Ovaries},
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    author = {Vitor C Piro and Temesgen H Dadi and Enrico Seiler and Knut Reinert and Bernhard Y Renard},
    title = {ganon: precise metagenomics classification against large and up-to-date sets of reference sequences},
    journal = {Bioinformatics},
    year = {2020},
    volume = {36},
    number = {Supplement{\_}1},
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    author = {Claudia Wylezich and Sten Calvelage and Kore Schlottau and Ute Ziegler and Anne Pohlmann and Dirk Höper and Martin Beer},
    title = {Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including {SARS}-{CoV}-2},
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    author = {Stefanie Deinhardt-Emmer and Daniel Wittschieber and Juliane Sanft and Sandra Kleemann and Stefan Elschner and Karoline F. Haupt and Vanessa Vau and Clio Häring and Jürgen Rödel and Andreas Henke and Christina Ehrhardt and Michael Bauer and Mike Philipp and Nikolaus Ga{\ss}ler and Sandor Nietzsche and Bettina Löffler and Gita Mall},
    title = {Early postmortem mapping of {SARS}-{CoV}-2 {RNA} in patients with {COVID}-19 and correlation to tissue damage},
    journal = {{bioRxiv}},
    year = {2020},
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    author = {Mathilde Foglierini and Leontios Pappas and Antonio Lanzavecchia and Davide Corti and Laurent Perez},
    title = {{AncesTree}: An interactive immunoglobulin lineage tree visualizer},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {7},
    pages = {e1007731},
    doi = {10.1371/journal.pcbi.1007731},
    editor = {Mihaela Pertea},
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    }
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    @Article{Mirzaei:20a,
    author = {Mohammadali Khan Mirzaei and Jinling Xue and Rita Costa and Jinlong Ru and Sarah Schulz and Zofia E. Taranu and Li Deng},
    title = {Challenges of Studying the Human Virome {\textendash} Relevant Emerging Technologies},
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    @Article{Sikkema:20,
    author = {Reina S Sikkema and Suzan D Pas and David F Nieuwenhuijse and {\'{A}}ine O'Toole and Jaco Verweij and Anne van der Linden and Irina Chestakova and Claudia Schapendonk and Mark Pronk and Pascal Lexmond and Theo Bestebroer and Ronald J Overmars and Stefan van Nieuwkoop and Wouter van den Bijllaardt and Robbert G Bentvelsen and Miranda M L van Rijen and Anton G M Buiting and Anne J G van Oudheusden and Bram M Diederen and Anneke M C Bergmans and Annemiek van der Eijk and Richard Molenkamp and Andrew Rambaut and Aura Timen and Jan A J W Kluytmans and Bas B {Oude Munnink} and Marjolein F Q Kluytmans van den Bergh and Marion P G Koopmans},
    title = {{COVID}-19 in health-care workers in three hospitals in the south of the {N}etherlands: a cross-sectional study},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    doi = {10.1016/s1473-3099(20)30527-2},
    publisher = {Elsevier {BV}},
    }
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    author = {Marcus Panning and and Julius Wiener and Kathrin Rothe and Jochen Schneider and Mathias W. Pletz and Gernot Rohde and Jan Rupp and Martin Witzenrath and Christoph D. Spinner},
    title = {No {SARS}-{CoV}-2 detection in the German {CAPNETZ} cohort of community acquired pneumonia before {COVID}-19 peak in {M}arch 2020},
    journal = {Infection},
    year = {2020},
    doi = {10.1007/s15010-020-01471-y},
    publisher = {Springer Science and Business Media {LLC}},
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    author = {Christoph B. Messner and Vadim Demichev and Daniel Wendisch and Laura Michalick and Matthew White and Anja Freiwald and Kathrin Textoris-Taube and Spyros I. Vernardis and Anna-Sophia Egger and Marco Kreidl and Daniela Ludwig and Christiane Kilian and Federica Agostini and Aleksej Zelezniak and Charlotte Thibeault and Moritz Pfeiffer and Stefan Hippenstiel and Andreas Hocke and Christof von Kalle and Archie Campbell and Caroline Hayward and David J. Porteous and Riccardo E. Marioni and Claudia Langenberg and Kathryn S. Lilley and Wolfgang M. Kuebler and Michael Mülleder and Christian Drosten and Norbert Suttorp and Martin Witzenrath and Florian Kurth and Leif Erik Sander and Markus Ralser},
    title = {Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of {COVID}-19 Infection},
    journal = {{Cell Syst}},
    year = {2020},
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    publisher = {Elsevier {BV}},
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    author = {Daniel Lule Bugembe and John Kayiwa and My V.T. Phan and Phiona Tushabe and Stephen Balinandi and Beatrice Dhaala and Jonas Lexow and Henry Mwebesa and Jane Aceng and Henry Kyobe and Deogratius Ssemwanga and Julius Lutwama and Pontiano Kaleebu and Matthew Cotten},
    title = {Main Routes of Entry and Genomic Diversity of {SARS}-{CoV}-2, {U}ganda},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {10},
    doi = {10.3201/eid2610.202575},
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    @Article{Beer:20,
    author = {Martin Beer and Marcus Doherr and Klaus Osterrieder and Dirk Pfeiffer and Jakob Trimpert},
    title = {{SARS}-{CoV}-2 vaccination{\textemdash}A plea for fast and coordinated action},
    journal = {{Zoonoses Public Health}},
    year = {2020},
    doi = {10.1111/zph.12740},
    publisher = {Wiley},
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    author = {Nicola Clementi and Roberto Ferrarese and Marco Tonelli and Virginia Amato and Sara Racca and Massimo Locatelli and Giuseppe Lippi and Guido Silvestri and Massimo Clementi and Nicasio Mancini},
    title = {Lower nasopharyngeal viral load during the latest phase of {COVID}-19 pandemic in a {N}orthern {I}taly {U}niversity {H}ospital},
    journal = {{Clin Chem Lab Med}},
    year = {2020},
    volume = {0},
    number = {0},
    doi = {10.1515/cclm-2020-0815},
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    author = {Ulrike Felgenhauer and Andreas Schoen and Hans Henrik Gad and Rune Hartmann and Andreas R Schaubmar and Klaus Failing and Christian Drosten and Friedemann Weber},
    title = {Inhibition of {SARS}-{CoV}-2 by type {I} and type {III} interferons},
    journal = {{J Biol Chem}},
    year = {2020},
    pages = {jbc.AC120.013788},
    doi = {10.1074/jbc.ac120.013788},
    publisher = {American Society for Biochemistry {\&} Molecular Biology ({ASBMB})},
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    @Article{Torneri:20,
    author = {Andrea Torneri and Pieter Libin and Joris Vanderlocht and Anne-Mieke Vandamme and Johan Neyts and Niel Hens},
    title = {A prospect on the use of antiviral drugs to control local outbreaks of {COVID}-19},
    journal = {{BMC Med}},
    year = {2020},
    volume = {18},
    pages = {191},
    doi = {10.1186/s12916-020-01636-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Muenchhoff:20,
    author = {Maximilian Muenchhoff and Helga Mairhofer and Hans Nitschko and Natascha Grzimek-Koschewa and Dieter Hoffmann and Annemarie Berger and Holger Rabenau and Marek Widera and Nikolaus Ackermann and Regina Konrad and Sabine Zange and Alexander Graf and Stefan Krebs and Helmut Blum and Andreas Sing and Bernhard Liebl and Roman Wölfel and Sandra Ciesek and Christian Drosten and Ulrike Protzer and Stephan Boehm and Oliver T Keppler},
    title = {Multicentre comparison of quantitative {PCR}-based assays to detect {SARS}-{CoV}-2, {G}ermany, {M}arch 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {24},
    pages = {2001057},
    doi = {10.2807/1560-7917.es.2020.25.24.2001057},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
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    [Bibtex]
    @Article{Baker:20,
    author = {Dave J. Baker and Gemma L. Kay and Alp Aydin and Thanh Le-Viet and Steven Rudder and Ana P. Tedim and Anastasia Kolyva and Maria Diaz and Leonardo de Oliveira Martins and Nabil-Fareed Alikhan and Lizzie Meadows and Andrew Bell and Ana Victoria Gutierrez and Alexander J. Trotter and Nicholas M. Thomson and Rachel Gilroy and Luke Griffith and Evelien M. Adriaenssens and Rachael Stanley and Ian G. Charles and Ngozi Elumogo and John Wain and Reenesh Prakash and Emma Meader and Alison E. Mather and Mark A. Webber and Samir Dervisevic and Andrew J. Page and Justin O'Grady},
    title = {{CoronaHiT}: large scale multiplexing of {SARS}-{CoV}-2 genomes using {N}anopore sequencing},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.24.162156},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Lemey:20,
    author = {Philippe Lemey and Samuel Hong and Verity Hill and Guy Baele and Chiara Poletto and Vittoria Colizza and {\'{A}}ine O'Toole and John T. McCrone and Kristian G. Andersen and Michael Worobey and Martha I. Nelson and Andrew Rambaut and Marc A. Suchard},
    title = {Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a {SARS}-{CoV}-2 case study},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.22.165464},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Kurth:20,
    author = {Florian Kurth and Maria Roennefarth and Charlotte Thibeault and Victor M. Corman and Holger Müller-Redetzky and Mirja Mittermaier and Christoph Ruwwe-Glösenkamp and Katrin M. Heim and Alexander Krannich and Saskia Zvorc and Sein Schmidt and Lucie Kretzler and Chantip Dang-Heine and Matthias Rose and Michael Hummel and Andreas Hocke and Ralf H. Hübner and Bastian Opitz and Marcus A. Mall and Jobst Röhmel and Ulf Landmesser and Burkert Pieske and Samuel Knauss and Matthias Endres and Joachim Spranger and Frank P. Mockenhaupt and Frank Tacke and Sascha Treskatsch and Stefan Angermair and Britta Siegmund and Claudia Spies and Steffen Weber-Carstens and Kai-Uwe Eckardt and Dirk Schürmann and Alexander Uhrig and Miriam S. Stegemann and Thomas Zoller and Christian Drosten and Norbert Suttorp and Martin Witzenrath and Stefan Hippenstiel and Christof von Kalle and Leif Erik Sander},
    title = {Studying the pathophysiology of coronavirus disease 2019: a protocol for the {B}erlin prospective {COVID}-19 patient cohort ({Pa}-{COVID}-19)},
    journal = {Infection},
    year = {2020},
    doi = {10.1007/s15010-020-01464-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Penzes:20,
    author = {Judit J. P{\'{e}}nzes and Maria Söderlund-Venermo and Marta Canuti and Anna Maria Eis-Hübinger and Joseph Hughes and Susan F. Cotmore and Bal{\'{a}}zs Harrach},
    title = {Reorganizing the family {P}arvoviridae: a revised taxonomy independent of the canonical approach based on host association},
    journal = {{Arch Virol}},
    year = {2020},
    doi = {10.1007/s00705-020-04632-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Broggi:20,
    author = {Achille Broggi and Sreya Ghosh and Benedetta Sposito and Roberto Spreafico and Fabio Balzarini and Antonino Lo Cascio and Nicola Clementi and Maria De Santis and Nicasio Mancini and Francesca Granucci and Ivan Zanoni},
    title = {Type {III} interferons disrupt the lung epithelial barrier upon viral recognition},
    journal = {Science},
    year = {2020},
    pages = {eabc3545},
    doi = {10.1126/science.abc3545},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
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    [Bibtex]
    @Article{Perot:20,
    author = {Philippe P{\'{e}}rot and Franck Bielle and Thomas Bigot and Vincent Foulongne and Karine Bollor{\'{e}} and Delphine Chr{\'{e}}tien and Patricia Gil and Seraf{\'{\i}}n Guti{\'{e}}rrez and Gr{\'{e}}gory L'Ambert and Karima Mokhtari and Jan Hellert and Marie Flamand and Carole Tamietti and Muriel Coulpier and Anne Huard de Verneuil and Sarah Temmam and Th{\'{e}}r{\`{e}}se Couderc and Edouard De Sousa Cunha and Susana Boluda and Isabelle Plu and Marie Bernadette Delisle and Fabrice Bonneville and David Brassat and Claire Fieschi and Marion Malphettes and Charles Duyckaerts and Bertrand Mathon and Sophie Demeret and Danielle Seilhean and Marc Eloit},
    title = {Identification of {Umbre} Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 {French} Patients with Hypogammaglobulinemia},
    journal = {{Clin Infect Dis}},
    year = {2020},
    pages = {ciaa308},
    doi = {10.1093/cid/ciaa308},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{SilvaCandido:20,
    author = {Darlan da Silva Candido and Ingra Morales Claro and Jaqueline Goes de Jesus and William Marciel de Souza and Filipe Romero Rebello Moreira and Simon Dellicour and Thomas A. Mellan and Louis du Plessis and Rafael Henrique Moraes Pereira and Flavia Cristina da Silva Sales and Erika Regina Manuli and Julien Theze and Luis Almeida and Mariane Talon de Menezes and Carolina Moreira Voloch and Marcilio Jorge Fumagalli and Thais de Moura Coletti and Camila Alves Maia Silva and Mariana Severo Ramundo and Mariene Ribeiro Amorim and Henrique Hoeltgebaum and Swapnil Mishra and Mandev Gill and Luiz Max Carvalho and Lewis Fletcher Buss and Carlos Augusto Prete and Jordan Ashworth and Helder Nakaya and Pedro da Silva Peixoto and Oliver J Brady and Samuel M. Nicholls and Amilcar Tanuri and Atila Duque Rossi and Carlos Kaue Vieira Braga and Alexandra Lehmkuhl Gerber and Ana Paula Guimaraes and Nelson Gaburo and Cecilia Salete Alencar and Alessandro Clayton de Souza Ferreira and Cristiano Xavier Lima and Jose Eduardo Levi and Celso Granato and Giula Magalhaes Ferreira and Ronaldo da Silva Francisco and Fabiana Granja and Marcia Teixeira Garcia and Maria Luiza Moretti and Mauricio Wesley Perroud and Terezinha Marta Pereira Pinto Castineiras and Carolina Dos Santos Lazari and Sarah C Hill and Andreza Aruska de Souza Santos and Camila Lopes Simeoni and Julia Forato and Andrei Carvalho Sposito and Angelica Zaninelli Schreiber and Magnun Nueldo Nunes Santos and Camila Zolini Sa and Renan Pedra Souza and Luciana Cunha Resende Moreira and Mauro Martins Teixeira and Josy Hubner and Patricia Asfora Falabella Leme and Rennan Garcias Moreira and Mauricio Lacerda Nogueira and Neil Ferguson and Silvia Figueiredo Costa and Jose Luiz Proenca-Modena and Ana Tereza Vasconcelos and Samir Bhatt and Philippe Lemey and Chieh-Hsi Wu and Andrew Rambaut and Nick J Loman and Renato Santana Aguiar and Oliver G Pybus and Ester Cerdeira Sabino and Nuno Rodrigues Faria},
    title = {Evolution and epidemic spread of {SARS}-{CoV}-2 in {Brazil}},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.11.20128249},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Singer:20,
    author = {Joshua Singer and Robert J. Gifford and Matthew Cotten and David L. Robertson},
    title = {{CoV}-{GLUE}: A Web Application for Tracking {SARS}-{CoV}-2 Genomic Variation},
    journal = {Preprints},
    year = {2020},
    doi = {10.20944/preprints202006.0225.v1},
    publisher = {{MDPI} {AG}},
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    [Bibtex]
    @Article{Martin:20,
    author = {Roman Martin and Hannah F. Löchel and Marius Welzel and Georges Hattab and Anne-Christin Hauschild and Dominik Heider},
    title = {{CORDITE}: The Curated {CORona} Drug {InTERactions} Database for {SARS}-{CoV}-2},
    journal = {{iScience}},
    year = {2020},
    volume = {23},
    number = {7},
    pages = {101297},
    doi = {10.1016/j.isci.2020.101297},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Stukalov:20,
    author = {Alexey Stukalov and Virginie Girault and Vincent Grass and Valter Bergant and Ozge Karayel and Christian Urban and Darya A. Haas and Yiqi Huang and Lila Oubraham and Anqi Wang and Sabri M. Hamad and Antonio Piras and Maria Tanzer and Fynn M. Hansen and Thomas Enghleitner and Maria Reinecke and Teresa M. Lavacca and Rosina Ehmann and Roman Wölfel and Jörg Jores and Bernhard Kuster and Ulrike Protzer and Roland Rad and John Ziebuhr and Volker Thiel and Pietro Scaturro and Matthias Mann and Andreas Pichlmair},
    title = {Multi-level proteomics reveals host-perturbation strategies of {SARS}-{CoV}-2 and {SARS}-{CoV}},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Ho:20,
    author = {Jessica Sook Yuin Ho and Matthew Angel and Yixuan Ma and Elizabeth Sloan and Guojun Wang and Carles Martinez-Romero and Marta Alenquer and Vladimir Roudko and Liliane Chung and Simin Zheng and Max Chang and Yesai Fstkchyan and Sara Clohisey and Adam M. Dinan and James Gibbs and Robert J. Gifford and Rong Shen and Quan Gu and Nerea Irigoyen and Laura Campisi and Cheng Huang and Nan Zhao and Joshua D. Jones and Ingeborg van Knippenberg and Zeyu Zhu and Natasha Moshkina and L{\'{e}}a Meyer and Justine Noel and Zuleyma Peralta and Veronica Rezelj and Robyn Kaake and Brad Rosenberg and Bo Wang and Jiajie Wei and Slobodan Paessler and Helen M. Wise and Jeffrey Johnson and Alessandro Vannini and Maria Jo{\~{a}}o Amorim and J. Kenneth Baillie and Emily R. Miraldi and Christopher Benner and Ian Brierley and Paul Digard and Marta {\L}uksza and Andrew E. Firth and Nevan Krogan and Benjamin D. Greenbaum and Megan K. MacLeod and Harm van Bakel and Adolfo Garc{\`{\i}}a-Sastre and Jonathan W. Yewdell and Edward Hutchinson and Ivan Marazzi},
    title = {Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection},
    journal = {Cell},
    year = {2020},
    volume = {181},
    pages = {1502--1517},
    doi = {10.1016/j.cell.2020.05.035},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Clementi:20a,
    author = {Nicola Clementi and Roberto Ferrarese and Elena Criscuolo and Roberta Antonia Diotti and Matteo Castelli and Carolina Scagnolari and Roberto Burioni and Guido Antonelli and Massimo Clementi and Nicasio Mancini},
    title = {Interferon-$\upbeta$ 1a inhibits {SARS}-{CoV}-2 in vitro when administered after virus infection},
    journal = {{J Infect Dis}},
    year = {2020},
    pages = {jiaa350},
    doi = {10.1093/infdis/jiaa350},
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    [Bibtex]
    @Article{Duex:20,
    author = {Ariane Düx and Sebastian Lequime and Livia Victoria Patrono and Bram Vrancken and Sengül Boral and Jan F. Gogarten and Antonia Hilbig and David Horst and Kevin Merkel and Baptiste Prepoint and Sabine Santibanez and Jasmin Schlotterbeck and Marc A. Suchard and Markus Ulrich and Navena Widulin and Annette Mankertz and Fabian H. Leendertz and Kyle Harper and Thomas Schnalke and Philippe Lemey and S{\'{e}}bastien Calvignac-Spencer},
    title = {Measles virus and rinderpest virus divergence dated to the sixth century {BCE}},
    journal = {Science},
    year = {2020},
    volume = {368},
    number = {6497},
    pages = {1367--1370},
    doi = {10.1126/science.aba9411},
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    [Bibtex]
    @Article{Capina:20,
    author = {Rupert Capina and Katherine Li and Levon Kearney and Anne-Mieke Vandamme and P. Richard Harrigan and Kristel Van Laethem},
    title = {Quality Control of Next-Generation Sequencing-Based {HIV}-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {6},
    pages = {645},
    doi = {10.3390/v12060645},
    publisher = {{MDPI} {AG}},
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    [Bibtex]
    @Article{Wernike:20a,
    author = {Kerstin Wernike and Markus Keller and Franz J. Conraths and Thomas C. Mettenleiter and Martin H. Groschup and Martin Beer},
    title = {Pitfalls in {SARS}-{CoV}-2 {PCR} diagnostics},
    journal = {{Transbound Emerg Dis}},
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    doi = {10.1111/tbed.13684},
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    [Bibtex]
    @Article{Guzman-Solis:20,
    author = {Axel A. Guzm{\'{a}}n-Sol{\'{\i}}s and Daniel Blanco-Melo and Viridiana Villa-Islas and Miriam J. Bravo-L{\'{o}}pez and Marcela Sandoval-Velasco and Julie K. Wesp and Jorge A. G{\'{o}}mez-Vald{\'{e}}s and Mar{\'{\i}}a de la Luz Moreno-Cabrera and Alejandro Meraz-Moreno and Gabriela Sol{\'{\i}}s-Pichardo and Peter Schaaf and Benjamin R. tenOever and Mar{\'{\i}}a C. {\'{A}}vila-Arcos},
    title = {Ancient viral genomes reveal introduction of {HBV} and {B19V} to {M}exico during the transatlantic slave trade},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.05.137083},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Jones:20,
    author = {Terry C Jones and Barbara Mühlemann and Talitha Veith and Guido Biele and Marta Zuchowski and Jörg Hoffmann and Angela Stein and Anke Edelmann and Victor Max Corman and Christian Drosten},
    title = {An analysis of {SARS}-{CoV}-2 viral load by patient age},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.08.20125484},
    publisher = {Cold Spring Harbor Laboratory},
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    [Bibtex]
    @Article{Cespedes:20,
    author = {Susana Posada Cespedes and David Seifert and Ivan Topolsky and Karin J Metzner and Niko Beerenwinkel},
    title = {V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.09.142919},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Filipe:20,
    author = {Ana Da Silva Filipe and James Shepherd and Thomas Williams and Joseph Hughes and Elihu Aranday-Cortes and Patawee Asamaphan and Carlos Balcazar and Kirstyn Brunker and Stephen Carmichael and Rebecca Dewar and Michael D Gallagher and Rory Gunson and Antonia Ho and Natasha Jesudason and Natasha Johnson and E. Carol McWilliam Leitch and Kathy Li and Alasdair MacLean and Daniel Mair and Sarah E. McDonald and Martin McHugh and Jenna Nichols and Marc Niebel and Kyriaki Nomikou and Richard J. Orton and Aine O'Toole and Massimo Palmarini and Yasmin A. Parr and Andrew Rambaut and Stefan Rooke and Sharif Shaaban and Rajiv Shah and Joshua B. Singer and Katherine Smollett and Igor Starinskij and Lily Tong and Vattipally B. Sreenu and Elizabeth Wastnedge and David L. Robertson and Matthew T.G. Holden and Kate Templeton and Emma C. Thomson},
    title = {Genomic epidemiology of {SARS}-{CoV}-2 spread in {S}cotland highlights the role of {E}uropean travel in {COVID}-19 emergence},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.08.20124834},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Murcia:20,
    author = {Pablo Murcia and Daniel Streiker and Ana Da Silva Philipe and David L. Robertson and Ruth Jarrett and Brian Willett and Margaret Hosie and Roman Biek and Kathryn Allan and William Weir},
    title = {Send cat and dog samples to test for {SARS}-{CoV}-2},
    journal = {{Vet Rec}},
    year = {2020},
    volume = {186},
    pages = {571},
    doi = {10.1136/vr.m2019},
    publisher = {{BMJ}},
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    [Bibtex]
    @Article{Young:20,
    author = {Francesca Young and Simon Rogers and David L. Robertson},
    title = {Predicting host taxonomic information from viral genomes: A comparison of feature representations},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {5},
    pages = {e1007894},
    doi = {10.1371/journal.pcbi.1007894},
    editor = {Morgan Langille},
    publisher = {Public Library of Science ({PLoS})},
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    @Article{Eizenga:20,
    author = {Jordan M. Eizenga and Adam M. Novak and Jonas A. Sibbesen and Simon Heumos and Ali Ghaffaari and Glenn Hickey and Xian Chang and Josiah D. Seaman and Robin Rounthwaite and Jana Ebler and Mikko Rautiainen and Shilpa Garg and Benedict Paten and Tobias Marschall and Jouni Sir{\'{e}}n and Erik Garrison},
    title = {Pangenome Graphs},
    journal = {{Annu Rev Genomics Hum Genet}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1146/annurev-genom-120219-080406},
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    @Article{Vandamme:20,
    author = {Anne-Mieke Vandamme and ToTran Nguyen},
    title = {{B}elgium -- concerns about coronavirus contact-tracing apps},
    journal = {Nature},
    year = {2020},
    volume = {581},
    pages = {384},
    doi = {10.1038/d41586-020-01552-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    @Article{Ji:20,
    author = {Xiang Ji and Zhenyu Zhang and Andrew Holbrook and Akihiko Nishimura and Guy Baele and Andrew Rambaut and Philippe Lemey and Marc A Suchard},
    title = {Gradients do grow on trees: a linear-time $\mathcal{O}$({N})-dimensional gradient for statistical phylogenetics},
    journal = {{Mol Biol Evol}},
    year = {2020},
    pages = {msaa130},
    doi = {10.1093/molbev/msaa130},
    editor = {Jeffrey Townsend},
    publisher = {Oxford University Press ({OUP})},
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    @Article{Bartolini:20,
    author = {Barbara Bartolini and Martina Rueca and Cesare Ernesto Maria Gruber and Francesco Messina and Fabrizio Carletti and Emanuela Giombini and Eleonora Lalle and Licia Bordi and Giulia Matusali and Francesca Colavita and Concetta Castilletti and Francesco Vairo and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro},
    title = {{SARS}-{CoV}-2 Phylogenetic Analysis, {L}azio Region, {I}taly, {F}ebruary--{M}arch 2020},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {8},
    doi = {10.3201/eid2608.201525},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
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    @Article{Randazzo:20a,
    author = {Walter Randazzo and Gloria S{\'{a}}nchez Moragas},
    title = {Hepatitis {A} infections from food},
    journal = {{J Appl Microbiol}},
    year = {2020},
    doi = {10.1111/jam.14727},
    publisher = {Wiley},
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    @Article{Kratzel:20a,
    author = {Annika Kratzel and Silvio Steiner and Daniel Todt and Philip V'Kovski and Yannick Brueggemann and Joerg Steinmann and Eike Steinmann and Volker Thiel and Stephanie Pfaender},
    title = {Temperature-dependent surface stability of {SARS}-{CoV}-2},
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    @Article{Kitsou:20,
    author = {Konstantina Kitsou and Anastasia Kotanidou and Dimitrios Paraskevis and Timokratis Karamitros and Aris Katzourakis and Richard Tedder and Tara Hurst and Spyros Sapounas and Athanassios Kotsinas and Vassilis Gorgoulis and Vana Spoulou and Sotirios Tsiodras and Pagona Lagiou and Gkikas Magiorkinis},
    title = {Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of {COVID}-19 Patients},
    journal = {{medRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Sypsa:20,
    author = {Vana Sypsa and Sotirios Roussos and Dimitrios Paraskevis and Theodore Lytras and Sotirios Tsiodras and Angelos Hatzakis},
    title = {Modelling the {SARS}-{CoV}-2 first epidemic wave in {G}reece: social contact patterns for impact assessment and an exit strategy from social distancing measures},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.27.20114017},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Kemenesi:20a,
    author = {G{\'{a}}bor Kemenesi and Safia Zeghbib and Bal{\'{a}}zs A Somogyi and G{\'{a}}bor Endre T{\'{o}}th and Kriszti{\'{a}}n B{\'{a}}nyai and Norbert Solymosi and Peter M Szabo and Istv{\'{a}}n Szab{\'{o}} and {\'{A}}d{\'{a}}m B{\'{a}}lint and P{\'{e}}ter Urb{\'{a}}n and R{\'{o}}bert Herczeg and Attila Gyenesei and {\'{A}}gnes Nagy and Csaba Istv{\'{a}}n Pereszl{\'{e}}nyi and Gergely Csaba Babinszky and G{\'{a}}bor Dud{\'{a}}s and Gabriella Terhes and Viktor Zöldi and R{\'{o}}bert Lovas and Szabolcs Tenczer and L{\'{a}}szl{\'{o}} Kornya and Ferenc Jakab},
    title = {Multiple {SARS}-{CoV}-2 introductions shaped the early outbreak in {C}entral {E}astern {E}urope: comparing {H}ungarian data to a worldwide sequence data-matrix},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.06.080119},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Collatz:20,
    author = {Maximilian Collatz and Florian Mock and Martin Hölzer and Emanuel Barth and Konrad Sachse and Manja Marz},
    title = {{EpiDope}: {A Deep} neural network for linear {B}-cell epitope prediction},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.12.090019},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Pach:20,
    author = {Szymon Pach and Trung Ngoc Nguyen and Jakob Trimpert and Dusan Kunec and Nikolaus Osterrieder and Gerhard Wolber},
    title = {{ACE}2-Variants Indicate Potential {SARS}-{CoV}-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Worobey:20,
    author = {Michael Worobey and Jonathan Pekar and Brendan B. Larsen and Martha I. Nelson and Verity Hill and Jeffrey B. Joy and Andrew Rambaut and Marc A. Suchard and Joel O. Wertheim and Philippe Lemey},
    title = {The emergence of {SARS}-{CoV}-2 in {Europe} and the {US}},
    journal = {{bioRxiv}},
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    @Article{MacLean:20,
    author = {Oscar A. MacLean and Spyros Lytras and Joshua B. Singer and Steven Weaver and Sergei L. Kosakovsky Pond and David L. Robertson},
    title = {Evidence of significant natural selection in the evolution of {SARS}-{CoV}-2 in bats, not humans},
    journal = {{bioRxiv}},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Grant:20,
    author = {Heather E Grant and Emma B Hodcroft and Deogratius Ssemwanga and John M Kitayimbwa and Gonzalo Yebra and Luis Roger Esquivel Gomez and Dan Frampton and Astrid Gall and Paul Kellam and Tulio de Oliveira and Nicholas Bbosa and Rebecca N Nsubuga and Freddie Kibengo and Tsz Ho Kwan and Samantha Lycett and Rowland Kao and David L Robertson and Oliver Ratmann and Christophe Fraser and Deenan Pillay and Pontiano Kaleebu and Andrew J Leigh Brown},
    title = {Pervasive and non-random recombination in near full-length {HIV} genomes from {U}ganda},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa004},
    doi = {10.1093/ve/veaa004},
    publisher = {Oxford University Press ({OUP})},
    }
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    @Article{Faye:20,
    author = {Oumar Faye and Maria de Lourdes Monteiro and Bram Vrancken and Matthieu Prot and Sebastian Lequime and Maryam Diarra and Oumar Ndiaye and Tomas Valdez and Sandra Tavarez and Jessica Ramos and Silv{\^{a}}nia da Veiga Leal and Cecilio Pires and Antonio Moreira and Maria Filomena Tavares and Linete Fernandes and Jorge Noel Barreto and Maria do C{\'{e}}u Teixeira and Maria da Luz de Lima Mendon{\c{c}}a and Carolina Cardoso da Silva Leite Gomes and Mariano Salazar Castellon and Laurence Ma and Fr{\'{e}}d{\'{e}}ric Lemoine and Fabiana G{\'{a}}mbaro-Roglia and D{\'{e}}borah Delaune and Gamou Fall and Ibrahima Soc{\'{e}} Fall and Mamadou Diop and Anavaj Sakuntabhai and Cheikh Loucoubar and Philippe Lemey and Edward C. Holmes and Ousmane Faye and Amadou Alpha Sall and Etienne Simon-Loriere},
    title = {Genomic Epidemiology of 2015{\textendash}2016 {Zika} Virus Outbreak in {Cape} {Verde}},
    journal = {{Emerg. Infect. Dis.}},
    year = {2020},
    volume = {26},
    number = {6},
    pages = {1084--1090},
    doi = {10.3201/eid2606.190928},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
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    [Bibtex]
    @Article{Gryseels:20,
    author = {Sophie Gryseels and Thomas D. Watts and Jean-Marie Kabongo Mpolesha and Brendan B. Larsen and Philippe Lemey and Jean-Jacques Muyembe-Tamfum and Dirk E. Teuwen and Michael Worobey},
    title = {A near full-length {HIV}-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {22},
    pages = {12222--12229},
    doi = {10.1073/pnas.1913682117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
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    [Bibtex]
    @Article{Kemenesi:20,
    author = {G{\'{a}}bor Kemenesi and L{\'{a}}szl{\'{o}} Kornya and G{\'{a}}bor Endre T{\'{o}}th and Korn{\'{e}}lia Kurucz and Safia Zeghbib and Bal{\'{a}}zs A. Somogyi and Viktor Zöldi and P{\'{e}}ter Urb{\'{a}}n and R{\'{o}}bert Herczeg and Ferenc Jakab},
    title = {Nursing homes and the elderly regarding the {COVID}-19 pandemic: situation report from {H}ungary},
    journal = {{GeroScience}},
    year = {2020},
    doi = {10.1007/s11357-020-00195-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Randazzo:20,
    author = {Walter Randazzo and Pilar Truchado and Enric Cuevas-Ferrando and Pedro Sim{\'{o}}n and Ana Allende and Gloria S{\'{a}}nchez Moragas},
    title = {{SARS}-{CoV}-2 {RNA} in wastewater anticipated {COVID}-19 occurrence in a low prevalence area},
    journal = {{Water Res}},
    year = {2020},
    volume = {181},
    pages = {115942},
    doi = {10.1016/j.watres.2020.115942},
    publisher = {Elsevier {BV}},
    }
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    @Article{Böhmer:20,
    author = {Merle M Böhmer and Udo Buchholz and Victor M Corman and Martin Hoch and Katharina Katz and Durdica V Marosevic and Stefanie Böhm and Tom Woudenberg and Nikolaus Ackermann and Regina Konrad and Ute Eberle and Bianca Treis and Alexandra Dangel and Katja Bengs and Volker Fingerle and Anja Berger and Stefan Hörmansdorfer and Siegfried Ippisch and Bernd Wicklein and Andreas Grahl and Kirsten Pörtner and Nadine Muller and Nadine Zeitlmann and T Sonia Boender and Wei Cai and Andreas Reich and Maria an der Heiden and Ute Rexroth and Osamah Hamouda and Julia Schneider and Talitha Veith and Barbara Mühlemann and Roman Wölfel and Markus Antwerpen and Mathias Walter and Ulrike Protzer and Bernhard Liebl and Walter Haas and Andreas Sing and Christian Drosten and Andreas Zapf},
    title = {Investigation of a {COVID}-19 outbreak in {G}ermany resulting from a single travel-associated primary case: a case series},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    doi = {10.1016/s1473-3099(20)30314-5},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Farkas:20,
    author = {Kata Farkas and David I. Walker and Evelien M. Adriaenssens and James E. McDonald and Luke S. Hillary and Shelagh K. Malham and Davey L. Jones},
    title = {Viral indicators for tracking domestic wastewater contamination in the aquatic environment},
    journal = {{Water Res}},
    year = {2020},
    volume = {181},
    pages = {115926},
    doi = {10.1016/j.watres.2020.115926},
    publisher = {Elsevier {BV}},
    }
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    @Article{Zitzmann:20,
    author = {Carolin Zitzmann and Bianca Schmid and Alessia Ruggieri and Alan S. Perelson and Marco Binder and Ralf Bartenschlager and Lars Kaderali},
    title = {A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    pages = {725},
    doi = {10.3389/fmicb.2020.00725},
    publisher = {Frontiers Media {SA}},
    }
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    @Article{He:20,
    author = {Wan-Ting He and Xiang Ji and Wei He and Simon Dellicour and Shilei Wang and Gairu Li and Letian Zhang and Marius Gilbert and Henan Zhu and Gang Xing and Michael Veit and Zhen Huang and Guan-Zhu Han and Yaowei Huang and Marc A Suchard and Guy Baele and Philippe Lemey and Shuo Su},
    title = {Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus},
    journal = {{Mol Biol Evol}},
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    author = {Gael Darren Maganga and Anaïs Pinto and Illich Manfred Mombo and Mankomra Madjitobaye and Antoine Mitte Mbeang Beyeme and Larson Boundenga and Meriadeg Ar Gouilh and Nadine N'Dilimabaka and Jan Felix Drexler and Christian Drosten and Eric Maurice Leroy},
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    author = {Dorothea Bestle and Miriam Ruth Heindl and Hannah Limburg and Thuy Van Lam van and Oliver Pilgram and Hong Moulton and David A. Stein and Kornelia Hardes and Markus Eickmann and Olga Dolnik and Cornelius Rohde and Stephan Becker and Hans-Dieter Klenk and Wolfgang Garten and Torsten Steinmetzer and Eva Böttcher-Friebertshäuser},
    title = {{TMPRSS}2 and furin are both essential for proteolytic activation and spread of {SARS}-{CoV}-2 in human airway epithelial cells and provide promising drug targets},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Hayward:20,
    author = {Joshua A. Hayward and Mary Tachedjian and Adam Johnson and Tamsin B. Gordon and Jie Cui and Glenn A. Marsh and Michelle L. Baker and Lin-Fa Wang and Gilda Tachedjian},
    title = {Bats Possess Unique Variants of the Antiviral Restriction Factor Tetherin},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Gogarten:20,
    author = {Jan F. Gogarten and Malte Rühlemann and Elizabeth Archie and Jenny Tung and Chantal Akoua-Koffi and Corinna Bang and Tobias Deschner and Jean-Jacques Muyembe-Tamfun and Martha M. Robbins and Grit Schubert and Martin Surbeck and Roman M. Wittig and Klaus Zuberbühler and John F. Baines and Andre Franke and Fabian H. Leendertz and S{\'{e}}bastien Calvignac-Spencer},
    title = {Primate phageomes are structured by superhost phylogeny and environment},
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    @Article{Navratil:20,
    author = {Vincent Navratil and Loic Lionnard and Sonia Longhi and Marie Hardwick and Christophe Combet and Abdel Aouacheria},
    title = {The severe acute respiratory syndrome coronavirus 2 ({SARS}-{CoV}-2) envelope ({E}) protein harbors a conserved {BH}3-like sequence},
    journal = {{bioRxiv}},
    year = {2020},
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    @Article{Hoffmann:20b,
    author = {Marie Hoffmann and Michael T. Monaghan and Knut Reinert},
    title = {{PriSeT}: Efficient De Novo Primer Discovery},
    journal = {{bioRxiv}},
    year = {2020},
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    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Vasylyeva:20,
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    title = {Phylodynamics Helps to Evaluate the Impact of an {HIV} Prevention Intervention},
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    title = {Safety and immunogenicity of a modified vaccinia virus {Ankara} vector vaccine candidate for {Middle East} respiratory syndrome: an open-label, phase 1 trial},
    journal = {{Lancet Infect Dis}},
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    @Article{Folegatti:20,
    author = {Pedro M Folegatti and Mustapha Bittaye and Amy Flaxman and Fernando Ramos Lopez and Duncan Bellamy and Alexandra Kupke and Catherine Mair and Rebecca Makinson and Jonathan Sheridan and Cornelius Rohde and Sandro Halwe and Yuji Jeong and Young-Shin Park and Jae-Ouk Kim and Manki Song and Amy Boyd and Nguyen Tran and Daniel Silman and Ian Poulton and Mehreen Datoo and Julia Marshal and Yrene Themistocleous and Alison Lawrie and Rachel Roberts and Eleanor Berrie and Stephan Becker and Teresa Lambe and Adrian Hill and Katie Ewer and Sarah Gilbert},
    title = {Safety and immunogenicity of a candidate {Middle East} respiratory syndrome coronavirus viral-vectored vaccine: a dose-escalation, open-label, non-randomised, uncontrolled, phase 1 trial},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    volume = {20},
    number = {7},
    pages = {816--826},
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    @Article{Wernike:20,
    author = {Kerstin Wernike and Martin Beer},
    title = {Re-circulation of {S}chmallenberg virus, {G}ermany, 2019},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
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    publisher = {Wiley},
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    @Article{Hoffmann:20c,
    author = {Markus Hoffmann and Simon Schroeder and Hannah Kleine-Weber and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {Nafamostat mesylate blocks activation of {SARS}-{CoV}-2: New treatment option for {COVID}-19},
    journal = {{Antimicrob Agents Chemother}},
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    author = {Philip V'Kovski and Silvio Steiner and Mitra Gultom and Jenna N Kelly and Julie Russeil and Bastien Mangeat and Elisa Cora and Joern Pezoldt and Melle Holwerda and Annika Kratzel and Laura Laloli and Manon Wider and Jasmine Portmann and Tran Thi Nhu Thao and Nadine Ebert and Hanspeter Stalder and Rune Hartmann and Vincent Gardeux and Daniel Alpern and Bart Deplancke and Volker Thiel and Ronald Dijkman},
    title = {Disparate temperature-dependent virus - host dynamics for {SARS}-{CoV}-2 and {SARS}-{CoV} in the human respiratory epithelium},
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    [Bibtex]
    @Article{Anzt:20,
    author = {Hartwig Anzt and Felix Bach and Stephan Druskat and Frank Löffler and Axel Loewe and Bernhard Y. Renard and Gunnar Seemann and Alexander Struck and Elke Achhammer and Piush Aggarwal and Franziska Appel and Michael Bader and Lutz Brusch and Christian Busse and Gerasimos Chourdakis and Piotr Wojciech Dabrowski and Peter Ebert and Bernd Flemisch and Sven Friedl and Bernadette Fritzsch and Maximilian D. Funk and Volker Gast and Florian Goth and Jean-Noël Grad and Sibylle Hermann and Florian Hohmann and Stephan Janosch and Dominik Kutra and Jan Linxweiler and Thilo Muth and Wolfgang Peters-Kottig and Fabian Rack and Fabian H.C. Raters and Stephan Rave and Guido Reina and Malte Rei{\ss}ig and Timo Ropinski and Joerg Schaarschmidt and Heidi Seibold and Jan P. Thiele and Benjamin Uekerman and Stefan Unger and Rudolf Weeber},
    title = {An environment for sustainable research software in {G}ermany and beyond: current state, open challenges, and call for action},
    journal = {{F1000Res}},
    year = {2020},
    volume = {9},
    pages = {295},
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    publisher = {F1000 Research Ltd},
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    [Bibtex]
    @Article{Hotez:20,
    author = {Peter J. Hotez and Maria E. Bottazzi and Sunit K. Singh and Paul J. Brindley and Shaden Kamhawi},
    title = {Will {COVID}-19 become the next neglected tropical disease?},
    journal = {{PLoS Negl Trop Dis}},
    year = {2020},
    volume = {14},
    number = {4},
    pages = {e0008271},
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    @Article{Okba:20,
    author = {Nisreen M.A. Okba and Marcel A. Müller and Wentao Li and Chunyan Wang and Corine H. GeurtsvanKessel and Victor M. Corman and Mart M. Lamers and Reina S. Sikkema and Erwin de Bruin and Felicity D. Chandler and Yazdan Yazdanpanah and Quentin Le Hingrat and Diane Descamps and Nadhira Houhou-Fidouh and Chantal B.E.M. Reusken and Berend-Jan Bosch and Christian Drosten and Marion P.G. Koopmans and Bart L. Haagmans},
    title = {Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibody Responses in Coronavirus Disease 2019 Patients},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {7},
    pages = {1478--1488},
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    publisher = {Centers for Disease Control and Prevention ({CDC})},
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    @Article{Venturi:20,
    author = {Giulietta Venturi and Stephan W Aberle and Tatjana Av{\v{s}}i{\v{c}}-{\v{Z}}upanc and Luisa Barzon and Christoph Batejat and Elisa Burdino and Fabrizio Carletti and R{\'{e}}mi Charrel and Iva Christova and Jeff Connell and Victor Max Corman and Mary Emmanouil and Anne J Jääskeläinen and Ivan Kurolt and Yaniv Lustig and Miguel J Martinez and Marion Koopmans and Orsolya Nagy and Trung Nguyen and Anna Papa and Mercedes P{\'{e}}rez-Ruiz and Martin Pfeffer and Jelena Protic and Johan Reimerink and Giada Rossini and Mar{\'{\i}}a Paz S{\'{a}}nchez-Seco Fari{\~{n}}as and Jonas Schmidt-Chanasit and Sandra Söderholm and Bertrand Sudre and Marjan Van Esbroeck and Chantal B Reusken and},
    title = {Specialist laboratory networks as preparedness and response tool - the {E}merging {V}iral {D}iseases-{E}xpert {L}aboratory {N}etwork and the {C}hikungunya outbreak, {T}hailand, 2019},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {13},
    pages = {1900438},
    doi = {10.2807/1560-7917.es.2020.25.13.1900438},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
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    @Article{Depledge:20,
    author = {Daniel P. Depledge and Angus C. Wilson},
    title = {Using Direct {RNA} Nanopore Sequencing to Deconvolute Viral Transcriptomes},
    journal = {{Curr Protoc Microbiol}},
    year = {2020},
    volume = {57},
    number = {1},
    doi = {10.1002/cpmc.99},
    publisher = {Wiley},
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    @Article{Wölfel:20,
    author = {Roman Wölfel and Victor M. Corman and Wolfgang Guggemos and Michael Seilmaier and Sabine Zange and Marcel A. Müller and Daniela Niemeyer and Terry C. Jones and Patrick Vollmar and Camilla Rothe and Michael Hoelscher and Tobias Bleicker and Sebastian Brünink and Julia Schneider and Rosina Ehmann and Katrin Zwirglmaier and Christian Drosten and Clemens Wendtner},
    title = {Virological assessment of hospitalized patients with {COVID}-2019},
    journal = {Nature},
    year = {2020},
    volume = {581},
    pages = {465--469},
    doi = {10.1038/s41586-020-2196-x},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Löchel:20,
    author = {Hannah F. Löchel and Dominik Heider},
    title = {Comparative analyses of error handling strategies for next-generation sequencing in precision medicine},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {5750},
    doi = {10.1038/s41598-020-62675-8},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Kelly:20,
    author = {Jenna N Kelly and Laura Laloli and Philip V'Kovski and Melle Holwerda and Jasmine Portmann and Volker Thiel and Ronald Dijkman},
    title = {Comprehensive single cell analysis of pandemic influenza {A} virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.},
    journal = {{bioRxiv}},
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    @Article{Bojkova:20,
    author = {Denisa Bojkova and Jake E McGreig and Katie-May McLaughlin and Stuart G Masterson and Marek Widera and Verena Kraehling and Sandra Ciesek and Mark N Wass and Martin Michaelis and Jindrich N Cinatl},
    title = {{SARS}-{CoV}-2 and {SARS}-{CoV} differ in their cell tropism and drug sensitivity profiles},
    journal = {{bioRxiv}},
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    @Article{Leal:20,
    author = {{\'{E}}lcio Leal and Claudia Regina Arrais and Marta Barreiros and Jessyca Kalynne Farias Rodrigues and Nilviane Pires Silva Sousa and Daniel Duarte Costa and Francisco Dimitre Rodrigo Pereira Santos and Antonio Dantas Silva and Antonia Iracilda e Silva Viana and Allan Kardec Barros and Kledoaldo Oliveira de Lima},
    title = {Characterization of {HIV}-1 genetic diversity and antiretroviral resistance in the state of {M}aranh{\~{a}}o, {Northeast Brazil}},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {3},
    pages = {e0230878},
    doi = {10.1371/journal.pone.0230878},
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    @Article{Capobianchi:20,
    author = {M.R. Capobianchi and M. Rueca and F. Messina and E. Giombini and F. Carletti and F. Colavita and C. Castilletti and E. Lalle and L. Bordi and F. Vairo and E. Nicastri and G. Ippolito and C.E.M. Gruber and B. Bartolini},
    title = {Molecular characterization of {SARS}-{CoV}-2 from the first case of {COVID}-19 in {Italy}},
    journal = {{Clin Microbiol Infect}},
    year = {2020},
    volume = {26},
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    @Article{Blanco-Melo:20a,
    author = {Daniel Blanco-Melo and Benjamin E. Nilsson-Payant and Wen-Chun Liu and Skyler Uhl and Daisy Hoagland and Rasmus M{\o}ller and Tristan X. Jordan and Kohei Oishi and Maryline Panis and David Sachs and Taia T. Wang and Robert E. Schwartz and Jean K. Lim and Randy A. Albrecht and Benjamin R. tenOever},
    title = {Imbalanced host response to {SARS}-{CoV}-2 drives development of {COVID}-19},
    journal = {{Cell}},
    year = {2020},
    volume = {181},
    number = {5},
    pages = {1036--1045.e9},
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    publisher = {Elsevier {BV}},
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    @Article{Corman:20a,
    author = {Victor M Corman and Holger F Rabenau and Ortwin Adams and Doris Oberle and Markus B Funk and Brigitte Keller-Stanislawski and Joerg Timm and Christian Drosten and Sandra Ciesek},
    title = {{SARS}-{CoV}-2 asymptomatic and symptomatic patients and risk for transfusion transmission},
    journal = {{Transfusion}},
    year = {2020},
    volume = {60},
    number = {6},
    pages = {1119--1122},
    doi = {10.1111/trf.15841},
    publisher = {Wiley},
    }
  • [DOI] V. Thiel, “Viral RNA in an m6A disguise,” Nat Microbiol, vol. 5, iss. 4, p. 531–532, 2020.
    [Bibtex]
    @Article{Thiel:20,
    author = {Volker Thiel},
    title = {Viral {RNA} in an m6{A} disguise},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {5},
    number = {4},
    pages = {531--532},
    doi = {10.1038/s41564-020-0689-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Pingarilho, V. F. Pimentel, I. Diogo, S. Fernandes, M. Miranda, A. Pineda-Pena, P. Libin, K. Theys, R. O. M. Martins, A. Vandamme, P. Gomes, and A. B. Abecasis, “Increasing prevalence of HIV-1 Transmitted Drug Resistance in Portugal: implications for first line treatment recommendations,” medRxiv, 2020.
    [Bibtex]
    @Article{Pingarilho:20,
    author = {Marta Pingarilho and Victor F Pimentel and Isabel Diogo and Sandra Fernandes and Mafalda Miranda and Andrea Pineda-Pena and Pieter Libin and Kristof Theys and M. Rosario Oliveira Martins and Annemieke Vandamme and Perpetua Gomes and Ana B. Abecasis},
    title = {Increasing prevalence of {HIV}-1 {Transmitted Drug Resistance} in {Portugal}: implications for first line treatment recommendations},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.17.20033092},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Paraskevis, E. Kostaki, G. Magiorkinis, G. Panayiotakopoulos, G. Sourvinos, and S. Tsiodras, “Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event,” Infect Genet Evol, vol. 79, p. 104212, 2020.
    [Bibtex]
    @Article{Paraskevis:20,
    author = {D. Paraskevis and E. Kostaki and G. Magiorkinis and G. Panayiotakopoulos and G. Sourvinos and S. Tsiodras},
    title = {Full-genome evolutionary analysis of the novel corona virus (2019-{nCoV}) rejects the hypothesis of emergence as a result of a recent recombination event},
    journal = {{Infect Genet Evol}},
    year = {2020},
    volume = {79},
    pages = {104212},
    doi = {10.1016/j.meegid.2020.104212},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Grifoni, J. Sidney, Y. Zhang, R. H. Scheuermann, B. Peters, and A. Sette, “A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2,” Cell Host Microbe, vol. 27, iss. 4, p. 671–680.e2, 2020.
    [Bibtex]
    @Article{Grifoni:20a,
    author = {Alba Grifoni and John Sidney and Yun Zhang and Richard H. Scheuermann and Bjoern Peters and Alessandro Sette},
    title = {A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to {SARS}-{CoV}-2},
    journal = {{Cell Host Microbe}},
    year = {2020},
    volume = {27},
    number = {4},
    pages = {671--680.e2},
    doi = {10.1016/j.chom.2020.03.002},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. Kaczorowska and L. van der Hoek, “Human Anelloviruses: diverse, omnipresent and commensal members of the virome,” FEMS Microbiol Rev, vol. 44, iss. 3, p. 305–313, 2020.
    [Bibtex]
    @Article{Kaczorowska:20,
    author = {Joanna Kaczorowska and Lia van der Hoek},
    title = {Human {A}nelloviruses: diverse, omnipresent and commensal members of the virome},
    journal = {{FEMS Microbiol Rev}},
    year = {2020},
    volume = {44},
    number = {3},
    pages = {305--313},
    doi = {10.1093/femsre/fuaa007},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] L. Zhang, D. Lin, X. Sun, U. Curth, C. Drosten, L. Sauerhering, S. Becker, K. Rox, and R. Hilgenfeld, “Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved $\alpha$-ketoamide inhibitors,” Science, vol. 368, iss. 6489, p. eabb3405, 2020.
    [Bibtex]
    @Article{Zhang:20,
    author = {Linlin Zhang and Daizong Lin and Xinyuanyuan Sun and Ute Curth and Christian Drosten and Lucie Sauerhering and Stephan Becker and Katharina Rox and Rolf Hilgenfeld},
    title = {Crystal structure of {SARS}-{CoV}-2 main protease provides a basis for design of improved $\alpha$-ketoamide inhibitors},
    journal = {Science},
    year = {2020},
    volume = {368},
    number = {6489},
    pages = {409--412},
    pages = {eabb3405},
    doi = {10.1126/science.abb3405},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] E. M. Adriaenssens, M. B. Sullivan, P. Knezevic, L. J. van Zyl, B. L. Sarkar, B. E. Dutilh, P. Alfenas-Zerbini, M. L, Y. Tong, J. R. Brister, A. M. I. Switt, J. Klumpp, R. K. Aziz, J. Barylski, J. Uchiyama, R. A. Edwards, A. M. Kropinski, N. K. Petty, M. R. J. Clokie, A. I. Kushkina, V. V. Morozova, S. Duffy, A. Gillis, J. Rumnieks, I. Kurtböke, N. Chanishvili, L. Goodridge, J. Wittmann, R. Lavigne, H. B. Jang, D. Prangishvili, F. Enault, D. Turner, M. M. Poranen, H. M. Oksanen, and M. Krupovic, “Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee,” Arch Virol, vol. 165, p. 1253–1260, 2020.
    [Bibtex]
    @Article{Adriaenssens:20,
    author = {Evelien M. Adriaenssens and Matthew B. Sullivan and Petar Knezevic and Leonardo J. van Zyl and B. L. Sarkar and Bas E. Dutilh and Poliane Alfenas-Zerbini and Ma{\l}gorzata {\L}obocka and Yigang Tong and James Rodney Brister and Andrea I. Moreno Switt and Jochen Klumpp and Ramy Karam Aziz and Jakub Barylski and Jumpei Uchiyama and Rob A. Edwards and Andrew M. Kropinski and Nicola K. Petty and Martha R. J. Clokie and Alla I. Kushkina and Vera V. Morozova and Siobain Duffy and Annika Gillis and Janis Rumnieks and Ipek Kurtböke and Nina Chanishvili and Lawrence Goodridge and Johannes Wittmann and Rob Lavigne and Ho Bin Jang and David Prangishvili and Francois Enault and Dann Turner and Minna M. Poranen and Hanna M. Oksanen and Mart Krupovic},
    title = {Taxonomy of prokaryotic viruses: 2018-2019 update from the {ICTV} {Bacterial} and {Archaeal Viruses Subcommittee}},
    journal = {{Arch Virol}},
    year = {2020},
    volume = {165},
    pages = {1253--1260},
    doi = {10.1007/s00705-020-04577-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. Blanco-Melo, B. E. Nilsson-Payant, S. Uhl, B. Escudero, S. Olschewski, P. Thibault, M. Panis, M. Rosenthal, C. Munoz-Fontela, B. Lee, and B. tenOever, “An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses,” bioRxiv, 2020.
    [Bibtex]
    @Article{Blanco-Melo:20,
    author = {Daniel Blanco-Melo and Benjamin E. Nilsson-Payant and Skyler Uhl and Beatriz Escudero and Silke Olschewski and Patricia Thibault and Maryline Panis and Maria Rosenthal and Cesar Munoz-Fontela and Benhur Lee and Benjamin tenOever},
    title = {An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense {RNA} viruses},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.12.989319},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hoffmann, H. Kleine-Weber, S. Schroeder, N. Krüger, T. Herrler, S. Erichsen, T. S. Schiergens, G. Herrler, N. Wu, A. Nitsche, M. A. Müller, C. Drosten, and S. Pöhlmann, “SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor,” Cell, vol. 181, iss. 2, p. 271–280.e8, 2020.
    [Bibtex]
    @Article{Hoffmann:20a,
    author = {Markus Hoffmann and Hannah Kleine-Weber and Simon Schroeder and Nadine Krüger and Tanja Herrler and Sandra Erichsen and Tobias S. Schiergens and Georg Herrler and Nai-Huei Wu and Andreas Nitsche and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {{SARS}-{CoV}-2 Cell Entry Depends on {ACE}2 and {TMPRSS}2 and Is Blocked by a Clinically Proven Protease Inhibitor},
    journal = {Cell},
    year = {2020},
    volume = {181},
    number = {2},
    pages = {271--280.e8},
    doi = {10.1016/j.cell.2020.02.052},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Pfaender, K. B. Mar, E. Michailidis, A. Kratzel, D. Hirt, P. V’Kovski, W. Fan, N. Ebert, H. Stalder, H. Kleine-Weber, M. Hoffmann, H. H. Hoffmann, M. Saeed, R. Dijkman, E. Steinmann, M. Wight-Carter, N. W. Hanners, S. Pohlmann, T. Gallagher, D. Todt, G. Zimmer, C. M. Rice, J. W. Schoggins, and V. Thiel, “LY6E impairs coronavirus fusion and confers immune control of viral disease,” bioRxiv, 2020.
    [Bibtex]
    @Article{Pfaender:20,
    author = {Stephanie Pfaender and Katrina B Mar and Eleftherios Michailidis and Annika Kratzel and Dagny Hirt and Philip V'Kovski and Wenchun Fan and Nadine Ebert and Hanspeter Stalder and Hannah Kleine-Weber and Markus Hoffmann and H. Heinrich Hoffmann and Mohsan Saeed and Ronald Dijkman and Eike Steinmann and Mary Wight-Carter and Natasha W Hanners and Stefan Pohlmann and Tom Gallagher and Daniel Todt and Gert Zimmer and Charles M Rice and John W Schoggins and Volker Thiel},
    title = {{LY}6{E} impairs coronavirus fusion and confers immune control of viral disease},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.05.979260},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. H. Forth, L. F. Forth, S. J. Lycett, L. Bell-Sakyi, G. M. Keil, S. Blome, S. Calvignac-Spencer, A. Wissgott, J. Krause, D. Hoeper, H. Kampen, and M. Beer, “African swine fever virus-like integrated elements in a soft tick genome – an ancient virus vector arms race?,” bioRxiv, 2020.
    [Bibtex]
    @Article{Forth:20,
    author = {Jan Hendrik Forth and Leonie Franziska Forth and Samantha J Lycett and Lesley Bell-Sakyi and Guenther Michael Keil and Sandra Blome and Sebastien Calvignac-Spencer and Antje Wissgott and Johannes Krause and Dirk Hoeper and Helge Kampen and Martin Beer},
    title = {African swine fever virus-like integrated elements in a soft tick genome {\textendash} an ancient virus vector arms race?},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.08.978106},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Woelfel, V. M. Corman, W. Guggemos, M. Seilmaier, S. Zange, M. A. Mueller, D. Niemeyer, P. Vollmar, C. Rothe, M. Hoelscher, T. Bleicker, S. Bruenink, J. Schneider, R. Ehmann, K. Zwirglmaier, C. Drosten, and C. Wendtner, “Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster,” medRxiv, 2020.
    [Bibtex]
    @Article{Woelfel:20,
    author = {Roman Woelfel and Victor Max Corman and Wolfgang Guggemos and Michael Seilmaier and Sabine Zange and Marcel A Mueller and Daniela Niemeyer and Patrick Vollmar and Camilla Rothe and Michael Hoelscher and Tobias Bleicker and Sebastian Bruenink and Julia Schneider and Rosina Ehmann and Katrin Zwirglmaier and Christian Drosten and Clemens Wendtner},
    title = {Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.05.20030502},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lequime, P. Bastide, S. Dellicour, P. Lemey, and G. Baele, “nosoi: A stochastic agent-based transmission chain simulation framework in R,” Methods Ecol Evol, 2020.
    [Bibtex]
    @Article{Lequime:20,
    author = {Sebastian Lequime and Paul Bastide and Simon Dellicour and Philippe Lemey and Guy Baele},
    title = {{nosoi}: {A} stochastic agent-based transmission chain simulation framework in {R}},
    journal = {{Methods Ecol Evol}},
    year = {2020},
    doi = {10.1111/2041-210X.13422},
    publisher = {Wiley},
    }
  • [DOI] C. Claus, M. Jung, and J. M. Hübschen, “Pluripotent stem cell-based models: a peephole into virus infections during early pregnancy,” Cells, vol. 9, iss. 3, p. 542, 2020.
    [Bibtex]
    @Article{Claus:20,
    author = {Claudia Claus and Matthias Jung and Judith M. Hübschen},
    title = {Pluripotent Stem Cell-Based Models: A Peephole into Virus Infections during Early Pregnancy},
    journal = {{Cells}},
    year = {2020},
    volume = {9},
    number = {3},
    pages = {542},
    doi = {10.3390/cells9030542},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. S. Gill, P. Lemey, M. A. Suchard, A. Rambaut, and G. Baele, “Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction,” Mol Biol Evol, vol. 37, iss. 6, p. 1832–1842, 2020.
    [Bibtex]
    @Article{Gill:20,
    author = {Mandev S Gill and Philippe Lemey and Marc A Suchard and Andrew Rambaut and Guy Baele},
    title = {Online {Bayesian} phylodynamic inference in {BEAST} with application to epidemic reconstruction},
    journal = {{Mol Biol Evol}},
    year = {2020},
    volume = {37},
    number = {6},
    pages = {1832--1842},
    doi = {10.1093/molbev/msaa047},
    editor = {Michael Rosenberg},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Tomazatos, R. E. Marschang, I. Maranda, H. Baum, A. Bialonski, M. Spînu, R. Lühken, J. Schmidt-Chanasit, and D. Cadar, “Letea virus: comparative genomics and phylogenetic analysis of a novel reassortant orbivirus discovered in grass snakes (Natrix natrix),” Viruses, vol. 12, iss. 2, p. 243, 2020.
    [Bibtex]
    @Article{Tomazatos:20,
    author = {Alexandru Tomazatos and Rachel E. Marschang and Iulia Maranda and Heike Baum and Alexandra Bialonski and Marina Sp{\^{\i}}nu and Renke Lühken and Jonas Schmidt-Chanasit and Daniel Cadar},
    title = {Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes ({N}atrix natrix)},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {2},
    pages = {243},
    doi = {10.3390/v12020243},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. Brunker, G. Jaswant, S. M. Thumbi, K. Lushasi, A. Lugelo, A. M. Czupryna, F. Ade, G. Wambura, V. Chuchu, R. Steenson, C. Ngeleja, C. Bautista, D. L. Manalo, M. R. R. Gomez, M. Y. J. V. Chu, M. E. Miranda, M. Kamat, K. Rysava, J. Espineda, E. A. V. Silo, A. M. Aringo, R. P. Bernales, F. F. Adonay, M. J. Tildesley, D. A. Marston, D. L. Jennings, A. R. Fooks, W. Zhu, L. W. Meredith, S. C. Hill, R. Poplawski, R. J. Gifford, J. B. Singer, M. Maturi, A. Mwatondo, R. Biek, and K. Hampson, “Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes,” Wellcome Open Res, vol. 5, p. 3, 2020.
    [Bibtex]
    @Article{Brunker:20,
    author = {Kirstyn Brunker and Gurdeep Jaswant and S.M. Thumbi and Kennedy Lushasi and Ahmed Lugelo and Anna M. Czupryna and Fred Ade and Gati Wambura and Veronicah Chuchu and Rachel Steenson and Chanasa Ngeleja and Criselda Bautista and Daria L. Manalo and Ma. Ricci R. Gomez and Maria Yna Joyce V. Chu and Mary Elizabeth Miranda and Maya Kamat and Kristyna Rysava and Jason Espineda and Eva Angelica V. Silo and Ariane Mae Aringo and Rona P. Bernales and Florencio F. Adonay and Michael J. Tildesley and Denise A. Marston and Daisy L. Jennings and Anthony R. Fooks and Wenlong Zhu and Luke W. Meredith and Sarah C. Hill and Radoslaw Poplawski and Robert J. Gifford and Joshua B. Singer and Mathew Maturi and Athman Mwatondo and Roman Biek and Katie Hampson},
    title = {Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {3},
    doi = {10.12688/wellcomeopenres.15518.1},
    publisher = {Faculty of 1000 Ltd},
    }
  • [DOI] R. Zell, A. E. Gorbalenya, N. J. Knowles, P. Simmonds, and T. Skern, “How to recognise and deal with dubious virus sequences?,” Infect Genet Evol, vol. 81, p. 104242, 2020.
    [Bibtex]
    @Article{Zell:20,
    author = {Roland Zell and Alexander E. Gorbalenya and Nick J. Knowles and Peter Simmonds and Tim Skern},
    title = {How to recognise and deal with dubious virus sequences?},
    journal = {{Infect Genet Evol}},
    year = {2020},
    volume = {81},
    pages = {104242},
    doi = {10.1016/j.meegid.2020.104242},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. M. Dinan, N. I. Lukhovitskaya, I. Olendraite, and A. E. Firth, “A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.,” Virus Evol, vol. 6, iss. 1, p. veaa007, 2020.
    [Bibtex]
    @Article{Dinan:20,
    author = {Dinan, Adam M and Lukhovitskaya, Nina I and Olendraite, Ingrida and Firth, Andrew E},
    title = {A case for a negative-strand coding sequence in a group of positive-sense {RNA} viruses.},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa007},
    abstract = {Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family which, together with RNA bacteriophages of the family , form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and origin of genes.},
    doi = {10.1093/ve/veaa007},
    issue = {1},
    keywords = {RNA virus; overlapping genes},
    pmid = {32064120},
    }
  • [DOI] B. B. Oude Munnink, E. Münger, D. F. Nieuwenhuijse, R. Kohl, A. van der Linden, C. M. E. Schapendonk, H. van der Jeugd, M. Kik, J. M. Rijks, C. B. E. M. Reusken, and M. Koopmans, “Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018.,” Sci Rep, vol. 10, p. 2798, 2020.
    [Bibtex]
    @Article{OudeMunnink:20a,
    author = {Oude Munnink, Bas B and Münger, E and Nieuwenhuijse, D F and Kohl, R and van der Linden, A and Schapendonk, C M E and van der Jeugd, H and Kik, M and Rijks, J M and Reusken, C B E M and Koopmans, M},
    title = {Genomic monitoring to understand the emergence and spread of {U}sutu virus in the {N}etherlands, 2016-2018.},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {2798},
    abstract = {Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula). In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to Nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. This analyses further suggest some extent of circulation of USUV between the Netherlands, Germany and Belgium, as well as likely overwintering of USUV in the Netherlands.},
    doi = {10.1038/s41598-020-59692-y},
    issue = {1},
    pmid = {32071379},
    }
  • [DOI] M. J. Poen, A. Pohlmann, C. Amid, T. M. Bestebroer, S. M. Brookes, I. H. Brown, H. Everett, C. M. E. Schapendonk, R. D. Scheuer, S. L. Smits, M. Beer, R. A. M. Fouchier, and R. J. Ellis, “Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak.,” PLoS One, vol. 15, iss. 2, p. e0229326, 2020.
    [Bibtex]
    @Article{Poen:20,
    author = {Poen, Marjolein J and Pohlmann, Anne and Amid, Clara and Bestebroer, Theo M and Brookes, Sharon M and Brown, Ian H and Everett, Helen and Schapendonk, Claudia M E and Scheuer, Rachel D and Smits, Saskia L and Beer, Martin and Fouchier, Ron A M and Ellis, Richard J},
    title = {Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (m{SNV}) analysis during an influenza {A/H5N8} outbreak.},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {2},
    pages = {e0229326},
    abstract = {As high-throughput sequencing technologies are becoming more widely adopted for analysing pathogens in disease outbreaks there needs to be assurance that the different sequencing technologies and approaches to data analysis will yield reliable and comparable results. Conversely, understanding where agreement cannot be achieved provides insight into the limitations of these approaches and also allows efforts to be focused on areas of the process that need improvement. This manuscript describes the next-generation sequencing of three closely related viruses, each analysed using different sequencing strategies, sequencing instruments and data processing pipelines. In order to determine the comparability of consensus sequences and minority (sub-consensus) single nucleotide variant (mSNV) identification, the biological samples, the sequence data from 3 sequencing platforms and the *.bam quality-trimmed alignment files of raw data of 3 influenza A/H5N8 viruses were shared. This analysis demonstrated that variation in the final result could be attributed to all stages in the process, but the most critical were the well-known homopolymer errors introduced by 454 sequencing, and the alignment processes in the different data processing pipelines which affected the consistency of mSNV detection. However, homopolymer errors aside, there was generally a good agreement between consensus sequences that were obtained for all combinations of sequencing platforms and data processing pipelines. Nevertheless, minority variant analysis will need a different level of careful standardization and awareness about the possible limitations, as shown in this study.},
    doi = {10.1371/journal.pone.0229326},
    issue = {2},
    pmid = {32078666},
    }
  • [DOI] A. Grifoni, J. Sidney, Y. Zhang, R. H. Scheuermann, B. Peters, and A. Sette, “Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions,” bioRxiv, 2020.
    [Bibtex]
    @Article{Grifoni:20,
    author = {Alba Grifoni and John Sidney and Yun Zhang and Richard H Scheuermann and Bjoern Peters and Alessandro Sette},
    title = {Candidate targets for immune responses to 2019-{N}ovel {C}oronavirus ({nCoV}): sequence homology- and bioinformatic-based predictions},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.02.12.946087},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. V. Damme, M. Hölzer, A. Viehweger, B. Müller, E. Bongcam-Rudloff, and C. Brandt, “Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN),” bioRxiv, 2020.
    [Bibtex]
    @Article{Damme:20,
    author = {Renaud Van Damme and Martin Hölzer and Adrian Viehweger and Bettina Müller and Erik Bongcam-Rudloff and Christian Brandt},
    title = {Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis ({MUFFIN})},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.02.08.939843},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hoffmann, H. Kleine-Weber, N. Krüger, M. Müller, C. Drosten, and S. Pöhlmann, “The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells,” bioRxiv, 2020.
    [Bibtex]
    @Article{Hoffmann:20,
    author = {Markus Hoffmann and Hannah Kleine-Weber and Nadine Krüger and Marcel Müller and Christian Drosten and Stefan Pöhlmann},
    title = {The novel coronavirus 2019 (2019-{nCoV}) uses the {SARS}-coronavirus receptor {ACE}2 and the cellular protease {TMPRSS}2 for entry into target cells},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.31.929042},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] G. Kampf, D. Todt, S. Pfaender, and E. Steinmann, “Persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents,” J Hosp Infect, vol. 104, iss. 3, p. 246–251, 2020.
    [Bibtex]
    @Article{Kampf:20,
    author = {Günter Kampf and Daniel Todt and Stephanie Pfaender and Eike Steinmann},
    title = {Persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents},
    journal = {{J Hosp Infect}},
    year = {2020},
    volume = {104},
    number = {3},
    pages = {246--251},
    doi = {10.1016/j.jhin.2020.01.022},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. L. Hong, S. Dellicour, B. Vrancken, M. A. Suchard, M. T. Pyne, D. R. Hillyard, P. Lemey, and G. Baele, “In search of covariates of HIV-1 subtype B spread in the United States – A cautionary tale of large-scale bayesian phylogeography,” Viruses, vol. 12, iss. 2, p. 182, 2020.
    [Bibtex]
    @Article{Hong:20,
    author = {Samuel L. Hong and Simon Dellicour and Bram Vrancken and Marc A. Suchard and Michael T. Pyne and David R. Hillyard and Philippe Lemey and Guy Baele},
    title = {In Search of Covariates of {HIV}-1 Subtype {B} Spread in the {United States} -- {A} Cautionary Tale of Large-Scale Bayesian Phylogeography},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {2},
    pages = {182},
    doi = {10.3390/v12020182},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Reimering, S. Muñoz, and A. C. McHardy, “Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic,” PLoS Comput Biol, vol. 16, iss. 2, p. e1007101, 2020.
    [Bibtex]
    @Article{Reimering:20,
    author = {Susanne Reimering and Sebastian Mu{\~{n}}oz and Alice C. McHardy},
    title = {Phylogeographic reconstruction using air transportation data and its application to the 2009 {H1N1} influenza {A} pandemic},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {2},
    pages = {e1007101},
    doi = {10.1371/journal.pcbi.1007101},
    editor = {Cecile Viboud},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] C. E. Brook, M. Boots, K. Chandran, A. P. Dobson, C. Drosten, A. L. Graham, B. T. Grenfell, M. A. Müller, M. Ng, L. Wang, and A. van Leeuwen, “Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence,” eLife, vol. 9, p. e48401, 2020.
    [Bibtex]
    @Article{Brook:20,
    author = {Cara E Brook and Mike Boots and Kartik Chandran and Andrew P Dobson and Christian Drosten and Andrea L Graham and Bryan T Grenfell and Marcel A Müller and Melinda Ng and Lin-Fa Wang and Anieke van Leeuwen},
    title = {Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence},
    journal = {{eLife}},
    year = {2020},
    volume = {9},
    pages = {e48401},
    doi = {10.7554/elife.48401},
    publisher = {{eLife} Sciences Publications, Ltd},
    }
  • [DOI] M. K. Mirzaei, M. A. A. Khan, P. Ghosh, Z. E. Taranu, M. Taguer, J. Ru, R. Chowdhury, M. M. Kabir, L. Deng, D. Mondal, and C. F. Maurice, “Bacteriophages isolated from stunted children can regulate gut bacterial communities in an age-specific manner,” Cell Host Microbe, vol. 27, iss. 2, p. 199–212.e5, 2020.
    [Bibtex]
    @Article{Mirzaei:20,
    author = {Mohammadali Khan Mirzaei and Md. Anik Ashfaq Khan and Prakash Ghosh and Zofia E. Taranu and Mariia Taguer and Jinlong Ru and Rajashree Chowdhury and Md. Mamun Kabir and Li Deng and Dinesh Mondal and Corinne F. Maurice},
    title = {Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner},
    journal = {{Cell Host Microbe}},
    year = {2020},
    volume = {27},
    number = {2},
    pages = {199--212.e5},
    doi = {10.1016/j.chom.2020.01.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. B. E. M. Reusken, E. K. Broberg, B. Haagmans, A. Meijer, V. M. Corman, A. Papa, R. Charrel, C. Drosten, M. Koopmans, and K. L. and, “Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020,” Euro Surveill, vol. 25, iss. 6, p. 2000082, 2020.
    [Bibtex]
    @Article{Reusken:20,
    author = {Chantal B.E.M. Reusken and Eeva K. Broberg and Bart Haagmans and Adam Meijer and Victor M. Corman and Anna Papa and Remi Charrel and Christian Drosten and Marion Koopmans and Katrin Leitmeyer and},
    title = {Laboratory readiness and response for novel coronavirus (2019-{nCoV}) in expert laboratories in 30 {EU}/{EEA} countries, {J}anuary 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {6},
    pages = {2000082},
    doi = {10.2807/1560-7917.es.2020.25.6.2000082},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] S. Dirmeier, C. Dächert, M. van Hemert, A. Tas, N. S. Ogando, F. van Kuppeveld, R. Bartenschlager, L. Kaderali, M. Binder, and N. Beerenwinkel, “Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation,” PLoS Comput Biol, vol. 16, iss. 2, p. e1007587, 2020.
    [Bibtex]
    @Article{Dirmeier:20,
    author = {Simon Dirmeier and Christopher Dächert and Martijn van Hemert and Ali Tas and Natacha S. Ogando and Frank van Kuppeveld and Ralf Bartenschlager and Lars Kaderali and Marco Binder and Niko Beerenwinkel},
    title = {Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {2},
    pages = {e1007587},
    doi = {10.1371/journal.pcbi.1007587},
    editor = {Natalia L. Komarova},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] A. A. Gulyaeva, A. I. Sigorskih, E. S. Ocheredko, D. V. Samborskiy, and A. E. Gorbalenya, “LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins,” Bioinformatics, vol. 36, iss. 9, p. 2731–2739, 2020.
    [Bibtex]
    @Article{Gulyaeva:20,
    author = {Anastasia A Gulyaeva and Andrey I Sigorskih and Elena S Ocheredko and Dmitry V Samborskiy and Alexander E Gorbalenya},
    title = {{LAMPA}, {LArge} {Multidomain Protein Annotator}, and its application to {RNA} virus polyproteins},
    journal = {Bioinformatics},
    year = {2020},
    volume = {36},
    number = {9},
    pages = {2731--2739},
    doi = {10.1093/bioinformatics/btaa065},
    editor = {Yann Ponty},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. Rothe, M. Schunk, P. Sothmann, G. Bretzel, G. Froeschl, C. Wallrauch, T. Zimmer, V. Thiel, C. Janke, W. Guggemos, M. Seilmaier, C. Drosten, P. Vollmar, K. Zwirglmaier, S. Zange, R. Wölfel, and M. Hoelscher, “Transmission of 2019-nCoV infection from an asymptomatic contact in Germany,” N Engl J Med, vol. 382, p. 970–971, 2020.
    [Bibtex]
    @Article{Rothe:20,
    author = {Camilla Rothe and Mirjam Schunk and Peter Sothmann and Gisela Bretzel and Guenter Froeschl and Claudia Wallrauch and Thorbjörn Zimmer and Verena Thiel and Christian Janke and Wolfgang Guggemos and Michael Seilmaier and Christian Drosten and Patrick Vollmar and Katrin Zwirglmaier and Sabine Zange and Roman Wölfel and Michael Hoelscher},
    title = {Transmission of 2019-{nCoV} Infection from an Asymptomatic Contact in {G}ermany},
    journal = {{N Engl J Med}},
    year = {2020},
    volume = {382},
    pages = {970--971},
    doi = {10.1056/nejmc2001468},
    publisher = {Massachusetts Medical Society},
    }
  • [DOI] R. J. Paxton, “A microbiome silver bullet for honey bees,” Science, vol. 367, iss. 6477, p. 504–506, 2020.
    [Bibtex]
    @Article{Paxton:20,
    author = {Robert J. Paxton},
    title = {A microbiome silver bullet for honey bees},
    journal = {Science},
    year = {2020},
    volume = {367},
    number = {6477},
    pages = {504--506},
    doi = {10.1126/science.aba6135},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, A. Meijer, D. K. Chu, T. Bleicker, S. Brünink, J. Schneider, M. L. Schmidt, D. G. Mulders, B. L. Haagmans, B. van der Veer, S. van den Brink, L. Wijsman, G. Goderski, J. Romette, J. Ellis, M. Zambon, M. Peiris, H. Goossens, C. Reusken, M. P. Koopmans, and C. Drosten, “Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR,” Euro Surveill, vol. 25, iss. 3, p. 2000045, 2020.
    [Bibtex]
    @Article{Corman:20,
    author = {Victor M Corman and Olfert Landt and Marco Kaiser and Richard Molenkamp and Adam Meijer and Daniel KW Chu and Tobias Bleicker and Sebastian Brünink and Julia Schneider and Marie Luisa Schmidt and Daphne GJC Mulders and Bart L Haagmans and Bas van der Veer and Sharon van den Brink and Lisa Wijsman and Gabriel Goderski and Jean-Louis Romette and Joanna Ellis and Maria Zambon and Malik Peiris and Herman Goossens and Chantal Reusken and Marion PG Koopmans and Christian Drosten},
    title = {Detection of 2019 novel coronavirus (2019-{nCoV}) by real-time {RT}-{PCR}},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {3},
    pages = {2000045},
    doi = {10.2807/1560-7917.es.2020.25.3.2000045},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] C. Kreer, M. Döring, N. Lehnen, M. S. Ercanoglu, L. Gieselmann, D. Luca, K. Jain, P. Schommers, N. Pfeifer, and F. Klein, “openPrimeR for multiplex amplification of highly diverse templates,” J Immunol Methods, vol. 480, p. 112752, 2020.
    [Bibtex]
    @Article{Kreer:20,
    author = {Christoph Kreer and Matthias Döring and Nathalie Lehnen and Meryem S. Ercanoglu and Lutz Gieselmann and Domnica Luca and Kanika Jain and Philipp Schommers and Nico Pfeifer and Florian Klein},
    title = {{openPrimeR} for multiplex amplification of highly diverse templates},
    journal = {{J Immunol Methods}},
    year = {2020},
    volume = {480},
    pages = {112752},
    doi = {10.1016/j.jim.2020.112752},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. T. T. Kwok, D. F. Nieuwenhuijse, M. V. T. Phan, and M. P. G. Koopmans, “Virus metagenomics in farm animals: a systematic review,” Viruses, vol. 12, iss. 1, p. 107, 2020.
    [Bibtex]
    @Article{Kwok:20,
    author = {Kirsty T. T. Kwok and David F. Nieuwenhuijse and My V. T. Phan and Marion P. G. Koopmans},
    title = {Virus Metagenomics in Farm Animals: A Systematic Review},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {1},
    pages = {107},
    doi = {10.3390/v12010107},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] H. Kleine-Weber, S. Schroeder, N. Krüger, A. Prokscha, H. Y. Naim, M. A. Müller, C. Drosten, S. Pöhlmann, and M. Hoffmann, “Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus,” Emerg Microbes Infect, vol. 9, iss. 1, p. 155–168, 2020.
    [Bibtex]
    @Article{Kleine-Weber:20,
    author = {Hannah Kleine-Weber and Simon Schroeder and Nadine Krüger and Alexander Prokscha and Hassan Y. Naim and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann and Markus Hoffmann},
    title = {Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of {Middle East} respiratory syndrome coronavirus},
    journal = {{Emerg Microbes Infect}},
    year = {2020},
    volume = {9},
    number = {1},
    pages = {155--168},
    doi = {10.1080/22221751.2020.1713705},
    publisher = {Informa {UK} Limited},
    }
  • [DOI] A. O. Abdelkareem, M. I. Khalil, A. H. Elbehery, and H. M. Abbas, “Viral sequence identification in metagenomes using natural language processing techniques,” bioRxiv, 2020.
    [Bibtex]
    @Article{Abdelkareem:20,
    author = {Aly O. Abdelkareem and Mahmoud I. Khalil and Ali H. Elbehery and Hazem M. Abbas},
    title = {Viral Sequence Identification in Metagenomes using Natural Language Processing Techniques},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.10.892158},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Masembe, M. V. T. Phan, D. L. Robertson, and M. Cotten, “Increased resolution of African Swine Fever Virus genome patterns based on profile HMM protein domains,” Virus Evolution, p. veaa044, 2020.
    [Bibtex]
    @Article{Masembe:20,
    author = {Charles Masembe and My V.T. Phan and David L. Robertson and Matthew Cotten},
    title = {Increased resolution of {African Swine Fever Virus} genome patterns based on profile {HMM} protein domains},
    journal = {{Virus Evolution}},
    year = {2020},
    pages = {veaa044},
    doi = {10.1093/ve/veaa044},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Scire, J. Barido-Sottani, D. Kühnert, T. G. Vaughan, and T. Stadler, “Improved multi-type birth-death phylodynamic inference in BEAST 2,” bioRxiv, 2020.
    [Bibtex]
    @Article{Scire:20,
    author = {J{\'{e}}r{\'{e}}mie Scire and Joëlle Barido-Sottani and Denise Kühnert and Timothy G. Vaughan and Tanja Stadler},
    title = {Improved multi-type birth-death phylodynamic inference in {BEAST} 2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.06.895532},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Todt, M. Friesland, N. Moeller, D. Praditya, V. Kinast, Y. Brüggemann, L. Knegendorf, T. Burkard, J. Steinmann, R. Burm, L. Verhoye, A. Wahid, T. L. Meister, M. Engelmann, V. M. Pfankuche, C. Puff, F. W. R. Vondran, W. Baumgärtner, P. Meuleman, P. Behrendt, and E. Steinmann, “Robust hepatitis E virus infection and transcriptional response in human hepatocytes,” Proc Natl Acad Sci USA, vol. 117, iss. 3, p. 1731–1741, 2020.
    [Bibtex]
    @Article{Todt:20,
    author = {Daniel Todt and Martina Friesland and Nora Moeller and Dimas Praditya and Volker Kinast and Yannick Brüggemann and Leonard Knegendorf and Thomas Burkard and Joerg Steinmann and Rani Burm and Lieven Verhoye and Avista Wahid and Toni Luise Meister and Michael Engelmann and Vanessa M. Pfankuche and Christina Puff and Florian W. R. Vondran and Wolfgang Baumgärtner and Philip Meuleman and Patrick Behrendt and Eike Steinmann},
    title = {Robust hepatitis {E} virus infection and transcriptional response in human hepatocytes},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {3},
    pages = {1731--1741},
    doi = {10.1073/pnas.1912307117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] E. Hietanen and P. Susi, “Recombination events and conserved nature of receptor binding motifs in coxsackievirus A9 isolates,” Viruses, vol. 12, iss. 1, p. 68, 2020.
    [Bibtex]
    @Article{Hietanen:20,
    author = {Eero Hietanen and Petri Susi},
    title = {Recombination Events and Conserved Nature of Receptor Binding Motifs in Coxsackievirus {A9} Isolates},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {1},
    pages = {68},
    doi = {10.3390/v12010068},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] H. H. Niller, K. Angstwurm, D. Rubbenstroth, K. Schlottau, A. Ebinger, S. Giese, S. Wunderlich, B. Banas, L. F. Forth, D. Hoffmann, D. Höper, M. Schwemmle, D. Tappe, J. Schmidt-Chanasit, D. Nobach, C. Herden, C. Brochhausen, N. Velez-Char, A. Mamilos, K. Utpatel, M. Evert, S. Zoubaa, M. J. Riemenschneider, V. Ruf, J. Herms, G. Rieder, M. Errath, K. Matiasek, J. Schlegel, F. Liesche-Starnecker, B. Neumann, K. Fuchs, R. A. Linker, B. Salzberger, T. Freilinger, L. Gartner, J. J. Wenzel, U. Reischl, W. Jilg, A. Gessner, J. Jantsch, M. Beer, and B. Schmidt, “Zoonotic spillover infections with Borna disease virus 1 leading to fatal human encephalitis, 1999-2019: an epidemiological investigation.,” Lancet Infect Dis, vol. 20, iss. 4, p. 467–477, 2020.
    [Bibtex]
    @Article{Niller:20,
    author = {Niller, Hans Helmut and Angstwurm, Klemens and Rubbenstroth, Dennis and Schlottau, Kore and Ebinger, Arnt and Giese, Sebastian and Wunderlich, Silke and Banas, Bernhard and Forth, Leonie F and Hoffmann, Donata and Höper, Dirk and Schwemmle, Martin and Tappe, Dennis and Schmidt-Chanasit, Jonas and Nobach, Daniel and Herden, Christiane and Brochhausen, Christoph and Velez-Char, Natalia and Mamilos, Andreas and Utpatel, Kirsten and Evert, Matthias and Zoubaa, Saida and Riemenschneider, Markus J and Ruf, Viktoria and Herms, Jochen and Rieder, Georg and Errath, Mario and Matiasek, Kaspar and Schlegel, Jürgen and Liesche-Starnecker, Friederike and Neumann, Bernhard and Fuchs, Kornelius and Linker, Ralf A and Salzberger, Bernd and Freilinger, Tobias and Gartner, Lisa and Wenzel, Jürgen J and Reischl, Udo and Jilg, Wolfgang and Gessner, André and Jantsch, Jonathan and Beer, Martin and Schmidt, Barbara},
    title = {Zoonotic spillover infections with {B}orna disease virus 1 leading to fatal human encephalitis, 1999-2019: an epidemiological investigation.},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    volume = {20},
    number = {4},
    pages = {467--477},
    abstract = {In 2018-19, Borna disease virus 1 (BoDV-1), the causative agent of Borna disease in horses, sheep, and other domestic mammals, was reported in five human patients with severe to fatal encephalitis in Germany. However, information on case frequencies, clinical courses, and detailed epidemiological analyses are still lacking. We report the occurrence of BoDV-1-associated encephalitis in cases submitted to the Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany, and provide a detailed description of newly identified cases of BoDV-1-induced encephalitis. All brain tissues from 56 encephalitis cases from Bavaria, Germany, of putative viral origin (1999-2019), which had been submitted for virological testing upon request of the attending clinician and stored for stepwise diagnostic procedure, were systematically screened for BoDV-1 RNA. Two additional BoDV-1-positive cases were contributed by other diagnostic centres. Positive results were confirmed by deep sequencing, antigen detection, and determination of BoDV-1-reactive antibodies in serum and cerebrospinal fluid. Clinical and epidemiological data from infected patients were collected and analysed. BoDV-1 RNA and bornavirus-reactive antibodies were detected in eight newly analysed encephalitis cases and the first human BoDV-1 isolate was obtained from an unequivocally confirmed human BoDV-1 infection from the endemic area. Six of the eight BoDV-1-positive patients had no record of immunosuppression before the onset of fatal disease, whereas two were immunocompromised after solid organ transplantation. Typical initial symptoms were headache, fever, and confusion, followed by various neurological signs, deep coma, and severe brainstem involvement. Seven of nine patients with fatal encephalitis of unclear cause were BoDV-1 positive within one diagnostic centre. BoDV-1 sequence information and epidemiological analyses indicated independent spillover transmissions most likely from the local wild animal reservoir. BoDV-1 infection has to be considered as a potentially lethal zoonosis in endemic regions with reported spillover infections in horses and sheep. BoDV-1 infection can result in fatal encephalitis in immunocompromised and apparently healthy people. Consequently, all severe encephalitis cases of unclear cause should be tested for bornaviruses especially in endemic regions. German Federal Ministry of Education and Research.},
    doi = {10.1016/S1473-3099(19)30546-8},
    pmid = {31924550},
    }
  • [DOI] O. Ratmann, J. Kagaayi, M. Hall, T. Golubchick, G. Kigozi, X. Xi, C. Wymant, G. Nakigozi, L. Abeler-Dörner, D. Bonsall, A. Gall, A. Hoppe, P. Kellam, J. Bazaale, S. Kalibbala, O. Laeyendecker, J. Lessler, F. Nalugoda, L. W. Chang, T. de Oliveira, D. Pillay, T. C. Quinn, S. J. Reynolds, S. E. F. Spencer, R. Ssekubugu, D. Serwadda, M. J. Wawer, R. H. Gray, C. Fraser, K. M. Grabowski, Rakai Health Sciences Program, and the Pangea HIV Consortium, “Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.,” Lancet HIV, vol. 7, iss. 3, p. e173–e183, 2020.
    [Bibtex]
    @Article{Ratmann:20,
    author = {Ratmann, Oliver and Kagaayi, Joseph and Hall, Matthew and Golubchick, Tanya and Kigozi, Godfrey and Xi, Xiaoyue and Wymant, Chris and Nakigozi, Gertrude and Abeler-Dörner, Lucie and Bonsall, David and Gall, Astrid and Hoppe, Anne and Kellam, Paul and Bazaale, Jeremiah and Kalibbala, Sarah and Laeyendecker, Oliver and Lessler, Justin and Nalugoda, Fred and Chang, Larry W and de Oliveira, Tulio and Pillay, Deenan and Quinn, Thomas C and Reynolds, Steven J and Spencer, Simon E F and Ssekubugu, Robert and Serwadda, David and Wawer, Maria J and Gray, Ronald H and Fraser, Christophe and Grabowski, M Kate and {Rakai Health Sciences Program} and {the Pangea HIV Consortium}},
    title = {Quantifying {HIV} transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in {R}akai, {U}ganda.},
    journal = {{Lancet HIV}},
    year = {2020},
    volume = {7},
    number = {3},
    pages = {e173--e183},
    abstract = {International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15-49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4-7·3) of transmissions occurred within lakeside areas, 89·2% (86·0-91·8) within inland areas, 1·3% (0·6-2·6) from lakeside to inland areas, and 3·7% (2·3-5·8) from inland to lakeside areas. Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention.},
    doi = {10.1016/S2352-3018(19)30378-9},
    investigator = {Ayles, Helen and Bowden, Rory and Calvez, Vincent and Cohen, Myron and Dennis, Anne and Essex, Max and Fidler, Sarah and Frampton, Dan and Hayes, Richard and Herbeck, Josh and Kaleebu, Pontiano and Kityo, Cissy and Lingappa, Jairam and Novitsky, Vladimir and Paton, Nick and Rambaut, Andrew and Seeley, Janet and Ssemwanga, Deogratius and Tanser, Frank and Lutalo, Tom and Galiwango, Ronald and Makumbi, Fred and Sewankambo, Nelson K and Nabukalu, Dorean and Ndyanabo, Anthony and Ssekasanvu, Joseph and Nakawooya, Hadijja and Nakukumba, Jessica and Kigozi, Grace N and Nantume, Betty S and Resty, Nampijja and Kambasu, Jedidah and Nalugemwa, Margaret and Nakabuye, Regina and Ssebanobe, Lawrence and Nankinga, Justine and Kayiira, Adrian and Nanfuka, Gorreth and Ahimbisibwe, Ruth and Tomusange, Stephen and Galiwango, Ronald M and Nakalanzi, Margaret and Otobi, Joseph O and Ankunda, Denis and Ssembatya, Joseph L and Ssemanda, John B and Kato, Emmanuel and Kairania, Robert and Kisakye, Alice and Batte, James and Ludigo, James and Nampijja, Abisagi and Watya, Steven and Nehemia, Kighoma and Anyokot, Sr Margaret and Mwinike, Joshua and Kibumba, George and Ssebowa, Paschal and Mondo, George and Wasswa, Francis and Nantongo, Agnes and Kakembo, Rebecca and Galiwango, Josephine and Ssemango, Geoffrey and Redd, Andrew D and Santelli, John and Kennedy, Caitlin E and Wagman, Jennifer and Tobian, Aaron},
    pmid = {31953184},
    }
  • [DOI] A. L. Monjane, S. Dellicour, P. Hartnady, K. A. Oyeniran, B. E. Owor, M. Bezeidenhout, D. Linderme, R. A. Syed, L. Donaldson, S. Murray, E. P. Rybicki, A. Kvarnheden, E. Yazdkhasti, P. Lefeuvre, R. Froissart, P. Roumagnac, D. N. Shepherd, G. W. Harkins, M. A. Suchard, P. Lemey, A. Varsani, and D. P. Martin, “Symptom evolution following the emergence of maize streak virus.,” eLife, vol. 9, p. e51984, 2020.
    [Bibtex]
    @Article{Monjane:20,
    author = {Monjane, Adérito L and Dellicour, Simon and Hartnady, Penelope and Oyeniran, Kehinde A and Owor, Betty E and Bezeidenhout, Marion and Linderme, Daphne and Syed, Rizwan A and Donaldson, Lara and Murray, Shane and Rybicki, Edward P and Kvarnheden, Anders and Yazdkhasti, Elhman and Lefeuvre, Pierre and Froissart, Rémy and Roumagnac, Philippe and Shepherd, Dionne N and Harkins, Gordon W and Suchard, Marc A and Lemey, Philippe and Varsani, Arvind and Martin, Darren P},
    title = {Symptom evolution following the emergence of maize streak virus.},
    journal = {{eLife}},
    year = {2020},
    volume = {9},
    pages = {e51984},
    abstract = {For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed. This demonstrates an evolutionary trade-off between amounts of pathogen-inflicted harm and how effectively viruses position themselves within plants to enable onward transmission.},
    doi = {10.7554/eLife.51984},
    keywords = {evolutionary biology; maize; viruses},
    pmid = {31939738},
    }
  • [DOI] X. Wang, T. Hennig, A. W. Whisnant, F. Erhard, B. K. Prusty, C. C. Friedel, E. Forouzmand, W. Hu, L. Erber, Y. Chen, R. M. Sandri-Goldin, L. Dölken, and Y. Shi, “Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27.,” Nat Commun, vol. 11, p. 293, 2020.
    [Bibtex]
    @Article{Wang:20,
    author = {Wang, Xiuye and Hennig, Thomas and Whisnant, Adam W and Erhard, Florian and Prusty, Bhupesh K and Friedel, Caroline C and Forouzmand, Elmira and Hu, William and Erber, Luke and Chen, Yue and Sandri-Goldin, Rozanne M and Dölken, Lars and Shi, Yongsheng},
    title = {Herpes simplex virus blocks host transcription termination via the bimodal activities of {ICP27}.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {293},
    abstract = {Infection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes. However, the underlying mechanisms remain unclear. Here, we demonstrate that the HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essential mRNA 3' processing factor CPSF. It thereby induces the assembly of a dead-end 3' processing complex, blocking mRNA 3' cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3' processing for viral and a subset of host transcripts. Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced host shutoff and identify CPSF as an important factor that mediates regulation of transcription termination. These findings have broad implications for understanding the regulation of transcription termination by other viruses, cellular stress and cancer.},
    doi = {10.1038/s41467-019-14109-x},
    issue = {1},
    pmid = {31941886},
    }
  • [DOI] A. Mathieu, M. Dion, L. Deng, D. Tremblay, E. Moncaut, S. A. Shah, J. Stokholm, K. A. Krogfelt, S. Schjørring, H. Bisgaard, D. S. Nielsen, S. Moineau, and M. A. Petit, “Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.,” Nat Commun, vol. 11, p. 378, 2020.
    [Bibtex]
    @Article{Mathieu:20,
    author = {Mathieu, Aurélie and Dion, Moïra and Deng, Ling and Tremblay, Denise and Moncaut, Elisabeth and Shah, Shiraz A and Stokholm, Jakob and Krogfelt, Karen A and Schjørring, Susanne and Bisgaard, Hans and Nielsen, Dennis S and Moineau, Sylvain and Petit, Marie Agnès},
    title = {Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {378},
    abstract = {Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics.},
    doi = {10.1038/s41467-019-14042-z},
    issue = {1},
    pmid = {31953385},
    }
  • [DOI] E. Dugat-Bony, J. Lossouarn, M. De Paepe, A. Sarthou, Y. Fedala, M. A. Petit, and S. Chaillou, “Viral metagenomic analysis of the cheese surface: a comparative study of rapid procedures for extracting viral particles.,” Food Microbiol, vol. 85, p. 103278, 2020.
    [Bibtex]
    @Article{Dugat-Bony:20,
    author = {Dugat-Bony, Eric and Lossouarn, Julien and De Paepe, Marianne and Sarthou, Anne-Sophie and Fedala, Yasmina and Petit, Marie Agnès and Chaillou, Stéphane},
    title = {Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.},
    journal = {{Food Microbiol}},
    year = {2020},
    volume = {85},
    pages = {103278},
    abstract = {The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.},
    doi = {10.1016/j.fm.2019.103278},
    keywords = {Cheese rind; Viral metagenomic; Viral particles extraction procedure},
    pmid = {31500705},
    }

2019

  • [DOI] M. Perotti and L. Perez, “Virus-like particles and nanoparticles for vaccine development against HCMV,” Viruses, vol. 12, iss. 1, p. 35, 2019.
    [Bibtex]
    @Article{Perotti:19,
    author = {Michela Perotti and Laurent Perez},
    title = {Virus-Like Particles and Nanoparticles for Vaccine Development against {HCMV}},
    journal = {Viruses},
    year = {2019},
    volume = {12},
    number = {1},
    pages = {35},
    doi = {10.3390/v12010035},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. C. Wolthers, P. Susi, D. Jochmans, J. Koskinen, O. Landt, N. Sanchez, K. Palm, J. Neyts, and S. J. Butcher, “Progress in human picornavirus research: new findings from the AIROPico consortium,” Antiviral Res, vol. 161, p. 100–107, 2019.
    [Bibtex]
    @Article{Wolthers:19,
    author = {Katja C. Wolthers and Petri Susi and Dirk Jochmans and Janne Koskinen and Olfert Landt and Neus Sanchez and Kaia Palm and Johan Neyts and Sarah J. Butcher},
    title = {Progress in human picornavirus research: New findings from the {AIROPico} consortium},
    journal = {{Antiviral Res}},
    year = {2019},
    volume = {161},
    pages = {100--107},
    doi = {10.1016/j.antiviral.2018.11.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. A. de Jonge, F. L. Nobrega, S. J. J. Brouns, and B. E. Dutilh, “Molecular and evolutionary determinants of bacteriophage host range,” Trends Microbiol, vol. 27, iss. 1, p. 51–63, 2019.
    [Bibtex]
    @Article{Jonge:19,
    author = {Patrick A. de Jonge and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {1},
    pages = {51--63},
    doi = {10.1016/j.tim.2018.08.006},
    publisher = {Elsevier {BV}},
    }
  • D. Desirò, M. Hölzer, B. Ibrahim, and M. Marz, “SilentMutations (SIM): a tool for analyzing long-range RNA–RNA interactions in viral genomes and structured RNAs,” Virus Res, vol. 260, p. 135–141, 2019.
    [Bibtex]
    @Article{Desiro:19,
    author = {Desir{\`{o}}, Daniel and H{\"o}lzer, Martin and Ibrahim, Bashar and Marz, Manja},
    title = {{S}ilent{M}utations ({SIM}): A tool for analyzing long-range {RNA}--{RNA} interactions in viral genomes and structured {RNA}s},
    journal = {{Virus Res}},
    year = {2019},
    volume = {260},
    pages = {135--141},
    publisher = {Elsevier},
    }
  • [DOI] J. D. Wuerth and F. Weber, “Ferreting out viral pathogenesis,” Nat Microbiol, vol. 4, iss. 3, p. 384–385, 2019.
    [Bibtex]
    @Article{Wuerth:19,
    author = {Jennifer Deborah Wuerth and Friedemann Weber},
    title = {Ferreting out viral pathogenesis},
    journal = {{Nat Microbiol}},
    year = {2019},
    volume = {4},
    number = {3},
    pages = {384--385},
    doi = {10.1038/s41564-019-0390-0},
    publisher = {Springer Nature},
    }
  • [DOI] A. Sulovari and D. Li, “VIpower: simulation-based tool for estimating power of viral integration detection via high-throughput sequencing,” Genomics, 2019.
    [Bibtex]
    @Article{Sulovari:19,
    author = {Arvis Sulovari and Dawei Li},
    title = {{VIpower}: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing},
    journal = {Genomics},
    year = {2019},
    doi = {10.1016/j.ygeno.2019.01.015},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Dröge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, and A. C. McHardy, “CAMISIM: simulating metagenomes and microbial communities,” Microbiome, vol. 7, iss. 1, 2019.
    [Bibtex]
    @Article{Fritz:19,
    author = {Adrian Fritz and Peter Hofmann and Stephan Majda and Eik Dahms and Johannes Dröge and Jessika Fiedler and Till R. Lesker and Peter Belmann and Matthew Z. DeMaere and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {{CAMISIM}: simulating metagenomes and microbial communities},
    journal = {Microbiome},
    year = {2019},
    volume = {7},
    number = {1},
    doi = {10.1186/s40168-019-0633-6},
    publisher = {Springer Nature},
    }
  • [DOI] T. Kustin, G. Ling, S. Sharabi, D. Ram, N. Friedman, N. Zuckerman, E. D. Bucris, A. Glatman-Freedman, A. Stern, and M. Mandelboim, “A method to identify respiratory virus infections in clinical samples using next-generation sequencing,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kustin:19,
    author = {Talia Kustin and Guy Ling and Sivan Sharabi and Daniela Ram and Nehemya Friedman and Neta Zuckerman and Efrat Dahan Bucris and Aharona Glatman-Freedman and Adi Stern and Michal Mandelboim},
    title = {A method to identify respiratory virus infections in clinical samples using next-generation sequencing},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-37483-w},
    publisher = {Springer Nature},
    }
  • [DOI] S. Kouchaki, A. Tapinos, and D. L. Robertson, “A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kouchaki:19,
    author = {Samaneh Kouchaki and Avraam Tapinos and David L. Robertson},
    title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38197-9},
    publisher = {Springer Nature},
    }
  • [DOI] V. Ravindran, J. C. Nacher, T. Akutsu, M. Ishitsuka, A. Osadcenco, V. Sunitha, G. Bagler, J. Schwartz, and D. L. Robertson, “Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Ravindran:19,
    author = {Vandana Ravindran and Jose C. Nacher and Tatsuya Akutsu and Masayuki Ishitsuka and Adrian Osadcenco and V. Sunitha and Ganesh Bagler and Jean-Marc Schwartz and David L. Robertson},
    title = {Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38224-9},
    publisher = {Springer Nature},
    }
  • [DOI] M. Ahmad, V. Helms, O. V. Kalinina, and T. Lengauer, “Relative principal components analysis: application to analyzing biomolecular conformational changes,” J Chem Theory Comput, 2019.
    [Bibtex]
    @Article{Ahmad:19,
    author = {Mazen Ahmad and Volkhard Helms and Olga V. Kalinina and Thomas Lengauer},
    title = {Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes},
    journal = {{J Chem Theory Comput}},
    year = {2019},
    doi = {10.1021/acs.jctc.8b01074},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, D. G. Daffonchio, A. Danchin, V. de Lorenzo, P. C. Dorrestein, R. D. Finn, C. M. Fraser, J. A. Gilbert, S. J. Hallam, P. Hugenholtz, J. P. A. Ioannidis, J. K. Jansson, J. F. Kim, H. Klenk, M. G. Klotz, R. Knight, K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason, A. C. McHardy, F. Meyer, C. A. Ouzounis, A. A. N. Patrinos, M. Podar, K. S. Pollard, J. Ravel, A. R. Muñoz, R. J. Roberts, R. Rosselló-Móra, S. Sansone, P. D. Schloss, L. M. Schriml, J. C. Setubal, R. Sorek, R. L. Stevens, J. M. Tiedje, A. Turjanski, G. W. Tyson, D. W. Ussery, G. M. Weinstock, O. White, W. B. Whitman, and I. Xenarios, “Toward unrestricted use of public genomic data,” Science, vol. 363, iss. 6425, p. 350–352, 2019.
    [Bibtex]
    @Article{Amann:19,
    author = {Rudolf I. Amann and Shakuntala Baichoo and Benjamin J. Blencowe and Peer Bork and Mark Borodovsky and Cath Brooksbank and Patrick S. G. Chain and Rita R. Colwell and Daniele G. Daffonchio and Antoine Danchin and Victor de Lorenzo and Pieter C. Dorrestein and Robert D. Finn and Claire M. Fraser and Jack A. Gilbert and Steven J. Hallam and Philip Hugenholtz and John P. A. Ioannidis and Janet K. Jansson and Jihyun F. Kim and Hans-Peter Klenk and Martin G. Klotz and Rob Knight and Konstantinos T. Konstantinidis and Nikos C. Kyrpides and Christopher E. Mason and Alice C. McHardy and Folker Meyer and Christos A. Ouzounis and Aristides A. N. Patrinos and Mircea Podar and Katherine S. Pollard and Jacques Ravel and Alejandro Reyes Mu{\~{n}}oz and Richard J. Roberts and Ramon Rossell{\'{o}}-M{\'{o}}ra and Susanna-Assunta Sansone and Patrick D. Schloss and Lynn M. Schriml and Jo{\~{a}}o C. Setubal and Rotem Sorek and Rick L. Stevens and James M. Tiedje and Adrian Turjanski and Gene W. Tyson and David W. Ussery and George M. Weinstock and Owen White and William B. Whitman and Ioannis Xenarios},
    title = {Toward unrestricted use of public genomic data},
    journal = {Science},
    year = {2019},
    volume = {363},
    number = {6425},
    pages = {350--352},
    doi = {10.1126/science.aaw1280},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. Golumbeanu, S. Desfarges, C. Hernandez, M. Quadroni, S. Rato, P. Mohammadi, A. Telenti, N. Beerenwinkel, and A. Ciuffi, “Proteo-transcriptomic dynamics of cellular response to HIV-1 infection,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Golumbeanu:19,
    author = {Monica Golumbeanu and S{\'{e}}bastien Desfarges and C{\'{e}}line Hernandez and Manfredo Quadroni and Sylvie Rato and Pejman Mohammadi and Amalio Telenti and Niko Beerenwinkel and Angela Ciuffi},
    title = {Proteo-Transcriptomic Dynamics of Cellular Response to {HIV}-1 Infection},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-36135-3},
    publisher = {Springer Nature},
    }
  • [DOI] C. M. Zmasek, D. M. Knipe, P. E. Pellett, and R. H. Scheuermann, “Classification of human Herpesviridae proteins using domain-architecture aware inference of orthologs (DAIO),” Virology, vol. 529, p. 29–42, 2019.
    [Bibtex]
    @Article{Zmasek:19,
    author = {Christian M. Zmasek and David M. Knipe and Philip E. Pellett and Richard H. Scheuermann},
    title = {Classification of human {H}erpesviridae proteins using Domain-architecture Aware Inference of Orthologs ({DAIO})},
    journal = {Virology},
    year = {2019},
    volume = {529},
    pages = {29--42},
    doi = {10.1016/j.virol.2019.01.005},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. F. Cotmore, M. Agbandje-McKenna, M. Canuti, J. A. Chiorini, A. Eis-Hubinger, J. Hughes, M. Mietzsch, S. Modha, M. Ogliastro, J. J. Pénzes, D. J. Pintel, J. Qiu, M. Soderlund-Venermo, P. Tattersall, and P. T. and, “ICTV virus taxonomy profile: Parvoviridae,” J Gen Virol, vol. 100, iss. 3, p. 367–368, 2019.
    [Bibtex]
    @Article{Cotmore:19,
    author = {Susan F. Cotmore and Mavis Agbandje-McKenna and Marta Canuti and John A. Chiorini and Anna-Maria Eis-Hubinger and Joseph Hughes and Mario Mietzsch and Sejal Modha and Myl{\`{e}}ne Ogliastro and Judit J. P{\'{e}}nzes and David J. Pintel and Jianming Qiu and Maria Soderlund-Venermo and Peter Tattersall and Peter Tijssen and},
    title = {{ICTV} Virus Taxonomy Profile: {P}arvoviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    volume = {100},
    number = {3},
    pages = {367--368},
    doi = {10.1099/jgv.0.001212},
    publisher = {Microbiology Society},
    }
  • [DOI] S. G. Siddell, P. J. Walker, E. J. Lefkowitz, A. R. Mushegian, M. J. Adams, B. E. Dutilh, A. E. Gorbalenya, B. Harrach, R. L. Harrison, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, H. Sanfaçon, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, “Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018),” Arch Virol, vol. 164, iss. 3, p. 943–946, 2019.
    [Bibtex]
    @Article{Siddell:19,
    author = {Stuart G. Siddell and Peter J. Walker and Elliot J. Lefkowitz and Arcady R. Mushegian and Michael J. Adams and Bas E. Dutilh and Alexander E. Gorbalenya and Bal{\'{a}}zs Harrach and Robert L. Harrison and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and H{\'{e}}l{\`{e}}ne Sanfa{\c{c}}on and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Additional changes to taxonomy ratified in a special vote by the {International Committee on Taxonomy of Viruses} ({O}ctober 2018)},
    journal = {{Arch Virol}},
    year = {2019},
    volume = {164},
    number = {3},
    pages = {943--946},
    doi = {10.1007/s00705-018-04136-2},
    publisher = {Springer Nature},
    }
  • [DOI] U. Ashraf, C. Benoit-Pilven, V. Lacroix, V. Navratil, and N. Naffakh, “Advances in analyzing virus-induced alterations of host cell splicing,” Trends Microbiol, vol. 27, iss. 3, p. 268–281, 2019.
    [Bibtex]
    @Article{Ashraf:19,
    author = {Usama Ashraf and Clara Benoit-Pilven and Vincent Lacroix and Vincent Navratil and Nadia Naffakh},
    title = {Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {3},
    pages = {268--281},
    doi = {10.1016/j.tim.2018.11.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. M. Kinsella, M. Deijs, and L. van der Hoek, “Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery,” Virus Res, vol. 263, p. 21–26, 2019.
    [Bibtex]
    @Article{Kinsella:19,
    author = {Cormac M. Kinsella and Martin Deijs and Lia van der Hoek},
    title = {Enhanced bioinformatic profiling of {VIDISCA} libraries for virus detection and discovery},
    journal = {{Virus Res}},
    year = {2019},
    volume = {263},
    pages = {21--26},
    doi = {10.1016/j.virusres.2018.12.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Wernike and M. Beer, “Misinterpretation of Schmallenberg virus sequence variations: the sample material makes the difference,” Virus Genes, 2019.
    [Bibtex]
    @Article{Wernike:19,
    author = {Kerstin Wernike and Martin Beer},
    title = {Misinterpretation of {S}chmallenberg virus sequence variations: the sample material makes the difference},
    journal = {{Virus Genes}},
    year = {2019},
    doi = {10.1007/s11262-018-1628-2},
    publisher = {Springer Nature},
    }
  • [DOI] P. Hubel, C. Urban, V. Bergant, W. M. Schneider, B. Knauer, A. Stukalov, P. Scaturro, A. Mann, L. Brunotte, H. H. Hoffmann, J. W. Schoggins, M. Schwemmle, M. Mann, C. M. Rice, and A. Pichlmair, “A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape,” Nat Immunol, 2019.
    [Bibtex]
    @Article{Hubel:19,
    author = {Philipp Hubel and Christian Urban and Valter Bergant and William M. Schneider and Barbara Knauer and Alexey Stukalov and Pietro Scaturro and Angelika Mann and Linda Brunotte and Heinrich H. Hoffmann and John W. Schoggins and Martin Schwemmle and Matthias Mann and Charles M. Rice and Andreas Pichlmair},
    title = {A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape},
    journal = {{Nat Immunol}},
    year = {2019},
    doi = {10.1038/s41590-019-0323-3},
    publisher = {Springer Nature},
    }
  • [DOI] K. Brown, I. Olendraite, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, “ICTV virus taxonomy profile: Solinviviridae,” J Gen Virol, 2019.
    [Bibtex]
    @Article{Brown:19,
    author = {Katherine Brown and Ingrida Olendraite and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {S}olinviviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001242},
    publisher = {Microbiology Society},
    }
  • [DOI] I. Olendraite, K. Brown, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, “ICTV virus taxonomy profile: Polycipiviridae,” J Gen Virol, 2019.
    [Bibtex]
    @Article{Olendraite:19,
    author = {Ingrida Olendraite and Katherine Brown and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {P}olycipiviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001241},
    publisher = {Microbiology Society},
    }
  • [DOI] S. Hansen, S. Hotop, O. Faye, O. Ndiaye, S. Böhlken-Fascher, R. Pessôa, F. Hufert, C. Stahl-Hennig, R. Frank, C. Czerny, J. Schmidt-Chanasit, S. S. Sanabani, A. A. Sall, M. Niedrig, M. Brönstrup, H. Fritz, and A. A. E. Wahed, “Diagnosing Zika virus infection against a background of other flaviviruses: studies in high resolution serological analysis,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Hansen:19,
    author = {Sören Hansen and Sven-Kevin Hotop and Oumar Faye and Oumar Ndiaye and Susanne B\"{o}hlken-Fascher and Rodrigo Pess{\^{o}}a and Frank Hufert and Christiane Stahl-Hennig and Ronald Frank and Claus-Peter Czerny and Jonas Schmidt-Chanasit and Sabri S. Sanabani and Amadou A. Sall and Matthias Niedrig and Mark Br\"{o}nstrup and Hans-Joachim Fritz and Ahmed Abd El Wahed},
    title = {Diagnosing {Z}ika virus infection against a background of other flaviviruses: Studies in high resolution serological analysis},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-40224-2},
    publisher = {Springer Nature},
    }
  • [DOI] M. Thijssen, P. Lemey, S. Amini-Bavil-Olyaee, S. Dellicour, S. M. Alavian, F. Tacke, C. Verslype, F. Nevens, and M. R. Pourkarim, “Mass migration to Europe: an opportunity for elimination of hepatitis B virus?,” Lancet Gastroenterol Hepatol, vol. 4, p. 315–323, 2019.
    [Bibtex]
    @Article{Thijssen:19,
    author = {Thijssen, Marijn and Lemey, Philippe and Amini-Bavil-Olyaee, Samad and Dellicour, Simon and Alavian, Seyed Moayed and Tacke, Frank and Verslype, Chris and Nevens, Frederik and Pourkarim, Mahmoud Reza},
    title = {Mass migration to {E}urope: an opportunity for elimination of hepatitis {B} virus?},
    journal = {{Lancet Gastroenterol Hepatol}},
    year = {2019},
    volume = {4},
    pages = {315--323},
    abstract = {People from low-to-middle income countries have been migrating to western Europe on a large scale in recent years. Data indicate that the number of first-time asylum applications by non-EU members increased from 290 000 in 2011 to more than 1·3 million in 2015. During the peak period of migration, The Global Health Sector Strategy on Viral Hepatitis was adopted by WHO. Viral hepatitis, and particularly hepatitis B virus (HBV), is an important disease because of its high prevalence and associated mortality. In some cases, HBV can be carried by refugees arriving from regions of high and intermediate prevalence. Refugees with HBV might not show clinical symptoms and not be diagnosed in destination countries with a low prevalence, where screening is not regularly done. Although transmission to the host population is low, dedicated surveillance and tailored public health policies are required. It is important to note that some of the countries that receive many migrants do not have a universal HBV vaccination programme. In this Viewpoint, we argue that the current large-scale movement from regions with high or intermediate HBV prevalence should be taken as an opportunity to achieve viral hepatitis elimination targets, by establishing a well prepared infrastructure for HBV screening, vaccination, and treatment.},
    doi = {10.1016/S2468-1253(19)30014-7},
    issue = {4},
    pmid = {30860067},
    }
  • [DOI] A. Jariani, C. Warth, K. Deforche, P. Libin, A. J. Drummond, A. Rambaut, F. A. Matsen IV, and K. Theys, “SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination,” Virus Evol, vol. 5, iss. 1, 2019.
    [Bibtex]
    @Article{Jariani:19,
    author = {Abbas Jariani and Christopher Warth and Koen Deforche and Pieter Libin and Alexei J Drummond and Andrew Rambaut and Frederick A {Matsen IV} and Kristof Theys},
    title = {{SANTA}-{SIM}: simulating viral sequence evolution dynamics under selection and recombination},
    journal = {{Virus Evol}},
    year = {2019},
    volume = {5},
    number = {1},
    doi = {10.1093/ve/vez003},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] X. Chen and D. Li, “ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data,” Bioinformatics, 2019.
    [Bibtex]
    @Article{Chen:19,
    author = {Xun Chen and Dawei Li},
    title = {{ERVcaller}: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data},
    journal = {Bioinformatics},
    year = {2019},
    doi = {10.1093/bioinformatics/btz205},
    editor = {Inanc Birol},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Altan-Bonnet, C. Perales, and E. Domingo, “Extracellular vesicles: vehicles of en bloc viral transmission.,” Virus Res, 2019.
    [Bibtex]
    @Article{Altan-Bonnet:19,
    author = {Altan-Bonnet, Nihal and Perales, Celia and Domingo, Esteban},
    title = {Extracellular vesicles: vehicles of en bloc viral transmission.},
    journal = {{Virus Res}},
    year = {2019},
    abstract = {En Bloc transmission of viruses allow multiple genomes to collectivelly penetrate and initiate infection in the same cell, often resulting in enhanced infectivity. Given the quasispecies (mutant cloud) nature of RNA viruses and many DNA viruses, the multiple genomes provide different starting points in sequence space to initiate adaptive walks. Moreover, en bloc transmission has implications for modulation of viral fitness and for the response of viral populations to lethal mutagenesis. Mechanisms that can enable multiple viral genomes to be transported en bloc among hosts has only recently been gaining attention. A growing body of research suggests that extracellular vesicles (EV) are highly prevalent and robust vehicles for en bloc delivery of viral particles and naked infectious genomes among organisms. Both RNA and DNA viruses exploit these vesicles to increase multiplicity of infection and enhance virulence.},
    doi = {10.1016/j.virusres.2019.03.023},
    pmid = {30928427},
    }
  • [DOI] O. Ratmann, K. M. and Grabowski, M. Hall, T. Golubchik, C. Wymant, L. Abeler-Dörner, D. Bonsall, A. Hoppe, A. L. Brown, T. de Oliveira, A. Gall, P. Kellam, D. Pillay, J. Kagaayi, G. Kigozi, T. C. Quinn, M. J. Wawer, O. Laeyendecker, D. Serwadda, R. H. Gray, and C. Fraser, “Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis,” Nat Commun, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Ratmann:19,
    author = {Oliver Ratmann and and M. Kate Grabowski and Matthew Hall and Tanya Golubchik and Chris Wymant and Lucie Abeler-Dörner and David Bonsall and Anne Hoppe and Andrew Leigh Brown and Tulio de Oliveira and Astrid Gall and Paul Kellam and Deenan Pillay and Joseph Kagaayi and Godfrey Kigozi and Thomas C. Quinn and Maria J. Wawer and Oliver Laeyendecker and David Serwadda and Ronald H. Gray and Christophe Fraser},
    title = {Inferring {HIV}-1 transmission networks and sources of epidemic spread in {A}frica with deep-sequence phylogenetic analysis},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1038/s41467-019-09139-4},
    publisher = {Springer Nature},
    }
  • [DOI] H. F. Löchel, D. Eger, T. Sperlea, and D. Heider, “Deep learning on chaos game representation for proteins,” bioRxiv, p. 575324, 2019.
    [Bibtex]
    @Article{Löchel:19,
    author = {Hannah F. Löchel and Dominic Eger and Theodor Sperlea and Dominik Heider},
    title = {Deep Learning on Chaos Game Representation for Proteins},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {575324},
    doi = {10.1101/575324},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. de Borba, S. M. Villordo, F. L. Marsico, J. M. Carballeda, C. V. Filomatori, L. G. Gebhard, H. M. Pallarés, S. Lequime, L. Lambrechts, I. S. Vargas, C. D. Blair, and A. V. Gamarnik, “RNA structure duplication in the dengue virus 3′ UTR: redundancy or host specificity?,” mBio, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Borba:19,
    author = {Luana de Borba and Sergio M. Villordo and Franco L. Marsico and Juan M. Carballeda and Claudia V. Filomatori and Leopoldo G. Gebhard and Horacio M. Pallar{\'{e}}s and Sebastian Lequime and Louis Lambrechts and Irma S{\'{a}}nchez Vargas and Carol D. Blair and Andrea V. Gamarnik},
    title = {{RNA} Structure Duplication in the Dengue Virus 3' {UTR}: Redundancy or Host Specificity?},
    journal = {{mBio}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1128/mbio.02506-18},
    editor = {Carolyn B. Coyne},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. D. Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C. Wu, D. Xie, C. Zhang, T. Stadler, and A. J. Drummond, “BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis,” PLOS Comput Biol, vol. 15, iss. 4, p. e1006650, 2019.
    [Bibtex]
    @Article{Bouckaert:19,
    author = {Remco Bouckaert and Timothy G. Vaughan and Joëlle Barido-Sottani and Sebasti{\'{a}}n Duch{\^{e}}ne and Mathieu Fourment and Alexandra Gavryushkina and Joseph Heled and Graham Jones and Denise Kühnert and Nicola De Maio and Michael Matschiner and F{\'{a}}bio K. Mendes and Nicola F. Müller and Huw A. Ogilvie and Louis du Plessis and Alex Popinga and Andrew Rambaut and David Rasmussen and Igor Siveroni and Marc A. Suchard and Chieh-Hsi Wu and Dong Xie and Chi Zhang and Tanja Stadler and Alexei J. Drummond},
    title = {{BEAST} 2.5: An advanced software platform for {B}ayesian evolutionary analysis},
    journal = {{PLOS Comput Biol}},
    year = {2019},
    volume = {15},
    number = {4},
    pages = {e1006650},
    doi = {10.1371/journal.pcbi.1006650},
    editor = {Mihaela Pertea},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] E. Domingo, A. I. de Ávila, I. Gallego, J. Sheldon, and C. Perales, “Viral fitness: history and relevance for viral pathogenesis and antiviral interventions,” Pathog Dis, 2019.
    [Bibtex]
    @Article{Domingo:19,
    author = {Esteban Domingo and Ana I de {\'{A}}vila and Isabel Gallego and Julie Sheldon and Celia Perales},
    title = {Viral fitness: history and relevance for viral pathogenesis and antiviral interventions},
    journal = {{Pathog Dis}},
    year = {2019},
    doi = {10.1093/femspd/ftz021},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. V. Membrebe, M. A. Suchard, A. Rambaut, G. Baele, and P. Lemey, “Bayesian inference of evolutionary histories under time-dependent substitution rates,” Mol Biol Evol, 2019.
    [Bibtex]
    @Article{Membrebe:19,
    author = {Jade Vincent Membrebe and Marc A Suchard and Andrew Rambaut and Guy Baele and Philippe Lemey},
    title = {Bayesian inference of evolutionary histories under time-dependent substitution rates},
    journal = {{Mol Biol Evol}},
    year = {2019},
    doi = {10.1093/molbev/msz094},
    editor = {Jeffrey Thorne},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Singer, E. Thomson, J. Hughes, E. Aranday-Cortes, J. McLauchlan, A. S. da Filipe, L. Tong, C. Manso, R. J. Gifford, D. L. Robertson, E. Barnes, M. Ansari, J. Mbisa, D. Bibby, D. Bradshaw, and D. Smith, “Interpreting viral deep sequencing data with GLUE,” Viruses, vol. 11, iss. 4, p. 323, 2019.
    [Bibtex]
    @Article{Singer:19,
    author = {Joshua Singer and Emma Thomson and Joseph Hughes and Elihu Aranday-Cortes and John McLauchlan and Ana da Silva Filipe and Lily Tong and Carmen Manso and Robert J. Gifford and David L. Robertson and Eleanor Barnes and M. Ansari and Jean Mbisa and David Bibby and Daniel Bradshaw and David Smith},
    title = {Interpreting Viral Deep Sequencing Data with {GLUE}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {4},
    pages = {323},
    doi = {10.3390/v11040323},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Nachtweide and M. Stanke, “Multi-genome annotation with AUGUSTUS,” in Methods Mol Biol, Springer new york, 2019, p. 139–160.
    [Bibtex]
    @InCollection{Nachtweide:19,
    author = {Stefanie Nachtweide and Mario Stanke},
    title = {Multi-Genome Annotation with {AUGUSTUS}},
    booktitle = {{Methods Mol Biol}},
    publisher = {Springer New York},
    year = {2019},
    pages = {139--160},
    doi = {10.1007/978-1-4939-9173-0_8},
    }
  • [DOI] A. B. de Schneider and M. T. Wolfinger, “Musashi binding elements in Zika and related Flavivirus 3’UTRs: a comparative study in silico,” Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{BernardiSchneider:19,
    author = {Adriano de Bernardi Schneider and Michael T. Wolfinger},
    title = {Musashi binding elements in {Z}ika and related {F}lavivirus 3'{UTRs}: A comparative study in silico},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-43390-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Hufsky, B. Ibrahim, S. Modha, M. R. J. Clokie, S. Deinhardt-Emmer, B. E. Dutilh, S. Lycett, P. Simmonds, V. Thiel, A. Abroi, E. M. Adriaenssens, M. Escalera-Zamudio, J. N. Kelly, K. Lamkiewicz, L. Lu, J. Susat, T. Sicheritz, D. L. Robertson, and M. Marz, “The third annual meeting of the European Virus Bioinformatics Center,” Viruses, vol. 11, iss. 5, p. 420, 2019.
    [Bibtex]
    @Article{Hufsky:19,
    author = {Franziska Hufsky and Bashar Ibrahim and Sejal Modha and Martha R. J. Clokie and Stefanie Deinhardt-Emmer and Bas E. Dutilh and Samantha Lycett and Peter Simmonds and Volker Thiel and Aare Abroi and Evelien M. Adriaenssens and Marina Escalera-Zamudio and Jenna Nicole Kelly and Kevin Lamkiewicz and Lu Lu and Julian Susat and Thomas Sicheritz and David L. Robertson and Manja Marz},
    title = {The Third Annual Meeting of the {E}uropean {V}irus {B}ioinformatics {C}enter},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {420},
    doi = {10.3390/v11050420},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Peter, M. Hölzer, K. Lamkiewicz, P. S. di Fenizio, H. A. Hwaeer, M. Marz, S. Schuster, P. Dittrich, and B. Ibrahim, “Structure and hierarchy of influenza virus models revealed by reaction network analysis,” Viruses, vol. 11, iss. 5, p. 449, 2019.
    [Bibtex]
    @Article{Peter:19,
    author = {Stephan Peter and Martin Hölzer and Kevin Lamkiewicz and Pietro Speroni di Fenizio and Hassan Al Hwaeer and Manja Marz and Stefan Schuster and Peter Dittrich and Bashar Ibrahim},
    title = {Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {449},
    doi = {10.3390/v11050449},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Kiening, R. Ochsenreiter, H. Hellinger, T. Rattei, I. L. Hofacker, and D. Frishman, “Conserved secondary structures in viral mRNAs,” Viruses, vol. 11, iss. 5, p. 401, 2019.
    [Bibtex]
    @Article{Kiening:19,
    author = {Michael Kiening and Roman Ochsenreiter and Hans-Jörg Hellinger and Thomas Rattei and Ivo L. Hofacker and Dmitrij Frishman},
    title = {Conserved Secondary Structures in Viral {mRNAs}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {401},
    doi = {10.3390/v11050401},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. C. Gregory, A. A. Zayed, N. Conceição-Neto, B. Temperton, B. Bolduc, A. Alberti, M. Ardyna, K. Arkhipova, M. Carmichael, C. Cruaud, C. Dimier, G. Domínguez-Huerta, J. Ferland, S. Kandels, Y. Liu, C. Marec, S. Pesant, M. Picheral, S. Pisarev, J. Poulain, J. Tremblay, D. Vik, M. Babin, C. Bowler, A. I. Culley, C. de Vargas, B. E. Dutilh, D. Iudicone, L. Karp-Boss, S. Roux, S. Sunagawa, P. Wincker, M. B. Sullivan, S. G. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, M. Follows, G. Gorsky, N. Grimsley, L. Guidi, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels-Lewis, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, S. Pesant, N. Poulton, J. Raes, C. Sardet, S. Speich, L. Stemmann, M. B. Sullivan, S. Sunagawa, and P. Wincker, “Marine DNA viral macro- and microdiversity from pole to pole,” Cell, vol. 177, iss. 5, p. 1109–1123.e14, 2019.
    [Bibtex]
    @Article{Gregory:19,
    author = {Ann C. Gregory and Ahmed A. Zayed and N{\'{a}}dia Concei{\c{c}}{\~{a}}o-Neto and Ben Temperton and Ben Bolduc and Adriana Alberti and Mathieu Ardyna and Ksenia Arkhipova and Margaux Carmichael and Corinne Cruaud and C{\'{e}}line Dimier and Guillermo Dom{\'{\i}}nguez-Huerta and Joannie Ferland and Stefanie Kandels and Yunxiao Liu and Claudie Marec and St{\'{e}}phane Pesant and Marc Picheral and Sergey Pisarev and Julie Poulain and Jean-{\'{E}}ric Tremblay and Dean Vik and Marcel Babin and Chris Bowler and Alexander I. Culley and Colomban de Vargas and Bas E. Dutilh and Daniele Iudicone and Lee Karp-Boss and Simon Roux and Shinichi Sunagawa and Patrick Wincker and Matthew B. Sullivan and Silvia G. Acinas and Marcel Babin and Peer Bork and Emmanuel Boss and Chris Bowler and Guy Cochrane and Colomban de Vargas and Michael Follows and Gabriel Gorsky and Nigel Grimsley and Lionel Guidi and Pascal Hingamp and Daniele Iudicone and Olivier Jaillon and Stefanie Kandels-Lewis and Lee Karp-Boss and Eric Karsenti and Fabrice Not and Hiroyuki Ogata and St{\'{e}}phane Pesant and Nicole Poulton and Jeroen Raes and Christian Sardet and Sabrina Speich and Lars Stemmann and Matthew B. Sullivan and Shinichi Sunagawa and Patrick Wincker},
    title = {Marine {DNA} Viral Macro- and Microdiversity from Pole to Pole},
    journal = {Cell},
    year = {2019},
    volume = {177},
    number = {5},
    pages = {1109--1123.e14},
    doi = {10.1016/j.cell.2019.03.040},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Tapinos, B. Constantinides, M. V. T. Phan, S. Kouchaki, M. Cotten, and D. L. Robertson, “The utility of data transformation for alignment, de novo assembly and classification of short read virus sequences,” Viruses, vol. 11, iss. 5, p. 394, 2019.
    [Bibtex]
    @Article{Tapinos:19a,
    author = {Avraam Tapinos and Bede Constantinides and My V. T. Phan and Samaneh Kouchaki and Matthew Cotten and David L. Robertson},
    title = {The Utility of Data Transformation for Alignment, de novo Assembly and Classification of Short Read Virus Sequences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {394},
    doi = {10.3390/v11050394},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Zhao, C. Dewald, M. Hennig, J. Bossert, M. Bauer, M. W. Pletz, and K. D. Jandt, “Microorganisms at materials surfaces in aircraft: potential risks for public health? – A systematic review,” Travel Med Infect Dis, vol. 28, p. 6–14, 2019.
    [Bibtex]
    @Article{Zhao:19,
    author = {Bin Zhao and Carolin Dewald and Max Hennig and Jörg Bossert and Michael Bauer and Mathias W. Pletz and Klaus D. Jandt},
    title = {Microorganisms at materials surfaces in aircraft: Potential risks for public health? - {A} systematic review},
    journal = {{Travel Med Infect Dis}},
    year = {2019},
    volume = {28},
    pages = {6--14},
    doi = {10.1016/j.tmaid.2018.07.011},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. Fonseca, P. J. K. Libin, K. Theys, N. R. Faria, M. R. T. Nunes, M. I. Restovic, M. Freire, M. Giovanetti, L. Cuypers, A. Nowé, A. B. Abecasis, K. Deforche, G. A. Santiago, I. C. de Siqueira, E. J. San, K. C. B. Machado, V. Azevedo, A. M. B. Filippis, R. V. da Cunha, O. G. Pybus, A. Vandamme, L. C. J. Alcantara, and T. de Oliveira, “A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes,” PLoS Negl Trop Dis, vol. 13, iss. 5, p. e0007231, 2019.
    [Bibtex]
    @Article{Fonseca:19,
    author = {Vagner Fonseca and Pieter J. K. Libin and Kristof Theys and Nuno R. Faria and Marcio R. T. Nunes and Maria I. Restovic and Murilo Freire and Marta Giovanetti and Lize Cuypers and Ann Now{\'{e}} and Ana B. Abecasis and Koen Deforche and Gilberto A. Santiago and Isadora C. de Siqueira and Emmanuel J. San and Kaliane C. B. Machado and Vasco Azevedo and Ana Maria Bispo-de Filippis and Rivaldo Ven{\^{a}}ncio da Cunha and Oliver G. Pybus and Anne-Mieke Vandamme and Luiz C. J. Alcantara and Tulio de Oliveira},
    title = {A computational method for the identification of {D}engue, {Z}ika and {C}hikungunya virus species and genotypes},
    journal = {{PLoS Negl Trop Dis}},
    year = {2019},
    volume = {13},
    number = {5},
    pages = {e0007231},
    doi = {10.1371/journal.pntd.0007231},
    editor = {Isabel Rodriguez-Barraquer},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. Hölzer and M. Marz, “De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-seq assemblers,” GigaScience, vol. 8, iss. 5, 2019.
    [Bibtex]
    @Article{Hölzer:19,
    author = {Martin Hölzer and Manja Marz},
    title = {{D}e novo transcriptome assembly: A comprehensive cross-species comparison of short-read {RNA}-Seq assemblers},
    journal = {{GigaScience}},
    year = {2019},
    volume = {8},
    number = {5},
    doi = {10.1093/gigascience/giz039},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Schuster, P. Miesen, and R. P. van Rij, “Antiviral RNAi in insects and mammals: parallels and differences,” Viruses, vol. 11, iss. 5, p. 448, 2019.
    [Bibtex]
    @Article{Schuster:19,
    author = {Susan Schuster and Pascal Miesen and Ronald P. van Rij},
    title = {Antiviral {RNAi} in Insects and Mammals: Parallels and Differences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {448},
    doi = {10.3390/v11050448},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Pfaff, S. Hägglund, M. Zoli, S. Blaise-Boisseau, E. Laloy, S. Koethe, D. Zühlke, K. Riedel, S. Zientara, L. Bakkali-Kassimi, J. Valarcher, D. Höper, M. Beer, and M. Eschbaumer, “Proteogenomics uncovers critical elements of host response in bovine soft palate epithelial cells following in vitro infection with foot-and-mouth disease virus,” Viruses, vol. 11, iss. 1, p. 53, 2019.
    [Bibtex]
    @Article{Pfaff:19,
    author = {Florian Pfaff and Sara Hägglund and Martina Zoli and Sandra Blaise-Boisseau and Eve Laloy and Susanne Koethe and Daniela Zühlke and Katharina Riedel and Stephan Zientara and Labib Bakkali-Kassimi and Jean-Fran{\c{c}}ois Valarcher and Dirk Höper and Martin Beer and Michael Eschbaumer},
    title = {Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {1},
    pages = {53},
    doi = {10.3390/v11010053},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Röder, N. Kersten, M. Herr, N. K. Speicher, and N. Pfeifer, “Web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning,” Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Röder:19,
    author = {Benedict Röder and Nicolas Kersten and Marius Herr and Nora K Speicher and Nico Pfeifer},
    title = {web-{rMKL}: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    doi = {10.1093/nar/gkz422},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. Theys, P. J. K. Libin, K. V. Laethem, and A. B. Abecasis, “An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors.,” Antimicrob Agents Chemother, 2019.
    [Bibtex]
    @Article{Theys:19,
    author = {Kristof Theys and Pieter J. K. Libin and Kristel Van Laethem and Ana B Abecasis},
    title = {An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to {HIV}-1 subtypes and integrase inhibitors.},
    journal = {{Antimicrob Agents Chemother}},
    year = {2019},
    doi = {10.1128/aac.00539-19},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Kallies, M. Hölzer, R. Brizola Toscan, U. Nunes da Rocha, J. Anders, M. Marz, and A. Chatzinotas, “Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters.,” Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kallies:19,
    author = {Kallies, René and Hölzer, Martin and Brizola Toscan, Rodolfo and Nunes da Rocha, Ulisses and Anders, John and Marz, Manja and Chatzinotas, Antonis},
    title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the order were the most abundant group (52.20 to 69.12%) dominated by and . Those, and the high number of unknown viral sequences, substantially expand the known virosphere.},
    doi = {10.3390/v11060484},
    issue = {6},
    keywords = {AquaDiva; aquifer; groundwater; sequencing library preparation; viral metagenome},
    pmid = {31141902},
    }
  • [DOI] A. Dukhovny, K. Lamkiewicz, Q. Chen, M. Fricke, N. Jabrane-Ferrat, M. Marz, J. U. Jung, and E. H. Sklan, “A CRISPR activation screen identifies genes protecting from Zika virus infection,” J Virol, 2019.
    [Bibtex]
    @Article{Dukhovny:19,
    author = {Dukhovny, Anna and Lamkiewicz, Kevin and Chen, Qian and Fricke, Markus and Jabrane-Ferrat, Nabila and Marz, Manja and Jung, Jae U. and Sklan, Ella H.},
    title = {A {CRISPR} activation screen identifies genes protecting from {Z}ika virus infection},
    journal = {{J Virol}},
    year = {2019},
    abstract = {Zika virus (ZIKV) is an arthropod borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barr{\'e} syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection we used a genome scale CRISPR activation screen. Our highly ranking hits included a short list of interferon stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted IFNL2 and IFI6 as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing sgRNAs for both of these genes displayed lower levels of cell death compared to controls. Furthermore, the identified genes were significantly induced in ZIKV infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiates CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barr{\'e} syndrome, neuropathy and myelitis. Vertical transmission of ZIKV can cause fetus demise, still birth or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.},
    doi = {10.1128/JVI.00211-19},
    elocation-id = {JVI.00211-19},
    eprint = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19.full.pdf},
    publisher = {American Society for Microbiology Journals},
    url = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19},
    }
  • [DOI] S. Jansen, A. Heitmann, R. Lühken, M. Leggewie, M. Helms, M. Badusche, G. Rossini, J. Schmidt-Chanasit, and E. Tannich, “Culex torrentium: a potent vector for the transmission of West Nile Virus in central europe,” Viruses, vol. 11, iss. 6, p. 492, 2019.
    [Bibtex]
    @Article{Jansen:19,
    author = {Stephanie Jansen and Anna Heitmann and Renke Lühken and Mayke Leggewie and Michelle Helms and Marlis Badusche and Giada Rossini and Jonas Schmidt-Chanasit and Egbert Tannich},
    title = {{C}ulex torrentium: A Potent Vector for the Transmission of {W}est {N}ile {V}irus in Central Europe},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {6},
    pages = {492},
    doi = {10.3390/v11060492},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. A. Carlisle, T. Turk, K. Kusejko, K. J. Metzner, C. Leemann, C. Schenkel, N. Bachmann, S. Posada, N. Beerenwinkel, J. Böni, S. Yerly, T. Klimkait, M. Perreau, D. L. Braun, A. Rauch, A. Calmy, M. Cavassini, M. Battegay, P. Vernazza, E. Bernasconi, H. F. Günthard, R. D. Kouyos, and Swiss HIV Cohort Study, “Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection.,” J Infect Dis, 2019.
    [Bibtex]
    @Article{Carlisle:19,
    author = {Carlisle, Louisa A and Turk, Teja and Kusejko, Katharina and Metzner, Karin J and Leemann, Christine and Schenkel, Corinne and Bachmann, Nadine and Posada, Susana and Beerenwinkel, Niko and Böni, Jürg and Yerly, Sabine and Klimkait, Thomas and Perreau, Matthieu and Braun, Dominique L and Rauch, Andri and Calmy, Alexandra and Cavassini, Matthias and Battegay, Manuel and Vernazza, Pietro and Bernasconi, Enos and Günthard, Huldrych F and Kouyos, Roger D and {Swiss HIV Cohort Study}},
    title = {Viral diversity from next-generation sequencing of {HIV}-1 samples provides precise estimates of infection recency and time since infection.},
    journal = {{J Infect Dis}},
    year = {2019},
    abstract = {HIV-1 genetic diversity increases over the course of infection, and can be used to infer time since infection (TSI) and consequently also infection recency, crucial quantities for HIV-1 surveillance and the understanding of viral pathogenesis. We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fraction of ambiguous nucleotides (FAN) obtained by population sequencing were available for 207 samples. We assessed whether average pairwise diversity (APD) calculated using NGS sequences provided a more exact prediction of TSI and classification of infection recency (<1 year post-infection) compared to FAN. NGS-derived APD classifies an infection as recent with a sensitivity of 88% and specificity of 85%. When considering only the 207 samples for which FAN were available, NGS-derived APD exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than FAN. Additionally, APD can estimate TSI with a mean absolute error of 0.84 years, compared to 1.03 years for FAN.},
    doi = {10.1093/infdis/jiz094},
    keywords = {HIV-1; diversity; infection recency; next-generation sequencing; time since infection},
    pmid = {30835266},
    }
  • [DOI] V. Kinast, T. L. Burkard, D. Todt, and E. Steinmann, "Hepatitis E virus drug development.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kinast:19,
    author = {Kinast, Volker and Burkard, Thomas L and Todt, Daniel and Steinmann, Eike},
    title = {Hepatitis {E} Virus Drug Development.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV.},
    doi = {10.3390/v11060485},
    issue = {6},
    keywords = {antivirals; drug development; hepatitis E virus; ribavirin; sofosbuvir; therapy; vaccine},
    pmid = {31141919},
    }
  • [DOI] A. Brinkmann, A. Andrusch, A. Belka, C. Wylezich, D. Höper, A. Pohlmann, T. N. Petersen, P. Lucas, Y. Blanchard, A. Papa, A. Melidou, B. B. Oude Munnink, J. Matthijnssens, W. Deboutte, R. J. Ellis, F. Hansmann, W. Baumgärtner, E. van der Vries, A. Osterhaus, C. Camma, I. Mangone, A. Lorusso, M. Maracci, A. Nunes, M. Pinto, V. Borges, A. Kroneman, D. Schmitz, V. M. Corman, C. Drosten, T. C. Jones, R. S. Hendriksen, F. M. Aarestrup, M. Koopmans, M. Beer, and A. Nitsche, "Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.," J Clin Microbiol, 2019.
    [Bibtex]
    @Article{Brinkmann:19,
    author = {Brinkmann, Annika and Andrusch, Andreas and Belka, Ariane and Wylezich, Claudia and Höper, Dirk and Pohlmann, Anne and Petersen, Thomas Nordahl and Lucas, Pierrick and Blanchard, Yannick and Papa, Anna and Melidou, Angeliki and Oude Munnink, Bas B and Matthijnssens, Jelle and Deboutte, Ward and Ellis, Richard J and Hansmann, Florian and Baumgärtner, Wolfgang and van der Vries, Erhard and Osterhaus, Albert and Camma, Cesare and Mangone, Iolanda and Lorusso, Alessio and Maracci, Maurilia and Nunes, Alexandra and Pinto, Miguel and Borges, Vítor and Kroneman, Annelies and Schmitz, Dennis and Corman, Victor Max and Drosten, Christian and Jones, Terry C and Hendriksen, Rene S and Aarestrup, Frank M and Koopmans, Marion and Beer, Martin and Nitsche, Andreas},
    title = {Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.},
    journal = {{J Clin Microbiol}},
    year = {2019},
    abstract = {Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. Sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing, using publicly available and custom tools and databases, and differ widely between individuals and institutions.Here, we present the results of the COMPARE (COllaborative Management Platform for detection and Analyses of [Re-] emerging and foodborne outbreaks in Europe) virus proficiency test. An artificial, simulated dataset of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis towards the identification of viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple dataset. The identification of slightly mutated and highly divergent virus genomes has been identified as being most challenging: Furthermore, the interpretation of the results together with a fictitious case report by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings.External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve harmonization, comparability, and reproducibility of results. Similar to what is established for conventional laboratory tests like PCR, there is a need for the establishment of international proficiency testing for bioinformatics pipelines and interpretation of such results.},
    doi = {10.1128/JCM.00466-19},
    pmid = {31167846},
    }
  • [DOI] P. J. Walker, S. G. Siddell, E. J. Lefkowitz, A. R. Mushegian, D. M. Dempsey, B. E. Dutilh, B. Harrach, R. L. Harrison, C. R. Hendrickson, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, "Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)," Arch Virol, 2019.
    [Bibtex]
    @Article{Walker:19,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the {I}nternational {C}ode of {V}irus {C}lassification and {N}omenclature ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2019)},
    journal = {{Arch Virol}},
    year = {2019},
    doi = {10.1007/s00705-019-04306-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. Lechner, F. Hartkopf, P. Hiort, A. Nitsche, M. Grossegesse, J. Doellinger, B. Y. Renard, and T. Muth, "Purple: a computational workflow for strategic selection of peptides for viral diagnostics using MS-based targeted proteomics.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Lechner:19,
    author = {Lechner, Johanna and Hartkopf, Felix and Hiort, Pauline and Nitsche, Andreas and Grossegesse, Marica and Doellinger, Joerg and Renard, Bernhard Y and Muth, Thilo},
    title = {Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using {MS}-Based Targeted Proteomics.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are required. Such assays can now be established using mass spectrometry-based targeted proteomics, by which viral proteins can be rapidly detected from complex samples down to the strain-level with high sensitivity and reproducibility. Developing such targeted assays involves tedious steps of peptide candidate selection, peptide synthesis, and assay optimization. Peptide selection requires extensive preprocessing by comparing candidate peptides against a large search space of background proteins. Here we present Purple (Picking unique relevant peptides for viral experiments), a software tool for selecting target-specific peptide candidates directly from given proteome sequence data. It comes with an intuitive graphical user interface, various parameter options and a threshold-based filtering strategy for homologous sequences. Purple enables peptide candidate selection across various taxonomic levels and filtering against backgrounds of varying complexity. Its functionality is demonstrated using data from different virus species and strains. Our software enables to build taxon-specific targeted assays and paves the way to time-efficient and robust viral diagnostics using targeted proteomics.},
    doi = {10.3390/v11060536},
    issue = {6},
    keywords = {data analysis; mass spectrometry; parallel reaction monitoring; peptide selection; targeted proteomics; virus diagnostics; virus proteomics},
    pmid = {31181768},
    }
  • [DOI] E. Karatzas, G. Kolios, and G. M. Spyrou, "An application of computational drug repurposing based on transcriptomic signatures.," Methods Mol Biol, vol. 1903, p. 149–177, 2019.
    [Bibtex]
    @Article{Karatzas:19,
    author = {Karatzas, Evangelos and Kolios, George and Spyrou, George M},
    title = {An Application of Computational Drug Repurposing Based on Transcriptomic Signatures.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {1903},
    pages = {149--177},
    abstract = {Drug repurposing is a methodology where already existing drugs are tested against diseases outside their initial usage, in order to reduce the high cost and long periods of new drug development. In silico drug repurposing further speeds up the process, by testing a large number of drugs against the biological signatures of known diseases. In this chapter, we present a step-by-step methodology of a transcriptomics-based computational drug repurposing pipeline providing a comprehensive guide to the whole procedure, from proper dataset selection to short list derivation of repurposed drugs which might act as inhibitors against the studied disease. The presented pipeline contains the selection and curation of proper transcriptomics datasets, statistical analysis of the datasets in order to extract the top over- and under-expressed gene identifiers, appropriate identifier conversion, drug repurposing analysis, repurposed drugs filtering, cross-tool screening, drug-list re-ranking, and results' validation.},
    doi = {10.1007/978-1-4939-8955-3_9},
    keywords = {Algorithms; Computational Biology, methods; Databases, Pharmaceutical; Drug Repositioning, methods; Gene Expression Profiling; Gene Expression Regulation, drug effects; Humans; Reproducibility of Results; Software; Transcriptome; User-Computer Interface; Web Browser; Workflow; Computational pipeline; Drug repositioning; Drug repurposing; Gene expression; Microarrays; RNA-Seq; Transcriptomics},
    pmid = {30547441},
    }
  • [DOI] L. Beller and J. Matthijnssens, "What is (not) known about the dynamics of the human gut virome in health and disease.," Curr Opin Virol, vol. 37, p. 52–57, 2019.
    [Bibtex]
    @Article{Beller:19,
    author = {Beller, Leen and Matthijnssens, Jelle},
    title = {What is (not) known about the dynamics of the human gut virome in health and disease.},
    journal = {{Curr Opin Virol}},
    year = {2019},
    volume = {37},
    pages = {52--57},
    abstract = {The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.},
    doi = {10.1016/j.coviro.2019.05.013},
    pmid = {31255903},
    }
  • [DOI] S. Tu and C. Upton, "Bioinformatics for analysis of poxvirus genomes.," Methods Mol Biol, vol. 2023, p. 29–62, 2019.
    [Bibtex]
    @Article{Tu:19,
    author = {Tu, Shin-Lin and Upton, Chris},
    title = {Bioinformatics for Analysis of Poxvirus Genomes.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {2023},
    pages = {29--62},
    abstract = {In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation sequencing of DNA genomes and mRNA transcripts and mass spectrometry of proteins. Perhaps, however, it is genome sequencing that impacts a virologist the most. In 2017, more than 480 complete genome sequences of poxviruses have been generated, and are constantly used in many different ways by almost all molecular virologists. Matching this growth in data acquisition is an explosion of the relatively new field of bioinformatics, providing databases to store and organize this valuable/expensive data and algorithms to analyze it. For the bench virologist, access to intuitive, easy-to-use, software is often critical for performing bioinformatics-based experiments. Three common hurdles for the researcher are (1) selection, retrieval, and reformatting genomics data from large databases; (2) use of tools to compare/analyze the genomics data; and (3) display and interpretation of complex sets of results. This chapter is directed at the bench virologist and describes the software that helps overcome these obstacles, with a focus on the comparison and analysis of poxvirus genomes. Although poxvirus genomes are stored in public databases such as GenBank, this resource can be cumbersome and tedious to use if large amounts of data must to be collected. Therefore, we also highlight our Viral Orthologous Clusters database system and integrated tools that we developed specifically for the management and analysis of complete viral genomes.},
    doi = {10.1007/978-1-4939-9593-6_2},
    keywords = {BBB; BLAST; Bioinformatics; Dotplot; Genomics; JDotter; MSA; Multiple sequence alignment; Poxvirus; Smallpox; VGO; VOCs; Vaccinia virus},
    pmid = {31240669},
    }
  • [DOI] A. Ariza-Mateos, C. Briones, C. Perales, E. Domingo, and J. Gómez, "The archaeology of coding RNA.," Ann NY Acad Sci, 2019.
    [Bibtex]
    @Article{Ariza-Mateos:19,
    author = {Ariza-Mateos, Ascensión and Briones, Carlos and Perales, Celia and Domingo, Esteban and Gómez, Jordi},
    title = {The archaeology of coding {RNA}.},
    journal = {{Ann NY Acad Sci}},
    year = {2019},
    abstract = {Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto-tRNA-like structures. Different biochemical and biophysical tools have been used to search for ancient-like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as "archaeological," and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA-like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon-alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA-like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA-like motif next to the tRNA-like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny-based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent "the losers" in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.},
    doi = {10.1111/nyas.14173},
    keywords = {RNA world; RNase III; RNase P; biocommunication; biosemiotics; quasispecies},
    pmid = {31237363},
    }
  • [DOI] R. A. Edwards, A. A. Vega, H. M. Norman, M. Ohaeri, K. Levi, E. A. Dinsdale, O. Cinek, R. K. Aziz, K. McNair, J. J. Barr, K. Bibby, S. J. J. Brouns, A. Cazares, P. A. de Jonge, C. Desnues, S. D. L. Muñoz, P. C. Fineran, A. Kurilshikov, R. Lavigne, K. Mazankova, D. T. McCarthy, F. L. Nobrega, A. R. Muñoz, G. Tapia, N. Trefault, A. V. Tyakht, P. Vinuesa, J. Wagemans, A. Zhernakova, F. M. Aarestrup, G. Ahmadov, A. Alassaf, J. Anton, A. Asangba, E. K. Billings, V. A. Cantu, J. M. Carlton, D. Cazares, G. Cho, T. Condeff, P. Cortés, M. Cranfield, D. A. Cuevas, R. D. la Iglesia, P. Decewicz, M. P. Doane, N. J. Dominy, L. Dziewit, B. M. Elwasila, M. A. Eren, C. Franz, J. Fu, C. Garcia-Aljaro, E. Ghedin, K. M. Gulino, J. M. Haggerty, S. R. Head, R. S. Hendriksen, C. Hill, H. Hyöty, E. N. Ilina, M. T. Irwin, T. C. Jeffries, J. Jofre, R. E. Junge, S. T. Kelley, M. K. Mirzaei, M. Kowalewski, D. Kumaresan, S. R. Leigh, D. Lipson, E. S. Lisitsyna, M. Llagostera, J. M. Maritz, L. C. Marr, A. McCann, S. Molshanski-Mor, S. Monteiro, B. Moreira-Grez, M. Morris, L. Mugisha, M. Muniesa, H. Neve, N. Nguyen, O. D. Nigro, A. S. Nilsson, T. O'Connell, R. Odeh, A. Oliver, M. Piuri, A. P. J. II, U. Qimron, Z. Quan, P. Rainetova, A. Ramírez-Rojas, R. Raya, K. Reasor, G. A. O. Rice, A. Rossi, R. Santos, J. Shimashita, E. N. Stachler, L. C. Stene, R. Strain, R. Stumpf, P. J. Torres, A. Twaddle, M. U. Ibekwe, N. Villagra, S. Wandro, B. White, A. Whiteley, K. L. Whiteson, C. Wijmenga, M. M. Zambrano, H. Zschach, and B. E. Dutilh, "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Edwards:19,
    author = {Robert A. Edwards and Alejandro A. Vega and Holly M. Norman and Maria Ohaeri and Kyle Levi and Elizabeth A. Dinsdale and Ondrej Cinek and Ramy K. Aziz and Katelyn McNair and Jeremy J. Barr and Kyle Bibby and Stan J. J. Brouns and Adrian Cazares and Patrick A. de Jonge and Christelle Desnues and Samuel L. D{\'{\i}}az Mu{\~{n}}oz and Peter C. Fineran and Alexander Kurilshikov and Rob Lavigne and Karla Mazankova and David T. McCarthy and Franklin L. Nobrega and Alejandro Reyes Mu{\~{n}}oz and German Tapia and Nicole Trefault and Alexander V. Tyakht and Pablo Vinuesa and Jeroen Wagemans and Alexandra Zhernakova and Frank M. Aarestrup and Gunduz Ahmadov and Abeer Alassaf and Josefa Anton and Abigail Asangba and Emma K. Billings and Vito Adrian Cantu and Jane M. Carlton and Daniel Cazares and Gyu-Sung Cho and Tess Condeff and Pilar Cort{\'{e}}s and Mike Cranfield and Daniel A. Cuevas and Rodrigo De la Iglesia and Przemyslaw Decewicz and Michael P. Doane and Nathaniel J. Dominy and Lukasz Dziewit and Bashir Mukhtar Elwasila and A. Murat Eren and Charles Franz and Jingyuan Fu and Cristina Garcia-Aljaro and Elodie Ghedin and Kristen M. Gulino and John M. Haggerty and Steven R. Head and Rene S. Hendriksen and Colin Hill and Heikki Hyöty and Elena N. Ilina and Mitchell T. Irwin and Thomas C. Jeffries and Juan Jofre and Randall E. Junge and Scott T. Kelley and Mohammadali Khan Mirzaei and Martin Kowalewski and Deepak Kumaresan and Steven R. Leigh and David Lipson and Eugenia S. Lisitsyna and Montserrat Llagostera and Julia M. Maritz and Linsey C. Marr and Angela McCann and Shahar Molshanski-Mor and Silvia Monteiro and Benjamin Moreira-Grez and Megan Morris and Lawrence Mugisha and Maite Muniesa and Horst Neve and Nam-phuong Nguyen and Olivia D. Nigro and Anders S. Nilsson and Taylor O'Connell and Rasha Odeh and Andrew Oliver and Mariana Piuri and Aaron J. Prussin II and Udi Qimron and Zhe-Xue Quan and Petra Rainetova and Ad{\'{a}}n Ram{\'{\i}}rez-Rojas and Raul Raya and Kim Reasor and Gillian A. O. Rice and Alessandro Rossi and Ricardo Santos and John Shimashita and Elyse N. Stachler and Lars C. Stene and Ronan Strain and Rebecca Stumpf and Pedro J. Torres and Alan Twaddle and MaryAnn Ugochi Ibekwe and Nicol{\'{a}}s Villagra and Stephen Wandro and Bryan White and Andy Whiteley and Katrine L. Whiteson and Cisca Wijmenga and Maria M. Zambrano and Henrike Zschach and Bas E. Dutilh},
    title = {Global phylogeography and ancient evolution of the widespread human gut virus {crAssphage}},
    journal = {{Nat Microbiol}},
    year = {2019},
    doi = {10.1038/s41564-019-0494-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. B. Jang, B. Bolduc, O. Zablocki, J. H. Kuhn, S. Roux, E. M. Adriaenssens, R. J. Brister, A. M. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. B. Sullivan, "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks," Nat Biotechnol, vol. 37, iss. 6, p. 632–639, 2019.
    [Bibtex]
    @Article{Jang:19,
    author = {Ho Bin Jang and Benjamin Bolduc and Olivier Zablocki and Jens H. Kuhn and Simon Roux and Evelien M. Adriaenssens and J. Rodney Brister and Andrew M Kropinski and Mart Krupovic and Rob Lavigne and Dann Turner and Matthew B. Sullivan},
    title = {Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks},
    journal = {{Nat Biotechnol}},
    year = {2019},
    volume = {37},
    number = {6},
    pages = {632--639},
    doi = {10.1038/s41587-019-0100-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Erhard, M. A. P. Baptista, T. Krammer, T. Hennig, M. Lange, P. Arampatzi, C. S. Jürges, F. J. Theis, A. Saliba, and L. Dölken, "scSLAM-seq reveals core features of transcription dynamics in single cells.," Nature, 2019.
    [Bibtex]
    @Article{Erhard:19,
    author = {Erhard, Florian and Baptista, Marisa A P and Krammer, Tobias and Hennig, Thomas and Lange, Marius and Arampatzi, Panagiota and Jürges, Christopher S and Theis, Fabian J and Saliba, Antoine-Emmanuel and Dölken, Lars},
    title = {{scSLAM-seq} reveals core features of transcription dynamics in single cells.},
    journal = {Nature},
    year = {2019},
    abstract = {Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease . However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling , biochemical nucleoside conversion and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.},
    doi = {10.1038/s41586-019-1369-y},
    pmid = {31292545},
    }
  • [DOI] C. N. Agoti, M. V. T. Phan, P. K. Munywoki, G. Githinji, G. F. Medley, P. A. Cane, P. Kellam, M. Cotten, and J. D. Nokes, "Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.," Sci Rep, vol. 9, p. 10076, 2019.
    [Bibtex]
    @Article{Agoti:19,
    author = {Agoti, Charles N and Phan, My V T and Munywoki, Patrick K and Githinji, George and Medley, Graham F and Cane, Patricia A and Kellam, Paul and Cotten, Matthew and Nokes, D James},
    title = {Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    pages = {10076},
    abstract = {Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3-4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0-21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0-17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.},
    doi = {10.1038/s41598-019-46509-w},
    issue = {1},
    pmid = {31296922},
    }
  • [DOI] J. M. Bartoszewicz, A. Seidel, R. Rentzsch, and B. Y. Renard, "DeePaC: predicting pathogenic potential of novel dna with reverse-complement neural networks.," Bioinformatics, 2019.
    [Bibtex]
    @Article{Bartoszewicz:19,
    author = {Bartoszewicz, Jakub M and Seidel, Anja and Rentzsch, Robert and Renard, Bernhard Y},
    title = {{DeePaC}: Predicting pathogenic potential of novel DNA with reverse-complement neural networks.},
    journal = {Bioinformatics},
    year = {2019},
    abstract = {We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized, and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable. We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art. The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC. Supplementary data are available at Bioinformatics online.},
    doi = {10.1093/bioinformatics/btz541},
    pmid = {31298694},
    }
  • [DOI] N. Bachmann, C. von Siebenthal, V. Vongrad, T. Turk, K. Neumann, N. Beerenwinkel, J. Bogojeska, J. Fellay, V. Roth, Y. L. Kok, C. W. Thorball, A. Borghesi, S. Parbhoo, M. Wieser, J. Böni, M. Perreau, T. Klimkait, S. Yerly, M. Battegay, A. Rauch, M. Hoffmann, E. Bernasconi, M. Cavassini, R. D. Kouyos, H. F. Günthard, K. J. Metzner, and S. H. C. Study, "Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.," Nat Commun, vol. 10, p. 3193, 2019.
    [Bibtex]
    @Article{Bachmann:19,
    author = {Bachmann, Nadine and von Siebenthal, Chantal and Vongrad, Valentina and Turk, Teja and Neumann, Kathrin and Beerenwinkel, Niko and Bogojeska, Jasmina and Fellay, Jaques and Roth, Volker and Kok, Yik Lim and Thorball, Christian W and Borghesi, Alessandro and Parbhoo, Sonali and Wieser, Mario and Böni, Jürg and Perreau, Matthieu and Klimkait, Thomas and Yerly, Sabine and Battegay, Manuel and Rauch, Andri and Hoffmann, Matthias and Bernasconi, Enos and Cavassini, Matthias and Kouyos, Roger D and Günthard, Huldrych F and Metzner, Karin J and Swiss HIV Cohort Study},
    title = {Determinants of {HIV}-1 reservoir size and long-term dynamics during suppressive {ART}.},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    pages = {3193},
    abstract = {The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies.},
    doi = {10.1038/s41467-019-10884-9},
    investigator = {Anagnostopoulos, Alexia and Battegay, Manuel and Bernasconi, Enos and Böni, Jürg and Braun, Dominique L and Bucher, Heiner C and Calmy, Alexandra and Cavassini, Matthias and Ciuffi, Angela and Dollenmaier, Günter and Egger, Matthias and Elzi, Luigia and Fehr, Jan and Fellay, Jacques and Furrer, Hansjakob and Fux, Christoph A and Günthard, Huldrych F and Haerry, David and Hasse, Barbara and Hirsch, Hans H and Hoffmann, Matthias and Hösli, Irene and Huber, Michael and Kahlert, Christian and Kaiser, Laurent and Keiser, Olivia and Klimkait, Thomas and Kouyos, Roger D and Kovari, Helen and Ledergerber, Bruno and Martinetti, Gladys and Tejada, Begona Martinez de and Marzolini, Catia and Metzner, Karin J and Müller, Nicolas and Nicca, Dunja and Paioni, Paolo and Pantaleo, Guiseppe and Perreau, Matthieu and Rauch, Andri and Rudin, Christoph and Scherrer, Alexandra U and Schmid, Patrick and Speck, Roberto and Stöckle, Marcel and Tarr, Philip and Trkola, Alexandra and Vernazza, Pietro and Wandeler, Gilles and Weber, Rainer and Yerly, Sabine},
    issue = {1},
    pmid = {31324762},
    }
  • [DOI] A. Michelitsch, K. Wernike, C. Klaus, G. Dobler, and M. Beer, "Exploring the reservoir hosts of tick-borne encephalitis virus," Viruses, vol. 11, iss. 7, p. 669, 2019.
    [Bibtex]
    @Article{Michelitsch:19,
    author = {Anna Michelitsch and Kerstin Wernike and Christine Klaus and Gerhard Dobler and Martin Beer},
    title = {Exploring the Reservoir Hosts of Tick-Borne Encephalitis Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {7},
    pages = {669},
    doi = {10.3390/v11070669},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Döring, C. Kreer, N. Lehnen, F. Klein, and N. Pfeifer, "Modeling the amplification of immunoglobulins through machine learning on sequence-specific features," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Döring:19,
    author = {Matthias Döring and Christoph Kreer and Nathalie Lehnen and Florian Klein and Nico Pfeifer},
    title = {Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-47173-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Wylezich, A. Belka, D. Hanke, M. Beer, S. Blome, and D. Höper, "Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.," Int J Parasitol, 2019.
    [Bibtex]
    @Article{Wylezich:19,
    author = {Wylezich, Claudia and Belka, Ariane and Hanke, Dennis and Beer, Martin and Blome, Sandra and Höper, Dirk},
    title = {Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.},
    journal = {{Int J Parasitol}},
    year = {2019},
    abstract = {Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics - an undirected, broad and sensitive method for the efficient identification of pathogens - was frequently used for virus and bacteria detection, but seldom applied to parasite identification. Here, metagenomics datasets prepared from swine faeces using an unbiased sample processing approach with RNA serving as starting material were re-analysed with respect to parasite detection. The taxonomic identification tool RIEMS, used for initial detection, provided basic hints on potential pathogens contained in the datasets. The suspected parasites/intestinal protists (Blastocystis, Entamoeba, Iodamoeba, Neobalantidium, Tetratrichomonas) were verified using subsequently applied reference mapping analyses on the base of rRNA sequences. Nearly full-length gene sequences could be extracted from the RNA-derived datasets. In the case of Blastocystis, subtyping was possible with subtype (ST)15 discovered for the first known time in swine faeces. Using RIEMS, some of the suspected candidates turned out to be false-positives caused by the poor status of sequences in publicly available databases. Altogether, 11 different species/STs of parasites/intestinal protists were detected in 34 out of 41 datasets extracted from metagenomics data. The approach operates without any primer bias that typically hampers the analysis of amplicon-based approaches, and allows the detection and taxonomic classification including subtyping of protist and metazoan endobionts (parasites, commensals or mutualists) based on an abundant biomarker, the 18S rRNA. The generic nature of the approach also allows evaluation of interdependencies that induce mutualistic or pathogenic effects that are often not clear for many intestinal protists and perhaps other parasites. Thus, metagenomics has the potential for generic pathogen identification beyond the characterization of viruses and bacteria when starting from RNA instead of DNA.},
    doi = {10.1016/j.ijpara.2019.04.007},
    keywords = {False-positives; Intestinal protists; Parasite detection; Pig faeces; RIEMS; Shotgun metagenomics; Subtyping; Taxonomic assignment},
    pmid = {31361998},
    }
  • [DOI] I. H. E. Korf, J. P. Meier-Kolthoff, E. M. Adriaenssens, A. M. Kropinski, M. Nimtz, M. Rohde, M. J. van Raaij, and J. Wittmann, "Still something to discover: novel insights into Escherichia coli phage diversity and taxonomy.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Korf:19,
    author = {Korf, Imke H E and Meier-Kolthoff, Jan P and Adriaenssens, Evelien M and Kropinski, Andrew M and Nimtz, Manfred and Rohde, Manfred and van Raaij, Mark J and Wittmann, Johannes},
    title = {Still Something to Discover: Novel Insights into {Escherichia coli} Phage Diversity and Taxonomy.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of phages.},
    doi = {10.3390/v11050454},
    issue = {5},
    keywords = {Escherichia coli; bacteriophage; diversity; genomics; taxonomy},
    pmid = {31109012},
    }
  • [DOI] M. Džunková, S. J. Low, J. N. Daly, L. Deng, C. Rinke, and P. Hugenholtz, "Defining the human gut host-phage network through single-cell viral tagging.," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Dzunkova:19,
    author = {Džunková, Mária and Low, Soo Jen and Daly, Joshua N and Deng, Li and Rinke, Christian and Hugenholtz, Philip},
    title = {Defining the human gut host-phage network through single-cell viral tagging.},
    journal = {{Nat Microbiol}},
    year = {2019},
    abstract = {Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.},
    doi = {10.1038/s41564-019-0526-2},
    pmid = {31384000},
    }
  • [DOI] M. Hölzer, A. Schoen, J. Wulle, M. A. Müller, C. Drosten, M. Marz, and F. Weber, "Virus- and interferon alpha-induced transcriptomes of cells from the microbat Myotis daubentonii," iScience, 2019.
    [Bibtex]
    @Article{Hölzer:19a,
    author = {Martin Hölzer and Andreas Schoen and Julia Wulle and Marcel A. Müller and Christian Drosten and Manja Marz and Friedemann Weber},
    title = {Virus- and interferon alpha-induced transcriptomes of cells from the microbat {Myotis daubentonii}},
    journal = {{iScience}},
    year = {2019},
    doi = {10.1016/j.isci.2019.08.016},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. C. Bilz, E. Willscher, H. Binder, J. Böhnke, M. L. Stanifer, D. Hübner, S. Boulant, U. G. Liebert, and C. Claus, "Teratogenic rubella virus alters the endodermal differentiation capacity of human induced pluripotent stem cells.," Cells, vol. 8, 2019.
    [Bibtex]
    @Article{Bilz:19,
    author = {Bilz, Nicole C and Willscher, Edith and Binder, Hans and Böhnke, Janik and Stanifer, Megan L and Hübner, Denise and Boulant, Steeve and Liebert, Uwe G and Claus, Claudia},
    title = {Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem Cells.},
    journal = {Cells},
    year = {2019},
    volume = {8},
    abstract = {The study of congenital virus infections in humans requires suitable ex vivo platforms for the species-specific events during embryonal development. A prominent example for these infections is rubella virus (RV) which most commonly leads to defects in ear, heart, and eye development. We applied teratogenic RV to human induced pluripotent stem cells (iPSCs) followed by differentiation into cells of the three embryonic lineages (ecto-, meso-, and endoderm) as a cell culture model for blastocyst- and gastrulation-like stages. In the presence of RV, lineage-specific differentiation markers were expressed, indicating that lineage identity was maintained. However, portrait analysis of the transcriptomic expression signatures of all samples revealed that mock- and RV-infected endodermal cells were less related to each other than their ecto- and mesodermal counterparts. Markers for definitive endoderm were increased during RV infection. Profound alterations of the epigenetic landscape including the expression level of components of the chromatin remodeling complexes and an induction of type III interferons were found, especially after endodermal differentiation of RV-infected iPSCs. Moreover, the eye field transcription factors RAX and SIX3 and components of the gene set vasculogenesis were identified as dysregulated transcripts. Although iPSC morphology was maintained, the formation of embryoid bodies as three-dimensional cell aggregates and as such cellular adhesion capacity was impaired during RV infection. The correlation of the molecular alterations induced by RV during differentiation of iPSCs with the clinical signs of congenital rubella syndrome suggests mechanisms of viral impairment of human development.},
    doi = {10.3390/cells8080870},
    issue = {8},
    keywords = {TGF-β and Wnt/β-catenin pathway; ectoderm; embryogenesis; embryoid body; epigenetic signature; human development; interferon response; interferon-induced genes; mesoderm; self-organizing map (SOM) data portrayal},
    pmid = {31405163},
    }
  • [DOI] H. R. Jonsdottir, S. Marti, D. Geerts, R. Rodriguez, V. Thiel, and R. Dijkman, "Establishment of primary transgenic human airway epithelial cell cultures to study respiratory virus-host interactions.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Jonsdottir:19,
    author = {Jonsdottir, Hulda R and Marti, Sabrina and Geerts, Dirk and Rodriguez, Regulo and Thiel, Volker and Dijkman, Ronald},
    title = {Establishment of Primary Transgenic Human Airway Epithelial Cell Cultures to Study Respiratory Virus-Host Interactions.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Primary human airway epithelial cell (hAEC) cultures represent a universal platform to propagate respiratory viruses and characterize their host interactions in authentic target cells. To further elucidate specific interactions between human respiratory viruses and important host factors in the airway epithelium, it is important to make hAEC cultures amenable to genetic modification. However, the short and finite lifespan of primary cells in cell culture creates a bottleneck for the genetic modification of these cultures. In the current study, we show that the incorporation of the Rho-associated protein kinase (ROCK) inhibitor (Y-27632) during cell propagation extends the life span of primary human cells in vitro and thereby facilitates the incorporation of lentivirus-based expression systems. Using fluorescent reporters for fluorescence-activated cell sorting (FACS)-based sorting, we generated homogenously fluorescent hAEC cultures that differentiate normally after lentiviral transduction. As a proof-of-principle, we demonstrate that host gene expression can be modulated post-differentiation via inducible short hairpin (sh)RNA-mediated knockdown. Importantly, functional characterization of these transgenic hAEC cultures with exogenous poly (I:C), as a proxy for virus infection, demonstrates that such modifications do not influence the host innate immune response. Moreover, the propagation kinetics of both human coronavirus 229E (HCoV-229E) and human respiratory syncytial virus (hRSV) were not affected. Combined, these results validate our newly established protocol for the genetic modification of hAEC cultures, thereby unlocking a unique potential for detailed molecular characterization of virus-host interactions in human respiratory epithelium.},
    doi = {10.3390/v11080747},
    issue = {8},
    keywords = {human airway epithelial cell cultures; respiratory viruses; virus-host interactions},
    pmid = {31412613},
    }
  • [DOI] A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, "Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.," Genome Res, 2019.
    [Bibtex]
    @Article{Viehweger:19,
    author = {Viehweger, Adrian and Krautwurst, Sebastian and Lamkiewicz, Kevin and Madhugiri, Ramakanth and Ziebuhr, John and Hölzer, Martin and Marz, Manja},
    title = {Direct {RNA} nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.},
    journal = {{Genome Res}},
    year = {2019},
    abstract = {Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses. Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called "quasispecies." Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous genome regions. Here, we used a full-length, direct RNA sequencing (DRS) approach based on nanopores to characterize viral RNAs produced in cells infected with a human coronavirus. By using DRS, we were able to map the longest (∼26-kb) contiguous read to the viral reference genome. By combining Illumina and Oxford Nanopore sequencing, we reconstructed a highly accurate consensus sequence of the human coronavirus (HCoV)-229E genome (27.3 kb). Furthermore, by using long reads that did not require an assembly step, we were able to identify, in infected cells, diverse and novel HCoV-229E sg RNAs that remain to be characterized. Also, the DRS approach, which circumvents reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. Our work paves the way for haplotype-based analyses of viral quasispecies by showing the feasibility of intra-sample haplotype separation. Even though several technical challenges remain to be addressed to exploit the potential of the nanopore technology fully, our work illustrates that DRS may significantly advance genomic studies of complex virus populations, including predictions on long-range interactions in individual full-length viral RNA haplotypes.},
    doi = {10.1101/gr.247064.118},
    pmid = {31439691},
    }
  • [DOI] S. Gago-Zachert, J. Schuck, C. Weinholdt, M. Knoblich, V. Pantaleo, I. Grosse, T. Gursinsky, and S. Behrens, "Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro.," Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Gago-Zachert:19,
    author = {Gago-Zachert, Selma and Schuck, Jana and Weinholdt, Claus and Knoblich, Marie and Pantaleo, Vitantonio and Grosse, Ivo and Gursinsky, Torsten and Behrens, Sven-Erik},
    title = {Highly efficacious antiviral protection of plants by small interfering {RNAs} identified in vitro.},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    abstract = {In response to a viral infection, the plant's RNA silencing machinery processes viral RNAs into a huge number of small interfering RNAs (siRNAs). However, a very few of these siRNAs actually interfere with viral replication. A reliable approach to identify these immunologically effective siRNAs (esiRNAs) and to define the characteristics underlying their activity has not been available so far. Here, we develop a novel screening approach that enables a rapid functional identification of antiviral esiRNAs. Tests on the efficacy of such identified esiRNAs of a model virus achieved a virtual full protection of plants against a massive subsequent infection in transient applications. We find that the functionality of esiRNAs depends crucially on two properties: the binding affinity to Argonaute proteins and the ability to access the target RNA. The ability to rapidly identify functional esiRNAs could be of great benefit for all RNA silencing-based plant protection measures against viruses and other pathogens.},
    doi = {10.1093/nar/gkz678},
    pmid = {31433052},
    }
  • [DOI] K. Theys, P. Lemey, A. Vandamme, and G. Baele, "Advances in visualization tools for phylogenomic and phylodynamic studies of viral diseases.," Front Public Health, vol. 7, p. 208, 2019.
    [Bibtex]
    @Article{Theys:19a,
    author = {Theys, Kristof and Lemey, Philippe and Vandamme, Anne-Mieke and Baele, Guy},
    title = {Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases.},
    journal = {{Front Public Health}},
    year = {2019},
    volume = {7},
    pages = {208},
    abstract = {Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.},
    doi = {10.3389/fpubh.2019.00208},
    keywords = {epidemiology; evolution; infectious disease; phylodynamics; phylogenetics; phylogenomics; visualization},
    pmid = {31428595},
    }
  • [DOI] C. Shi, L. Beller, W. Deboutte, K. C. Yinda, L. Delang, A. Vega-Rúa, A. Failloux, and J. Matthijnssens, "Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics.," Microbiome, vol. 7, p. 121, 2019.
    [Bibtex]
    @Article{Shi:19,
    author = {Shi, Chenyan and Beller, Leen and Deboutte, Ward and Yinda, Kwe Claude and Delang, Leen and Vega-Rúa, Anubis and Failloux, Anna-Bella and Matthijnssens, Jelle},
    title = {Stable distinct core eukaryotic viromes in different mosquito species from {G}uadeloupe, using single mosquito viral metagenomics.},
    journal = {Microbiome},
    year = {2019},
    volume = {7},
    pages = {121},
    abstract = {Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of the viral diversity in individual mosquitoes. To address this issue, we applied our optimized viral metagenomics protocol (NetoVIR) to compare the virome of single and pooled Aedes aegypti and Culex quinquefasciatus mosquitoes collected from different locations in Guadeloupe, in 2016 and 2017. The total read number and viral reads proportion of samples containing a single mosquito have no significant difference compared with those of pools containing five mosquitoes, which proved the feasibility of using single mosquito for viral metagenomics. A comparative analysis of the virome revealed a higher abundance and more diverse eukaryotic virome in Aedes aegypti, whereas Culex quinquefasciatus harbors a richer and more diverse phageome. The majority of the identified eukaryotic viruses were mosquito-species specific. We further characterized the genomes of 11 novel eukaryotic viruses. Furthermore, qRT-PCR analyses of the six most abundant eukaryotic viruses indicated that the majority of individual mosquitoes were infected by several of the selected viruses with viral genome copies per mosquito ranging from 267 to 1.01 × 10 (median 7.5 × 10 ) for Ae. aegypti and 192 to 8.69 × 10 (median 4.87 × 10 ) for Cx. quinquefasciatus. Additionally, in Cx. quinquefasciatus, a number of phage contigs co-occurred with several marker genes of Wolbachia sp. strain wPip. We firstly demonstrate the feasibility to use single mosquito for viral metagenomics, which can provide much more precise virome profiles of mosquito populations. Interspecific comparisons show striking differences in abundance and diversity between the viromes of Ae. aegypti and Cx. quinquefasciatus. Those two mosquito species seem to have their own relatively stable "core eukaryotic virome", which might have important implications for the competence to transmit important medically relevant arboviruses. The presence of Wolbachia in Cx. quinquefasciatus might explain (1) the lower overall viral load compared to Ae. aegypti, (2) the identification of multiple unknown phage contigs, and (3) the difference in competence for important human pathogens. How these viruses, phages, and bacteria influence the physiology and vector competence of mosquito hosts warrants further research.},
    doi = {10.1186/s40168-019-0734-2},
    issue = {1},
    keywords = {Aedes aegypti; Core virome; Culex quinquefasciatus; Eukaryotic virome; Guadeloupe; Phageome; Single mosquito; Viral metagenomics},
    pmid = {31462331},
    }
  • [DOI] T. Junier, M. Huber, S. Schmutz, V. Kufner, O. Zagordi, S. Neuenschwander, A. Ramette, J. Kubacki, C. Bachofen, W. Qi, F. Laubscher, S. Cordey, L. Kaiser, C. Beuret, V. Barbié, J. Fellay, and A. Lebrand, "Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial.," Genes, vol. 10, 2019.
    [Bibtex]
    @Article{Junier:19,
    author = {Junier, Thomas and Huber, Michael and Schmutz, Stefan and Kufner, Verena and Zagordi, Osvaldo and Neuenschwander, Stefan and Ramette, Alban and Kubacki, Jakub and Bachofen, Claudia and Qi, Weihong and Laubscher, Florian and Cordey, Samuel and Kaiser, Laurent and Beuret, Christian and Barbié, Valérie and Fellay, Jacques and Lebrand, Aitana},
    title = {Viral Metagenomics in the Clinical Realm: Lessons Learned from a {S}wiss-Wide Ring Trial.},
    journal = {Genes},
    year = {2019},
    volume = {10},
    abstract = {Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5-10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.},
    doi = {10.3390/genes10090655},
    issue = {9},
    keywords = {EQA; external quality assessment; quality control; ring trial; viral metagenomics},
    pmid = {31466373},
    }
  • [DOI] M. De Scheerder, B. Vrancken, S. Dellicour, T. Schlub, E. Lee, W. Shao, S. Rutsaert, C. Verhofstede, T. Kerre, T. Malfait, D. Hemelsoet, M. Coppens, A. Dhondt, D. De Looze, F. Vermassen, P. Lemey, S. Palmer, and L. Vandekerckhove, "HIV rebound is predominantly fueled by genetically identical viral expansions from diverse reservoirs.," Cell Host Microbe, 2019.
    [Bibtex]
    @Article{DeScheerder:19,
    author = {De Scheerder, Marie-Angélique and Vrancken, Bram and Dellicour, Simon and Schlub, Timothy and Lee, Eunok and Shao, Wei and Rutsaert, Sofie and Verhofstede, Chris and Kerre, Tessa and Malfait, Thomas and Hemelsoet, Dimitri and Coppens, Marc and Dhondt, Annemieke and De Looze, Danny and Vermassen, Frank and Lemey, Philippe and Palmer, Sarah and Vandekerckhove, Linos},
    title = {{HIV} Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.},
    journal = {{Cell Host Microbe}},
    year = {2019},
    abstract = {Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject of ardent debate, despite extensive research efforts. To unravel the source of rebounding viruses, we conducted a large-scale HIV-STAR (HIV-1 sequencing before analytical treatment interruption to identify the anatomically relevant HIV reservoir) clinical trial. We collected samples from 11 participants and compared the genetic composition of (pro)viruses collected under treatment from different cellular and anatomical compartments with that of plasma viruses sampled during analytical treatment interruption. We found a remarkably heterogeneous source of viral rebound. In addition, irrespective of the compartment or cell subset, genetically identical viral expansions played a significant role in viral rebound. Our study suggests that although there does not seem to be a primary source for rebound HIV, cellular proliferation is an important driver of HIV persistence and should therefore be considered in future curative strategies.},
    doi = {10.1016/j.chom.2019.08.003},
    keywords = {HIV persistence; HIV rebound; HIV-1 reservoir; analytical treatment interruption; cellular and anatomical compartments; cellular proliferation; cure research; in-depth sampling; single-genome sequencing},
    pmid = {31471273},
    }
  • [DOI] R. Connor, R. Brister, J. P. Buchmann, W. Deboutte, R. Edwards, J. Martí-Carreras, M. Tisza, V. Zalunin, J. Andrade-Martínez, A. Cantu, M. D'Amour, A. Efremov, L. Fleischmann, L. Forero-Junco, S. Garmaeva, M. Giluso, C. Glickman, M. Henderson, B. Kellman, D. Kristensen, C. Leubsdorf, K. Levi, S. Levi, S. Pakala, V. Peddu, A. Ponsero, E. Ribeiro, F. Roy, L. Rutter, S. Saha, M. Shakya, R. Shean, M. Miller, B. Tully, C. Turkington, K. Youens-Clark, B. Vanmechelen, and B. Busby, "NCBI's virus discovery hackathon: engaging research communities to identify cloud infrastructure requirements," Genes, vol. 10, iss. 9, p. 714, 2019.
    [Bibtex]
    @Article{Connor:19,
    author = {Ryan Connor and Rodney Brister and Jan P. Buchmann and Ward Deboutte and Rob Edwards and Joan Mart{\'{\i}}-Carreras and Mike Tisza and Vadim Zalunin and Juan Andrade-Mart{\'{\i}}nez and Adrian Cantu and Michael D'Amour and Alexandre Efremov and Lydia Fleischmann and Laura Forero-Junco and Sanzhima Garmaeva and Melissa Giluso and Cody Glickman and Margaret Henderson and Benjamin Kellman and David Kristensen and Carl Leubsdorf and Kyle Levi and Shane Levi and Suman Pakala and Vikas Peddu and Alise Ponsero and Eldred Ribeiro and Farrah Roy and Lindsay Rutter and Surya Saha and Migun Shakya and Ryan Shean and Matthew Miller and Benjamin Tully and Christopher Turkington and Ken Youens-Clark and Bert Vanmechelen and Ben Busby},
    title = {{NCBI}'s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements},
    journal = {Genes},
    year = {2019},
    volume = {10},
    number = {9},
    pages = {714},
    doi = {10.3390/genes10090714},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] J. H. Forth, L. F. Forth, J. King, O. Groza, A. Hübner, A. S. Olesen, D. Höper, L. K. Dixon, C. L. Netherton, T. B. Rasmussen, S. Blome, A. Pohlmann, and M. Beer, "A deep-sequencing workflow for the fast and efficient generation of high-quality african swine fever virus whole-genome sequences.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Forth:19,
    author = {Forth, Jan H and Forth, Leonie F and King, Jacqueline and Groza, Oxana and Hübner, Alexandra and Olesen, Ann Sofie and Höper, Dirk and Dixon, Linda K and Netherton, Christopher L and Rasmussen, Thomas Bruun and Blome, Sandra and Pohlmann, Anne and Beer, Martin},
    title = {A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing. Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.},
    doi = {10.3390/v11090846},
    issue = {9},
    keywords = {African swine fever virus (ASFV); Nanopore sequencing; next-generation sequencing (NGS); target enrichment; whole-genome sequencing},
    pmid = {31514438},
    }
  • [DOI] M. Maabar, A. J. Davison, M. Vučak, F. Thorburn, P. R. Murcia, R. Gunson, M. Palmarini, and J. Hughes, "DisCVR: rapid viral diagnosis from high-throughput sequencing data.," Virus Evol, vol. 5, p. vez033, 2019.
    [Bibtex]
    @Article{Maabar:19,
    author = {Maabar, Maha and Davison, Andrew J and Vučak, Matej and Thorburn, Fiona and Murcia, Pablo R and Gunson, Rory and Palmarini, Massimo and Hughes, Joseph},
    title = {{DisCVR}: Rapid viral diagnosis from high-throughput sequencing data.},
    journal = {{Virus Evol}},
    year = {2019},
    volume = {5},
    pages = {vez033},
    abstract = {High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample -mers (twenty-two nucleotide sequences) to -mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.},
    doi = {10.1093/ve/vez033},
    issue = {2},
    keywords = {diagnosis; high-throughput sequencing; k-mer; virus},
    pmid = {31528358},
    }
  • [DOI] S. Dellicour, C. Troupin, F. Jahanbakhsh, A. Salama, S. Massoudi, M. K. Moghaddam, G. Baele, P. Lemey, A. Gholami, and H. Bourhy, "Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - application to rabies virus spread in Iran.," Mol Ecol, 2019.
    [Bibtex]
    @Article{Dellicour:19,
    author = {Dellicour, Simon and Troupin, Cécile and Jahanbakhsh, Fatemeh and Salama, Akram and Massoudi, Siamak and Moghaddam, Madjid K and Baele, Guy and Lemey, Philippe and Gholami, Alireza and Bourhy, Hervé},
    title = {Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in {I}ran.},
    journal = {{Mol Ecol}},
    year = {2019},
    abstract = {Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.},
    doi = {10.1111/mec.15222},
    keywords = {Iran; dogs; molecular epidemiology; phylogeography; rabies},
    pmid = {31535448},
    }
  • [DOI] S. Modha, J. Hughes, G. Bianco, H. M. Ferguson, B. Helm, L. Tong, G. S. Wilkie, A. Kohl, and E. Schnettler, "Metaviromics reveals unknown viral diversity in the biting midge Culicoides impunctatus," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Modha:19,
    author = {Modha, Sejal and Hughes, Joseph and Bianco, Giovanni and Ferguson, Heather M and Helm, Barbara and Tong, Lily and Wilkie, Gavin S and Kohl, Alain and Schnettler, Esther},
    title = {Metaviromics Reveals Unknown Viral Diversity in the Biting Midge {C}ulicoides impunctatus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Biting midges ( species) are vectors of arboviruses and were responsible for the emergence and spread of (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors.},
    doi = {10.3390/v11090865},
    issue = {9},
    keywords = {Culicoides impunctatus; RNA viruses; metaviromics},
    pmid = {31533247},
    }
  • [DOI] S. Schuster, G. J. Overheul, L. Bauer, F. J. M. van Kuppeveld, and R. P. van Rij, "No evidence for viral small RNA production and antiviral function of Argonaute 2 in human cells.," Sci Rep, vol. 9, p. 13752, 2019.
    [Bibtex]
    @Article{Schuster:19a,
    author = {Schuster, Susan and Overheul, Gijs J and Bauer, Lisa and van Kuppeveld, Frank J M and van Rij, Ronald P},
    title = {No evidence for viral small {RNA} production and antiviral function of {A}rgonaute 2 in human cells.},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    pages = {13752},
    abstract = {RNA interference (RNAi) has strong antiviral activity in a range of animal phyla, but the extent to which RNAi controls virus infection in chordates, and specifically mammals remains incompletely understood. Here we analyze the antiviral activity of RNAi against a number of positive-sense RNA viruses using Argonaute-2 deficient human cells. In line with absence of virus-derived siRNAs, Sindbis virus, yellow fever virus, and encephalomyocarditis virus replicated with similar kinetics in wildtype cells and Argonaute-2 deficient cells. Coxsackievirus B3 (CVB3) carrying mutations in the viral 3A protein, previously proposed to be a virus-encoded suppressor of RNAi in another picornavirus, human enterovirus 71, had a strong replication defect in wildtype cells. However, this defect was not rescued in Argonaute-2 deficient cells, arguing against a role of CVB3 3A as an RNAi suppressor. In agreement, neither infection with wildtype nor 3A mutant CVB3 resulted in small RNA production with the hallmarks of canonical vsiRNAs. Together, our results argue against strong antiviral activity of RNAi under these experimental conditions, but do not exclude that antiviral RNAi may be functional under other cellular, experimental, or physiological conditions in mammals.},
    doi = {10.1038/s41598-019-50287-w},
    issue = {1},
    pmid = {31551491},
    }
  • [DOI] C. Büttner, M. Heer, J. Traichel, M. Schwemmle, and B. Heimrich, "Zika virus-mediated death of hippocampal neurons is independent from maturation state.," Front Cell Neurosci, vol. 13, p. 389, 2019.
    [Bibtex]
    @Article{Büttner:19,
    author = {Büttner, Caroline and Heer, Maxi and Traichel, Jasmin and Schwemmle, Martin and Heimrich, Bernd},
    title = {Zika Virus-Mediated Death of Hippocampal Neurons Is Independent From Maturation State.},
    journal = {{Front Cell Neurosci}},
    year = {2019},
    volume = {13},
    pages = {389},
    abstract = {Zika virus (ZIKV) infection of pregnant women and diaplazental transmission to the fetus is linked to the congenital syndrome of microcephaly in newborns. This neuropathology is believed to result from significant death of neuronal progenitor cells (NPC). Here, we examined the fate of neurons in the developing hippocampus, a brain structure which houses neuronal populations of different maturation states. For this purpose, we infected hippocampal slice cultures from immunocompetent newborn mice with ZIKV and monitored changes in hippocampal architecture. In neurons of all hippocampal subfields ZIKV was detected by immunofluorescence labeling and electron microscopy. This includes pyramidal neurons that maturate during the embryonic phase. In the dentate gyrus, ZIKV could be found in the Cajal-Retzius (CR) cells which belong to the earliest born cortical neurons, but also in granule cells that are predominantly generated postnatally. Intriguingly, virus particles were also present in the correctly outgrowing mossy fiber axons of juvenile granule cells, suggesting that viral infection does not impair region- and layer-specific formation of this projection. ZIKV infection of hippocampal tissue was accompanied by both a profound astrocyte reaction indicating tissue injury and a microglia response suggesting phagocytotic activity. Furthermore, depending on the viral load and incubation time, we observed extensive overall neuronal loss in the cultured hippocampal slice cultures. Thus, we conclude ZIKV can replicate in various neuronal populations and trigger neuronal death independent of the maturation state of infected cells.},
    doi = {10.3389/fncel.2019.00389},
    keywords = {Zika virus; cell death; electron microscopy; hippocampus; organotypic slice culture},
    pmid = {31551711},
    }
  • [DOI] M. T. Jahn, K. Arkhipova, S. M. Markert, C. Stigloher, T. Lachnit, L. Pita, A. Kupczok, M. Ribes, S. T. Stengel, P. Rosenstiel, B. E. Dutilh, and U. Hentschel, "A phage protein aids bacterial symbionts in eukaryote immune evasion.," Cell Host Microbe, 2019.
    [Bibtex]
    @Article{Jahn:19,
    author = {Jahn, Martin T and Arkhipova, Ksenia and Markert, Sebastian M and Stigloher, Christian and Lachnit, Tim and Pita, Lucia and Kupczok, Anne and Ribes, Marta and Stengel, Stephanie T and Rosenstiel, Philip and Dutilh, Bas E and Hentschel, Ute},
    title = {A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.},
    journal = {{Cell Host Microbe}},
    year = {2019},
    abstract = {Phages are increasingly recognized as important members of host-associated microbiomes, with a vast genomic diversity. The new frontier is to understand how phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we use marine sponges as a model to investigate the interplay between phages, bacterial symbionts, and eukaryotic hosts. Using viral metagenomics, we find that sponges, although massively filtering seawater, harbor species-specific and even individually unique viral signatures that are taxonomically distinct from other environments. We further discover a symbiont phage-encoded ankyrin-domain-containing protein, which is widely spread in phages of many host-associated contexts including human. We confirm in macrophage infection assays that the ankyrin protein (ANKp) modulates the eukaryotic host immune response against bacteria. We predict that the role of ANKp in nature is to facilitate coexistence in the tripartite interplay between phages, symbionts, and sponges and possibly many other host-microbe associations.},
    doi = {10.1016/j.chom.2019.08.019},
    keywords = {ankyrin; community ecology; immune evasion; innate immunity; marine sponge; phage; symbiosis; viromics},
    pmid = {31561965},
    }
  • [DOI] R. Jones, S. Lessoued, K. Meier, S. Devignot, S. Barata-García, M. Mate, G. Bragagnolo, F. Weber, M. Rosenthal, and J. Reguera, "Structure and function of the Toscana virus cap-snatching endonuclease.," Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Jones:19,
    author = {Jones, Rhian and Lessoued, Sana and Meier, Kristina and Devignot, Stéphanie and Barata-García, Sergio and Mate, Maria and Bragagnolo, Gabriel and Weber, Friedemann and Rosenthal, Maria and Reguera, Juan},
    title = {Structure and function of the {T}oscana virus cap-snatching endonuclease.},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    abstract = {Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important human pathogens such as Rift Valley fever virus (RVFV). Here, we carried out a structural and functional characterization of the TOSV cap-snatching endonuclease, an N terminal domain of the viral polymerase (L protein) that provides capped 3'OH primers for transcription. We report TOSV endonuclease crystal structures in the apo form, in complex with a di-ketoacid inhibitor (DPBA) and in an intermediate state of inhibitor release, showing details on substrate binding and active site dynamics. The structure reveals substantial folding rearrangements absent in previously reported cap-snatching endonucleases. These include the relocation of the N terminus and the appearance of new structural motifs important for transcription and replication. The enzyme shows high activity rates comparable to other His+ cap-snatching endonucleases. Moreover, the activity is dependent on conserved residues involved in metal ion and substrate binding. Altogether, these results bring new light on the structure and function of cap-snatching endonucleases and pave the way for the development of specific and broad-spectrum antivirals.},
    doi = {10.1093/nar/gkz838},
    pmid = {31584100},
    }
  • [DOI] L. Fries, I. Cho, V. Krähling, S. K. Fehling, T. Strecker, S. Becker, J. W. Hooper, S. A. Kwilas, S. Agrawal, J. Wen, M. Lewis, A. Fix, N. Thomas, D. Flyer, G. Smith, and G. Glenn, "A randomized, blinded, dose-ranging trial of an Ebola virus glycoprotein (EBOV GP) nanoparticle vaccine with Matrix-M™ adjuvant in healthy adults.," J Infect Dis, 2019.
    [Bibtex]
    @Article{Fries:19,
    author = {Fries, Louis and Cho, Iksung and Krähling, Verena and Fehling, Sarah K and Strecker, Thomas and Becker, Stephan and Hooper, Jay W and Kwilas, Steven A and Agrawal, Sapeckshita and Wen, Judy and Lewis, Maggie and Fix, Amy and Thomas, Nigel and Flyer, David and Smith, Gale and Glenn, Gregory},
    title = {A Randomized, Blinded, Dose-Ranging Trial of an {E}bola Virus Glycoprotein ({EBOV GP}) Nanoparticle Vaccine with {Matrix-M}\™ Adjuvant in Healthy Adults.},
    journal = {{J Infect Dis}},
    year = {2019},
    abstract = {Ebola virus (EBOV) epidemics pose a major public health risk. There currently is no licensed human vaccine against EBOV. The safety and immunogenicity of a recombinant EBOV glycoprotein (GP) nanoparticle vaccine formulated with or without Matrix-M™ adjuvant were evaluated to support vaccine development. A phase 1, placebo-controlled, dose-escalation trial was conducted in 230 healthy adults to evaluate 4 EBOV GP antigen doses as single- or 2-dose regimens with or without adjuvant. Safety and immunogenicity were assessed through 1-year post-dosing. All EBOV GP vaccine formulations were well tolerated. Receipt of 2 doses of EBOV GP with adjuvant showed a rapid increase in anti-EBOV GP IgG titers with peak titers observed on Day 35 representing 498- to 754-fold increases from baseline; no evidence of an antigen dose-response was observed. Serum EBOV-neutralizing and binding antibodies using wild-type ZEBOV or pseudovirion assays were 3- to 9-fold higher among recipients of 2-dose EBOV GP with adjuvant, compared with placebo on Day 35, which persisted through 1 year. EBOV GP vaccine with Matrix-M adjuvant is well tolerated and elicits a robust and persistent immune response. These data suggest that further development of this candidate vaccine for prevention of EBOV disease is warranted. ClinicalTrials.gov [NCT02370589]; anzctr.org.au [EBOV-H-101].},
    doi = {10.1093/infdis/jiz518},
    keywords = {Ebola virus; Matrix-M adjuvant; glycoprotein; nanoparticle vaccine},
    pmid = {31603201},
    }
  • [DOI] S. A. Ehrhardt, M. Zehner, V. Krähling, H. Cohen-Dvashi, C. Kreer, N. Elad, H. Gruell, M. S. Ercanoglu, P. Schommers, L. Gieselmann, R. Eggeling, C. Dahlke, T. Wolf, N. Pfeifer, M. M. Addo, R. Diskin, S. Becker, and F. Klein, "Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV.," Nat Med, 2019.
    [Bibtex]
    @Article{Ehrhardt:19,
    author = {Ehrhardt, Stefanie A and Zehner, Matthias and Krähling, Verena and Cohen-Dvashi, Hadas and Kreer, Christoph and Elad, Nadav and Gruell, Henning and Ercanoglu, Meryem S and Schommers, Philipp and Gieselmann, Lutz and Eggeling, Ralf and Dahlke, Christine and Wolf, Timo and Pfeifer, Nico and Addo, Marylyn M and Diskin, Ron and Becker, Stephan and Klein, Florian},
    title = {Polyclonal and convergent antibody response to {E}bola virus vaccine {rVSV}-{ZEBOV}.},
    journal = {{Nat Med}},
    year = {2019},
    abstract = {Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC). Here we examine the humoral immune response in a subset of human volunteers enrolled in a phase 1 rVSV-ZEBOV vaccination trial by performing comprehensive single B cell and electron microscopy structure analyses. Four studied vaccinees show polyclonal, yet reproducible and convergent B cell responses with shared sequence characteristics. EBOV-targeting antibodies cross-react with other Ebolavirus species, and detailed epitope mapping revealed overlapping target epitopes with antibodies isolated from EVD survivors. Moreover, in all vaccinees, we detected highly potent EBOV-neutralizing antibodies with activities comparable or superior to the monoclonal antibodies currently used in clinical trials. These include antibodies combining the IGHV3-15/IGLV1-40 immunoglobulin gene segments that were identified in all investigated individuals. Our findings will help to evaluate and direct current and future vaccination strategies and offer opportunities for novel EVD therapies.},
    doi = {10.1038/s41591-019-0602-4},
    pmid = {31591605},
    }
  • [DOI] A. Tamošiūnaitė, S. Weber, T. Schippers, A. Franke, Z. Xu, M. Jenckel, F. Pfaff, D. Hoffmann, M. Newell, K. B. Tischer, M. Beer, and N. Osterrieder, "What a difference a gene makes - identification of virulence factors of Cowpox virus.," J Virol, 2019.
    [Bibtex]
    @Article{Tamosiunaite:19,
    author = {Tamošiūnaitė, Aistė and Weber, Saskia and Schippers, Timo and Franke, Annika and Xu, Zhiyong and Jenckel, Maria and Pfaff, Florian and Hoffmann, Donata and Newell, Maegan and Tischer, B Karsten and Beer, Martin and Osterrieder, Nikolaus},
    title = {What a difference a gene makes - identification of virulence factors of {C}owpox virus.},
    journal = {{J Virol}},
    year = {2019},
    abstract = {Cowpox virus (CPXV) is a zoonotic Orthopoxvirus (OPV) that causes spill-over infections from their animal hosts to humans. In 2009, several human CPXV cases occurred through transmission from pet rats. An isolate from a diseased rat, RatPox09, exhibited significantly increased virulence in Wistar rats and caused high mortality when compared to the mildly virulent laboratory strain Brighton Red (BR). RatPox09 encodes four genes which are absent in the BR genome. We hypothesized that their gene products could be major factors influencing its high virulence. To address this hypothesis, we employed several BR/RatPox09 chimeric viruses using Red-mediated mutagenesis to generate BR knock-in mutants with single or multiple insertions of the respective RatPox09 genes based on BR. High-throughput sequencing was used to verify the genomic integrity of all recombinant viruses; and transcriptomic analyses confirmed the expression profile of genes adjacent to the ones modified be unaltered. While growth kinetics were comparable to those of BR and RatPox09, we discovered that a knock-in BR mutant containing the four RatPox09-specific genes was as virulent as the RatPox09 isolate causing death in over 75% of infected Wistar rats. Unexpectedly, the insertion of gCPXV0030 (7tGP) alone into the BR genome resulted in significantly higher clinical scores and lower survival rates matching that of RatPox09. The insertion of gCPXV0284 encoding the BTB domain protein D7L also increased the virulence of BR, while the other two ORFs failed to rescue virulence independently. In summary, our results confirmed our hypothesis that a relatively small set of four genes can contribute significantly to CPXV virulence in the natural rat animal model. With the cessation of vaccination against smallpox, and its assumed cross-protectivity against other OPV infections, waning immunity could open up new niches for related poxviruses. Therefore, the identification of virulence mechanisms in CPXV is of general interest. Here, we aimed to identify virulence markers in an experimental rodent CPXV infection model using bacterial artificial chromosome (BAC)-based virus recombineering. We focused our work on the recent zoonotic CPXV isolate RatPox09, which is highly pathogenic in Wistar rats when compared to the avirulent BR reference strain. In several animal studies, we were able to identify a novel set of CPXV virulence genes. Two of the identified virulence genes, encoding a putative BTB/POZ protein (CPXVD7L) and a B22R-family protein (CPXV7tGP), respectively, have not yet been described to be involved in CPXV virulence. Our results also show that single genes can significantly affect virulence, thus facilitating adaptation to other hosts.},
    doi = {10.1128/JVI.01625-19},
    pmid = {31645446},
    }
  • [DOI] B. F. A. von Meijenfeldt, K. Arkhipova, D. D. Cambuy, F. H. Coutinho, and B. E. Dutilh, "Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.," Genome Biol, vol. 20, p. 217, 2019.
    [Bibtex]
    @Article{Meijenfeldt:19,
    author = {von Meijenfeldt, F A Bastiaan and Arkhipova, Ksenia and Cambuy, Diego D and Coutinho, Felipe H and Dutilh, Bas E},
    title = {Robust taxonomic classification of uncharted microbial sequences and bins with {CAT} and {BAT}.},
    journal = {{Genome Biol}},
    year = {2019},
    volume = {20},
    pages = {217},
    abstract = {Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.},
    doi = {10.1186/s13059-019-1817-x},
    issue = {1},
    pmid = {31640809},
    }
  • [DOI] E. Sloan, M. Alenquer, L. Chung, S. Clohisey, A. M. Dinan, R. J. Gifford, Q. Gu, N. Irigoyen, J. D. Jones, I. van Knippenberg, V. Rezelj, B. Wang, H. M. Wise, M. J. Amorim, K. J. Baillie, I. Brierley, P. Digard, A. E. Firth, M. K. MacLeod, and E. Hutchinson, "Upstream translation initiation expands the coding capacity of segmented negative-strand RNA viruses," bioRxiv, 2019.
    [Bibtex]
    @Article{Sloan:19,
    author = {Elizabeth Sloan and Marta Alenquer and Liliane Chung and Sara Clohisey and Adam M. Dinan and Robert J. Gifford and Quan Gu and Nerea Irigoyen and Joshua D. Jones and Ingeborg van Knippenberg and Veronica Rezelj and Bo Wang and Helen M. Wise and Maria Joao Amorim and J Kenneth Baillie and Ian Brierley and Paul Digard and Andrew E. Firth and Megan K. MacLeod and Edward Hutchinson},
    title = {Upstream translation initiation expands the coding capacity of segmented negative-strand {RNA} viruses},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/795815},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Serdari, E. Kostaki, D. Paraskevis, A. Stamatakis, and P. Kapli, "Automated, phylogeny-based genotype delimitation of the hepatitis viruses HBV and HCV.," PeerJ, vol. 7, p. e7754, 2019.
    [Bibtex]
    @Article{Serdari:19,
    author = {Serdari, Dora and Kostaki, Evangelia-Georgia and Paraskevis, Dimitrios and Stamatakis, Alexandros and Kapli, Paschalia},
    title = {Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses {HBV} and {HCV}.},
    journal = {{PeerJ}},
    year = {2019},
    volume = {7},
    pages = {e7754},
    abstract = {The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.},
    doi = {10.7717/peerj.7754},
    keywords = {DNA-barcoding; HBV; HCV; Phylogeny; Species delimitation; Virus},
    pmid = {31667012},
    }
  • [DOI] U. Fahnøe, A. G. Pedersen, C. M. Johnston, R. J. Orton, D. Höper, M. Beer, J. Bukh, G. J. Belsham, and T. B. Rasmussen, "Virus adaptation and selection following challenge of animals vaccinated against classical swine fever virus.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Fahnoe:19,
    author = {Fahnøe, Ulrik and Pedersen, Anders Gorm and Johnston, Camille Melissa and Orton, Richard J and Höper, Dirk and Beer, Martin and Bukh, Jens and Belsham, Graham J and Rasmussen, Thomas Bruun},
    title = {Virus Adaptation and Selection Following Challenge of Animals Vaccinated against Classical Swine Fever Virus.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Vaccines against classical swine fever have proven very effective in protecting pigs from this deadly disease. However, little is known about how vaccination impacts the selective pressures acting on the classical swine fever virus (CSFV). Here we use high-throughput sequencing of viral genomes to investigate evolutionary changes in virus populations following the challenge of naïve and vaccinated pigs with the highly virulent CSFV strain "Koslov". The challenge inoculum contained an ensemble of closely related viral sequences, with three major haplotypes being present, termed A, B, and C. After the challenge, the viral haplotype A was preferentially located within the tonsils of naïve animals but was highly prevalent in the sera of all vaccinated animals. We find that the viral population structure in naïve pigs after infection is very similar to that in the original inoculum. In contrast, the viral population in vaccinated pigs, which only underwent transient low-level viremia, displayed several distinct changes including the emergence of 16 unique non-synonymous single nucleotide polymorphisms (SNPs) that were not detectable in the challenge inoculum. Further analysis showed a significant loss of heterogeneity and an increasing positive selection acting on the virus populations in the vaccinated pigs. We conclude that vaccination imposes a strong selective pressure on viruses that subsequently replicate within the vaccinated animal.},
    doi = {10.3390/v11100932},
    issue = {10},
    keywords = {CSFV; classical swine fever virus; deep sequencing; haplotype selection; vaccination; viral populations; virulence; virus evolution},
    pmid = {31658773},
    }
  • [DOI] S. Strubbia, J. Schaeffer, B. B. Oude Munnink, A. Besnard, M. V. T. Phan, D. F. Nieuwenhuijse, M. de Graaf, C. M. E. Schapendonk, C. Wacrenier, M. Cotten, M. P. G. Koopmans, and F. S. Le Guyader, "Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters.," Front Microbiol, vol. 10, p. 2394, 2019.
    [Bibtex]
    @Article{Strubbia:19,
    author = {Strubbia, Sofia and Schaeffer, Julien and Oude Munnink, Bas B and Besnard, Alban and Phan, My V T and Nieuwenhuijse, David F and de Graaf, Miranda and Schapendonk, Claudia M E and Wacrenier, Candice and Cotten, Matthew and Koopmans, Marion P G and Le Guyader, Françoise S},
    title = {Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters.},
    journal = {{Front Microbiol}},
    year = {2019},
    volume = {10},
    pages = {2394},
    abstract = {Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.},
    doi = {10.3389/fmicb.2019.02394},
    keywords = {metagenomic sequencing; metavirome; norovirus; oysters; sewage},
    pmid = {31681246},
    }
  • [DOI] D. Ji, P. Putzel, Y. Qian, I. Chang, A. Mandava, R. H. Scheuermann, J. D. Bui, H. Wang, and P. Smyth, "Machine learning of discriminative gate locations for clinical diagnosis.," Cytometry A, 2019.
    [Bibtex]
    @Article{Ji:19,
    author = {Ji, Disi and Putzel, Preston and Qian, Yu and Chang, Ivan and Mandava, Aishwarya and Scheuermann, Richard H and Bui, Jack D and Wang, Huan-You and Smyth, Padhraic},
    title = {Machine Learning of Discriminative Gate Locations for Clinical Diagnosis.},
    journal = {{Cytometry A}},
    year = {2019},
    abstract = {High-throughput single-cell cytometry technologies have significantly improved our understanding of cellular phenotypes to support translational research and the clinical diagnosis of hematological and immunological diseases. However, subjective and ad hoc manual gating analysis does not adequately handle the increasing volume and heterogeneity of cytometry data for optimal diagnosis. Prior work has shown that machine learning can be applied to classify cytometry samples effectively. However, many of the machine learning classification results are either difficult to interpret without using characteristics of cell populations to make the classification, or suboptimal due to the use of inaccurate cell population characteristics derived from gating boundaries. To date, little has been done to optimize both the gating boundaries and the diagnostic accuracy simultaneously. In this work, we describe a fully discriminative machine learning approach that can simultaneously learn feature representations (e.g., combinations of coordinates of gating boundaries) and classifier parameters for optimizing clinical diagnosis from cytometry measurements. The approach starts from an initial gating position and then refines the position of the gating boundaries by gradient descent until a set of globally-optimized gates across different samples are achieved. The learning procedure is constrained by regularization terms encoding domain knowledge that encourage the algorithm to seek interpretable results. We evaluate the proposed approach using both simulated and real data, producing classification results on par with those generated via human expertise, in terms of both the positions of the gating boundaries and the diagnostic accuracy. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.},
    doi = {10.1002/cyto.a.23906},
    keywords = {automated gating; cancer diagnosis; chronic lymphocytic leukemia; discriminative gates; flow cytometry; supervised machine learning},
    pmid = {31691488},
    }
  • [DOI] A. L. Mitchell, A. Almeida, M. Beracochea, M. Boland, J. Burgin, G. Cochrane, M. R. Crusoe, V. Kale, S. C. Potter, L. J. Richardson, E. Sakharova, M. Scheremetjew, A. Korobeynikov, A. Shlemov, O. Kunyavskaya, A. Lapidus, and R. D. Finn, "MGnify: the microbiome analysis resource in 2020.," Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Mitchell:19,
    author = {Mitchell, Alex L and Almeida, Alexandre and Beracochea, Martin and Boland, Miguel and Burgin, Josephine and Cochrane, Guy and Crusoe, Michael R and Kale, Varsha and Potter, Simon C and Richardson, Lorna J and Sakharova, Ekaterina and Scheremetjew, Maxim and Korobeynikov, Anton and Shlemov, Alex and Kunyavskaya, Olga and Lapidus, Alla and Finn, Robert D},
    title = {{MGnify}: the microbiome analysis resource in 2020.},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    abstract = {MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.},
    doi = {10.1093/nar/gkz1035},
    pmid = {31696235},
    }
  • [DOI] A. Hawksworth, M. Jayachander, S. Hester, S. Mohammed, and E. Hutchinson, "Proteomics as a tool for live attenuated influenza vaccine characterisation.," Vaccine, 2019.
    [Bibtex]
    @Article{Hawksworth:19,
    author = {Hawksworth, Amy and Jayachander, Mahesh and Hester, Svenja and Mohammed, Shabaz and Hutchinson, Edward},
    title = {Proteomics as a tool for live attenuated influenza vaccine characterisation.},
    journal = {Vaccine},
    year = {2019},
    abstract = {Many viral vaccines, including the majority of influenza vaccines, are grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation. For influenza vaccines this process is well established, but the viral strains recommended for use in vaccines are updated frequently. As viral strains can have different growth properties and responses to purification, these updates risk changes in the composition of the vaccine product. Changes of this sort are hard to assess, as influenza virions are complex structures containing variable ratios of both viral and host proteins. To address this, we used liquid chromatography and tandem mass spectrometry (LC-MS/MS), a flexible and sensitive method ideally suited to identifying and quantifying the proteins present in complex mixtures. By applying LC-MS/MS to the pilot scale manufacturing process of the live attenuated influenza vaccine (LAIV) FluMist® Quadrivalent vaccine (AstraZeneca), we were able to obtain a detailed description of how viral and host proteins are removed or retained at each stage of LAIV purification. LC-MS/MS allowed us to quantify the removal of individual host proteins at each stage of the purification process, confirming that LAIV purification efficiently depletes the majority of host proteins and identifying the small subset of host proteins which are associated with intact virions. LC-MS/MS also identified substantial differences in the retention of the immunosuppressive viral protein NS1 in purified virions. Finally, LC-MS/MS allowed us to detect subtle variations in the LAIV production process, both upstream of purification and during downstream purification stages. This demonstrates the potential utility of LC-MS/MS for optimising the purification of complex biological mixtures and shows that it is a promising approach for process optimisation in a wide variety of vaccine manufacturing platforms.},
    doi = {10.1016/j.vaccine.2019.10.082},
    keywords = {Influenza virus; LAIV; Live-attenuated influenza vaccine; Mass spectrometry; Vaccine manufacturing},
    pmid = {31708181},
    }
  • [DOI] A. W. Bronkhorst, R. Vogels, G. J. Overheul, B. Pennings, V. Gausson-Dorey, P. Miesen, and R. P. van Rij, "A DNA virus-encoded immune antagonist fully masks the potent antiviral activity of RNAi in Drosophila.," Proc Natl Acad Sci USA, 2019.
    [Bibtex]
    @Article{Bronkhorst:19,
    author = {Bronkhorst, Alfred W and Vogels, Rob and Overheul, Gijs J and Pennings, Bas and Gausson-Dorey, Valérie and Miesen, Pascal and van Rij, Ronald P},
    title = {A {DNA} virus-encoded immune antagonist fully masks the potent antiviral activity of {RNAi} in {D}rosophila.},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2019},
    abstract = {Coevolution of viruses and their hosts may lead to viral strategies to avoid, evade, or suppress antiviral immunity. An example is antiviral RNA interference (RNAi) in insects: the host RNAi machinery processes viral double-stranded RNA into small interfering RNAs (siRNAs) to suppress viral replication, whereas insect viruses encode suppressors of RNAi, many of which inhibit viral small interfering RNA (vsiRNA) production. Yet, many studies have analyzed viral RNAi suppressors in heterologous systems, due to the lack of experimental systems to manipulate the viral genome of interest, raising questions about in vivo functions of RNAi suppressors. To address this caveat, we generated an RNAi suppressor-defective mutant of invertebrate iridescent virus 6 (IIV6), a large DNA virus in which we previously identified the 340R protein as a suppressor of RNAi. Loss of 340R did not affect vsiRNA production, indicating that 340R binds siRNA duplexes to prevent RNA-induced silencing complex assembly. Indeed, vsiRNAs were not efficiently loaded into Argonaute 2 during wild-type IIV6 infection. Moreover, IIV6 induced a limited set of mature microRNAs in a 340R-dependent manner, most notably miR-305-3p, which we attribute to stabilization of the miR-305-5p:3p duplex by 340R. The IIV6 340R deletion mutant did not have a replication defect in cells, but was strongly attenuated in adult This in vivo replication defect was completely rescued in RNAi mutant flies, indicating that 340R is a bona fide RNAi suppressor, the absence of which uncovers a potent antiviral immune response that suppresses virus accumulation ∼100-fold. Together, our work indicates that viral RNAi suppressors may completely mask antiviral immunity.},
    doi = {10.1073/pnas.1909183116},
    keywords = {RNAi; antiviral defense; insect immunity; insect virus; viral suppressor of RNAi},
    pmid = {31712431},
    }
  • [DOI] T. P. Loka, S. H. Tausch, and B. Y. Renard, "Reliable variant calling during runtime of Illumina sequencing.," Sci Rep, vol. 9, p. 16502, 2019.
    [Bibtex]
    @Article{Loka:19,
    author = {Loka, Tobias P and Tausch, Simon H and Renard, Bernhard Y},
    title = {Reliable variant calling during runtime of {I}llumina sequencing.},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    pages = {16502},
    abstract = {The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby, our new algorithm allows for accurate read mapping results for intermediate cycles and supports large reference genomes such as the complete human reference. This enables the combination of real-time read mapping results with complex follow-up analysis. In this study, we showed the accuracy and scalability of our approach by applying real-time read mapping and variant calling to seven publicly available human whole exome sequencing datasets. Thereby, up to 89% of all detected SNPs were already identified after 40 sequencing cycles while showing similar precision as at the end of sequencing. Final results showed similar accuracy to those of conventional post-hoc analysis methods. When compared to standard routines, our live approach enables considerably faster interventions in clinical applications and infectious disease outbreaks. Besides variant calling, our approach can be adapted for a plethora of other mapping-based analyses.},
    doi = {10.1038/s41598-019-52991-z},
    issue = {1},
    pmid = {31712740},
    }
  • [DOI] A. Fusaro, B. Zecchin, B. Vrancken, C. Abolnik, R. Ademun, A. Alassane, A. Arafa, J. A. Awuni, E. Couacy-Hymann, B. M. '. Coulibaly, N. Gaidet, E. Go-Maro, T. Joannis, S. D. Jumbo, G. Minoungou, C. Meseko, M. M. Souley, D. B. Ndumu, I. Shittu, A. Twabela, A. Wade, L. Wiersma, Y. P. Akpeli, G. Zamperin, A. Milani, P. Lemey, and I. Monne, "Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza.," Nat Commun, vol. 10, p. 5310, 2019.
    [Bibtex]
    @Article{Fusaro:19,
    author = {Fusaro, Alice and Zecchin, Bianca and Vrancken, Bram and Abolnik, Celia and Ademun, Rose and Alassane, Abdou and Arafa, Abdelsatar and Awuni, Joseph Adongo and Couacy-Hymann, Emmanuel and Coulibaly, M ' Bétiégué and Gaidet, Nicolas and Go-Maro, Emilie and Joannis, Tony and Jumbo, Simon Dickmu and Minoungou, Germaine and Meseko, Clement and Souley, Maman Moutari and Ndumu, Deo Birungi and Shittu, Ismaila and Twabela, Augustin and Wade, Abel and Wiersma, Lidewij and Akpeli, Yao P and Zamperin, Gianpiero and Milani, Adelaide and Lemey, Philippe and Monne, Isabella},
    title = {Disentangling the role of {A}frica in the global spread of {H5} highly pathogenic avian influenza.},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    pages = {5310},
    abstract = {The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.},
    doi = {10.1038/s41467-019-13287-y},
    issue = {1},
    pmid = {31757953},
    }
  • [DOI] M. Cacciabue, A. Currá, E. Carrillo, G. König, and M. I. Gismondi, "A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.," Briefings Bioinf, 2019.
    [Bibtex]
    @Article{Cacciabue:19,
    author = {Cacciabue, Marco and Currá, Anabella and Carrillo, Elisa and König, Guido and Gismondi, María Inés},
    title = {A beginner's guide for {FMDV} quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.},
    journal = {{Briefings Bioinf}},
    year = {2019},
    abstract = {Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.},
    doi = {10.1093/bib/bbz086},
    keywords = {Illumina sequencing platform; analysis workflow; haplotype reconstruction; open-source software; sub-consensus SNV; viral quasispecies},
    pmid = {31697321},
    }
  • [DOI] C. Davis, T. Tipton, S. Sabir, C. Aitken, S. Bennett, S. Becker, T. Evans, S. K. Fehling, R. Gunson, Y. Hall, C. Jackson, I. Johanssen, M. P. Kieny, J. McMenamin, E. Spence, T. Strecker, C. Sykes, K. Templeton, F. Thorburn, E. Peters, A. M. Henao Restrepo, B. White, M. Zambon, M. W. Carroll, and E. C. Thomson, "Post-exposure prophylaxis with rVSV-ZEBOV following exposure to a patient with Ebola virus disease relapse in the UK: an operational, safety and immunogenicity report.," Clin Infect Dis, 2019.
    [Bibtex]
    @Article{Davis:19,
    author = {Davis, Chris and Tipton, Tom and Sabir, Suleman and Aitken, Celia and Bennett, Susan and Becker, Stephan and Evans, Tom and Fehling, Sarah Katharina and Gunson, Rory and Hall, Yper and Jackson, Celia and Johanssen, Ingolfur and Kieny, Marie Paule and McMenamin, Jim and Spence, Elizabeth and Strecker, Thomas and Sykes, Catie and Templeton, Kate and Thorburn, Fiona and Peters, Erica and Henao Restrepo, Ana Maria and White, Beth and Zambon, Maria and Carroll, Miles W and Thomson, Emma C},
    title = {Post-exposure prophylaxis with {rVSV-ZEBOV} following exposure to a patient with {E}bola virus disease relapse in the {UK}: an operational, safety and immunogenicity report.},
    journal = {{Clin Infect Dis}},
    year = {2019},
    abstract = {In October 2015, 65 people came into direct contact with a healthcare worker presenting with a late reactivation of Ebola virus disease (EVD) in the UK. Vaccination was offered to 45 individuals with an initial assessment of high exposure risk. Approval for rapid expanded access to the recombinant vesicular stomatitis virus-Zaire Ebola virus vaccine (rVSV-ZEBOV) as an unlicensed emergency medicine was obtained from the relevant authorities. An observational follow-up study was carried out for 1 year following vaccination. 26/45 individuals elected to receive vaccination between October 10th and 11th 2015 following written informed consent. By day 14, 39% had seroconverted, rising to 87% by day 28 and 100% by 3 months, although these responses were not always sustained. Neutralising antibody responses were detectable in 36% by day 14 and 73% at 12 months. Common side effects included fatigue, myalgia, headache, arthralgia and fever. These were positively associated with glycoprotein (GP)-specific T-cell but not IgM or IgG antibody responses. No severe vaccine-related adverse events were reported. No-one exposed to the virus became infected. This paper reports the use of the rVSV-ZEBOV vaccine given as an emergency intervention to individuals exposed to a patient presenting with a late reactivation of EVD. The vaccine was relatively well tolerated but a high percentage developed a fever ≥37.5oC necessitating urgent screening for Ebola virus and a small number developed persistent arthralgia.},
    doi = {10.1093/cid/ciz1165},
    keywords = {Ebola virus; T cell; rVSV-ZEBOV; vaccine},
    pmid = {31784751},
    }
  • [DOI] S. Dellicour, P. Lemey, J. Artois, T. T. Lam, A. Fusaro, I. Monne, G. Cattoli, D. Kuznetsov, I. Xenarios, G. Dauphin, W. Kalpravidh, S. Von Dobschuetz, F. Claes, S. H. Newman, M. A. Suchard, G. Baele, and M. Gilbert, "Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region.," Bioinformatics, 2019.
    [Bibtex]
    @Article{Dellicour:19a,
    author = {Dellicour, Simon and Lemey, Philippe and Artois, Jean and Lam, Tommy T and Fusaro, Alice and Monne, Isabella and Cattoli, Giovanni and Kuznetsov, Dmitry and Xenarios, Ioannis and Dauphin, Gwenaelle and Kalpravidh, Wantanee and Von Dobschuetz, Sophie and Claes, Filip and Newman, Scott H and Suchard, Marc A and Baele, Guy and Gilbert, Marius},
    title = {Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to {H5N1} spread in the {M}ekong region.},
    journal = {{Bioinformatics}},
    year = {2019},
    abstract = {The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences are geo-referenced at broad spatial scale such as, for example, the administrative unit of origin rather than more exact locations (e.g. GPS coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better possibility. We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza (HPAI) H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities. Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10. Supplementary data are available at Bioinformatics online and on figshare.com.},
    doi = {10.1093/bioinformatics/btz882},
    pmid = {31790143},
    }
  • [DOI] N. R. Faria, N. Vidal, J. Lourenco, J. Raghwani, K. C. E. Sigaloff, A. J. Tatem, D. A. M. van de Vijver, A. Pineda-Peña, R. Rose, C. L. Wallis, S. Ahuka-Mundeke, J. Muyembe-Tamfum, J. Muwonga, M. A. Suchard, T. F. Rinke de Wit, R. L. Hamers, N. Ndembi, G. Baele, M. Peeters, O. G. Pybus, P. Lemey, and S. Dellicour, "Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.," PLoS Pathog, vol. 15, p. e1007976, 2019.
    [Bibtex]
    @Article{Faria:19,
    author = {Faria, Nuno R and Vidal, Nicole and Lourenco, José and Raghwani, Jayna and Sigaloff, Kim C E and Tatem, Andy J and van de Vijver, David A M and Pineda-Peña, Andrea-Clemencia and Rose, Rebecca and Wallis, Carole L and Ahuka-Mundeke, Steve and Muyembe-Tamfum, Jean-Jacques and Muwonga, Jérémie and Suchard, Marc A and Rinke de Wit, Tobias F and Hamers, Raph L and Ndembi, Nicaise and Baele, Guy and Peeters, Martine and Pybus, Oliver G and Lemey, Philippe and Dellicour, Simon},
    title = {Distinct rates and patterns of spread of the major {HIV}-1 subtypes in {C}entral and {E}ast {A}frica.},
    journal = {{PLoS Pathog}},
    year = {2019},
    volume = {15},
    pages = {e1007976},
    abstract = {Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.},
    doi = {10.1371/journal.ppat.1007976},
    issue = {12},
    pmid = {31809523},
    }
  • [DOI] P. A. de Jonge, B. F. A. von Meijenfeldt, L. E. van Rooijen, S. J. J. Brouns, and B. E. Dutilh, "Evolution of BACON domain tandem repeats in crAssphage and novel gut bacteriophage lineages.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Jonge:19a,
    author = {Jonge, Patrick A de and Meijenfeldt, F A Bastiaan von and Rooijen, Laura E van and Brouns, Stan J J and Dutilh, Bas E},
    title = {Evolution of {BACON} Domain Tandem Repeats in cr{A}ssphage and Novel Gut Bacteriophage Lineages.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a -associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.},
    doi = {10.3390/v11121085},
    issue = {12},
    keywords = {BACON domain; Bacteroides-associated carbohydrate-binding often N-terminal domain; bacteriophage; crAssphage; genome evolution; gut virome; metagenomics; phage tail-associated protein domains; protein domain tandem arrays},
    pmid = {31766550},
    }
  • [DOI] S. Käfer, S. Paraskevopoulou, F. Zirkel, N. Wieseke, A. Donath, M. Petersen, T. C. Jones, S. Liu, X. Zhou, M. Middendorf, S. Junglen, B. Misof, and C. Drosten, "Re-assessing the diversity of negative strand RNA viruses in insects.," PLoS Pathog, vol. 15, p. e1008224, 2019.
    [Bibtex]
    @Article{Käfer:19,
    author = {Käfer, Simon and Paraskevopoulou, Sofia and Zirkel, Florian and Wieseke, Nicolas and Donath, Alexander and Petersen, Malte and Jones, Terry C and Liu, Shanlin and Zhou, Xin and Middendorf, Martin and Junglen, Sandra and Misof, Bernhard and Drosten, Christian},
    title = {Re-assessing the diversity of negative strand {RNA} viruses in insects.},
    journal = {{PLoS Pathog}},
    year = {2019},
    volume = {15},
    pages = {e1008224},
    abstract = {The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.},
    doi = {10.1371/journal.ppat.1008224},
    issue = {12},
    pmid = {31830128},
    }
  • [DOI] M. Wąchalska, M. Graul, P. Praest, R. D. Luteijn, A. W. Babnis, E. J. H. J. Wiertz, K. Bieńkowska-Szewczyk, and A. D. Lipińska, "Fluorescent TAP as a platform for virus-induced degradation of the antigenic peptide transporter.," Cells, vol. 8, 2019.
    [Bibtex]
    @Article{Wachalska:19,
    author = {Wąchalska, Magda and Graul, Małgorzata and Praest, Patrique and Luteijn, Rutger D and Babnis, Aleksandra W and Wiertz, Emmanuel J H J and Bieńkowska-Szewczyk, Krystyna and Lipińska, Andrea D},
    title = {Fluorescent {TAP} as a Platform for Virus-Induced Degradation of the Antigenic Peptide Transporter.},
    journal = {Cells},
    year = {2019},
    volume = {8},
    abstract = {Transporter associated with antigen processing (TAP), a key player in the major histocompatibility complex class I-restricted antigen presentation, makes an attractive target for viruses that aim to escape the immune system. Mechanisms of TAP inhibition vary among virus species. Bovine herpesvirus 1 (BoHV-1) is unique in its ability to target TAP for proteasomal degradation following conformational arrest by the UL49.5 gene product. The exact mechanism of TAP removal still requires elucidation. For this purpose, a TAP-GFP (green fluorescent protein) fusion protein is instrumental, yet GFP-tagging may affect UL49.5-induced degradation. Therefore, we constructed a series of TAP-GFP variants using various linkers to obtain an optimal cellular fluorescent TAP platform. Mel JuSo (MJS) cells with CRISPR/Cas9 TAP1 or TAP2 knockouts were reconstituted with TAP-GFP constructs. Our results point towards a critical role of GFP localization on fluorescent properties of the fusion proteins and, in concert with the type of a linker, on the susceptibility to virally-induced inhibition and degradation. The fluorescent TAP platform was also used to re-evaluate TAP stability in the presence of other known viral TAP inhibitors, among which only UL49.5 was able to reduce TAP levels. Finally, we provide evidence that BoHV-1 UL49.5-induced TAP removal is p97-dependent, which indicates its degradation via endoplasmic reticulum-associated degradation (ERAD).},
    doi = {10.3390/cells8121590},
    issue = {12},
    keywords = {BoHV-1 UL49.5; MHC I; TAP-GFP; antigen presentation; fluorescent TAP platform; immune evasion},
    pmid = {31817841},
    }
  • [DOI] K. S. Makarova, Y. I. Wolf, J. Iranzo, S. A. Shmakov, O. S. Alkhnbashi, S. J. J. Brouns, E. Charpentier, D. Cheng, D. H. Haft, P. Horvath, S. Moineau, F. J. M. Mojica, D. Scott, S. A. Shah, V. Siksnys, M. P. Terns, Č. Venclovas, M. F. White, A. F. Yakunin, W. Yan, F. Zhang, R. A. Garrett, R. Backofen, J. van der Oost, R. Barrangou, and E. V. Koonin, "Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.," Nat Rev Microbiol, 2019.
    [Bibtex]
    @Article{Makarova:19,
    author = {Makarova, Kira S and Wolf, Yuri I and Iranzo, Jaime and Shmakov, Sergey A and Alkhnbashi, Omer S and Brouns, Stan J J and Charpentier, Emmanuelle and Cheng, David and Haft, Daniel H and Horvath, Philippe and Moineau, Sylvain and Mojica, Francisco J M and Scott, David and Shah, Shiraz A and Siksnys, Virginijus and Terns, Michael P and Venclovas, Česlovas and White, Malcolm F and Yakunin, Alexander F and Yan, Winston and Zhang, Feng and Garrett, Roger A and Backofen, Rolf and van der Oost, John and Barrangou, Rodolphe and Koonin, Eugene V},
    title = {Evolutionary classification of {CRISPR-Cas }systems: a burst of class 2 and derived variants.},
    journal = {{Nat Rev Microbiol}},
    year = {2019},
    abstract = {The number and diversity of known CRISPR-Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR-Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR-Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR-Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR-Cas.},
    doi = {10.1038/s41579-019-0299-x},
    pmid = {31857715},
    }
  • [DOI] R. Muñoz-Moreno, C. Martínez-Romero, D. Blanco-Melo, C. V. Forst, R. Nachbagauer, A. A. Benitez, I. Mena, S. Aslam, V. Balasubramaniam, I. Lee, M. Panis, J. Ayllón, D. Sachs, M. Park, F. Krammer, B. R. tenOever, and A. García-Sastre, "Viral fitness landscapes in diverse host species reveal multiple evolutionary lines for the NS1 gene of influenza A viruses.," Cell Rep, vol. 29, p. 3997–4009.e5, 2019.
    [Bibtex]
    @Article{Muñoz-Moreno:19,
    author = {Muñoz-Moreno, Raquel and Martínez-Romero, Carles and Blanco-Melo, Daniel and Forst, Christian V and Nachbagauer, Raffael and Benitez, Asiel Arturo and Mena, Ignacio and Aslam, Sadaf and Balasubramaniam, Vinod and Lee, Ilseob and Panis, Maryline and Ayllón, Juan and Sachs, David and Park, Man-Seong and Krammer, Florian and tenOever, Benjamin R and García-Sastre, Adolfo},
    title = {Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the {NS1} Gene of Influenza {A} Viruses.},
    journal = {{Cell Rep}},
    year = {2019},
    volume = {29},
    pages = {3997--4009.e5},
    abstract = {Influenza A viruses (IAVs) have a remarkable tropism in their ability to circulate in both mammalian and avian species. The IAV NS1 protein is a multifunctional virulence factor that inhibits the type I interferon host response through a myriad of mechanisms. How NS1 has evolved to enable this remarkable property across species and its specific impact in the overall replication, pathogenicity, and host preference remain unknown. Here we analyze the NS1 evolutionary landscape and host tropism using a barcoded library of recombinant IAVs. Results show a surprisingly great variety of NS1 phenotypes according to their ability to replicate in different hosts. The IAV NS1 genes appear to have taken diverse and random evolutionary pathways within their multiple phylogenetic lineages. In summary, the high evolutionary plasticity of this viral protein underscores the ability of IAVs to adapt to multiple hosts and aids in our understanding of its global prevalence.},
    doi = {10.1016/j.celrep.2019.11.070},
    issue = {12},
    keywords = {IFN response; NS1 evolution; barcoded library; influenza virus; innate immunity; orthomyxovirus},
    pmid = {31851929},
    }
  • [DOI] K. Ciminski and M. Schwemmle, "Bat-borne influenza A viruses: an awakening.," Cold Spring Harb Perspect Med, 2019.
    [Bibtex]
    @Article{Ciminski:19,
    author = {Ciminski, Kevin and Schwemmle, Martin},
    title = {Bat-Borne Influenza {A} Viruses: An Awakening.},
    journal = {{Cold Spring Harb Perspect Med}},
    year = {2019},
    abstract = {Influenza A viruses (IAVs) originating from aquatic waterfowl recurrently cross interspecies barriers, which is greatly facilitated by utilizing cell surface-exposed monosaccharide sialic acids located on vertebrate cells as a universal host cell receptor. These glycan structures are first bound by the viral hemagglutinin (HA) for cell entry and then cleaved by the viral neuraminidase (NA) for particle release. In contrast, viruses of the recently identified bat-borne IAV subtypes H17N10 and H18N11 encode HA and NA homologs unable to interact with sialic acid residues despite a high degree of structural homology with their conventional counterparts. However, the most recent findings show that bat IAV HAs make use of the major histocompatibility complex class II proteins of different vertebrate species to gain entry into host cells, potentially permitting a broader host tropism. This review recapitulates current progress in the field of bat IAV research including the first assessment of the spillover potential of these bat viruses into other mammals.},
    doi = {10.1101/cshperspect.a038612},
    pmid = {31871229},
    }
  • [DOI] C. Amid, N. Pakseresht, N. Silvester, S. Jayathilaka, O. Lund, L. D. Dynovski, B. Á. Pataki, D. Visontai, B. B. Xavier, B. T. F. Alako, A. Belka, J. L. B. Cisneros, M. Cotten, G. B. Haringhuizen, P. W. Harrison, D. Höper, S. Holt, C. Hundahl, A. Hussein, R. S. Kaas, X. Liu, R. Leinonen, S. Malhotra-Kumar, D. F. Nieuwenhuijse, N. Rahman, C. Dos S Ribeiro, J. E. Skiby, D. Schmitz, J. Stéger, J. M. Szalai-Gindl, M. C. F. Thomsen, S. M. Cacciò, I. Csabai, A. Kroneman, M. Koopmans, F. Aarestrup, and G. Cochrane, "The COMPARE data hubs.," Database (Oxford), vol. 2019, 2019.
    [Bibtex]
    @Article{Amid:19,
    author = {Amid, Clara and Pakseresht, Nima and Silvester, Nicole and Jayathilaka, Suran and Lund, Ole and Dynovski, Lukasz D and Pataki, Bálint Á and Visontai, Dávid and Xavier, Basil Britto and Alako, Blaise T F and Belka, Ariane and Cisneros, Jose L B and Cotten, Matthew and Haringhuizen, George B and Harrison, Peter W and Höper, Dirk and Holt, Sam and Hundahl, Camilla and Hussein, Abdulrahman and Kaas, Rolf S and Liu, Xin and Leinonen, Rasko and Malhotra-Kumar, Surbhi and Nieuwenhuijse, David F and Rahman, Nadim and Dos S Ribeiro, Carolina and Skiby, Jeffrey E and Schmitz, Dennis and Stéger, József and Szalai-Gindl, János M and Thomsen, Martin C F and Cacciò, Simone M and Csabai, István and Kroneman, Annelies and Koopmans, Marion and Aarestrup, Frank and Cochrane, Guy},
    title = {The {COMPARE} Data Hubs.},
    journal = {{Database (Oxford)}},
    year = {2019},
    volume = {2019},
    abstract = {Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.},
    doi = {10.1093/database/baz136},
    keywords = {FAIR principles; data hubs; data sharing platform; pathogen portal; pathogen sequencing data},
    pmid = {31868882},
    }
  • [DOI] A. Duex, S. Lequime, L. V. Patrono, B. Vrancken, S. Boral, J. F. Gogarten, A. Hilbig, D. Horst, K. Merkel, B. Prepoint, S. Santibanez, J. Schlotterbeck, M. A. Suchard, M. Ulrich, N. Widulin, A. Mankertz, F. H. Leendertz, K. Harper, P. Lemey, and S. Calvignac-Spencer, "The history of measles: from a 1912 genome to an antique origin," bioRxiv, 2019.
    [Bibtex]
    @Article{Duex:19,
    author = {Ariane Duex and Sebastian Lequime and Livia V. Patrono and Bram Vrancken and Senguel Boral and Jan F. Gogarten and Antonia Hilbig and David Horst and Kevin Merkel and Baptiste Prepoint and Sabine Santibanez and Jasmin Schlotterbeck and Marc A. Suchard and Markus Ulrich and Navena Widulin and Annette Mankertz and Fabian H. Leendertz and Kyle Harper and Philippe Lemey and Sebastien Calvignac-Spencer},
    title = {The history of measles: from a 1912 genome to an antique origin},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/2019.12.29.889667},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. M. Price, K. E. Hayer, A. B. R. McIntyre, N. S. Gokhale, A. D. N. Fera, C. E. Mason, S. M. Horner, A. C. Wilson, D. P. Depledge, and M. D. Weitzman, "Direct RNA sequencing reveals m6a modifications on adenovirus RNA are necessary for efficient splicing," bioRxiv, 2019.
    [Bibtex]
    @Article{Price:19,
    author = {Alexander M. Price and Katharina E. Hayer and Alexa B.R. McIntyre and Nandan S. Gokhale and Ashley N. Della Fera and Christopher E. Mason and Stacy M. Horner and Angus C. Wilson and Daniel P. Depledge and Matthew D. Weitzman},
    title = {Direct {RNA} sequencing reveals m6A modifications on adenovirus {RNA} are necessary for efficient splicing},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/865485},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. A. Overholt, M. Hölzer, P. Geesink, C. Diezel, M. Marz, and K. Küsel, "Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system," bioRxiv, 2019.
    [Bibtex]
    @Article{Overholt:19,
    author = {Will A. Overholt and Martin Hölzer and Patricia Geesink and Celia Diezel and Manja Marz and Kirsten Küsel},
    title = {Inclusion of {O}xford {N}anopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/2019.12.18.880807},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. E. M. Gruber, B. Bartolini, C. Castilletti, A. Mirazimi, R. Hewson, I. Christova, T. Avšič, R. Grunow, A. Papa, M. P. Sánchez-Seco, M. Kopmans, G. Ippolito, M. R. Capobianchi, C. B. E. M. Reusken, and A. Di Caro, "Geographical variability affects CCHFV detection by RT-PCR: a tool for in-silico evaluation of molecular assays.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Gruber:19,
    author = {Gruber, Cesare E M and Bartolini, Barbara and Castilletti, Concetta and Mirazimi, Ali and Hewson, Roger and Christova, Iva and Avšič, Tatjana and Grunow, Roland and Papa, Anna and Sánchez-Seco, María P and Kopmans, Marion and Ippolito, Giuseppe and Capobianchi, Maria R and Reusken, Chantal B E M and Di Caro, Antonino},
    title = {Geographical Variability Affects {CCHFV} Detection by {RT-PCR}: A Tool for In-Silico Evaluation of Molecular Assays.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.},
    doi = {10.3390/v11100953},
    issue = {10},
    keywords = {CCHFV; Crimean–Congo hemorrhagic fever virus; arthropod-borne virus; emerging diseases; laboratory preparedness; molecular detection},
    pmid = {31623214},
    }

2018

  • [DOI] T. R. Klingen, S. Reimering, C. A. Guzmán, and A. C. McHardy, "In silico vaccine strain prediction for human influenza viruses," Trends Microbiol, vol. 26, p. 119–131, 2018.
    [Bibtex]
    @Article{Klingen:18,
    author = {Klingen, Thorsten R and Reimering, Susanne and Guzmán, Carlos A and McHardy, Alice C},
    title = {In Silico Vaccine Strain Prediction for Human Influenza Viruses},
    journal = {{Trends Microbiol}},
    year = {2018},
    volume = {26},
    pages = {119--131},
    abstract = {Vaccines preventing seasonal influenza infections save many lives every year; however, due to rapid viral evolution, they have to be updated frequently to remain effective. To identify appropriate vaccine strains, the World Health Organization (WHO) operates a global program that continually generates and interprets surveillance data. Over the past decade, sophisticated computational techniques, drawing from multiple theoretical disciplines, have been developed that predict viral lineages rising to predominance, assess their suitability as vaccine strains, link genetic to antigenic alterations, as well as integrate and visualize genetic, epidemiological, structural, and antigenic data. These could form the basis of an objective and reproducible vaccine strain-selection procedure utilizing the complex, large-scale data types from surveillance. To this end, computational techniques should already be incorporated into the vaccine-selection process in an independent, parallel track, and their performance continuously evaluated.},
    doi = {10.1016/j.tim.2017.09.001},
    issue = {2},
    keywords = {Antibodies, Viral, immunology; Antigens, Viral, immunology; Biological Evolution; Computational Biology; Forecasting; Global Health; Humans; Influenza A Virus, H3N2 Subtype, immunology; Influenza Vaccines, immunology; Influenza, Human, epidemiology, prevention & control, virology; Orthomyxoviridae, immunology; Seasons; Vaccination, methods; World Health Organization; GISRS; computational predictions; influenza viruses; vaccine; viral evolution},
    pmid = {29032900},
    }
  • [DOI] V. Lulla, A. M. Dinan, M. Hosmillo, Y. Chaudhry, L. Sherry, N. Irigoyen, K. M. Nayak, N. J. Stonehouse, M. Zilbauer, I. Goodfellow, and A. E. Firth, "An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells," Nat Microbiol, vol. 4, iss. 2, p. 280–292, 2018.
    [Bibtex]
    @Article{Lulla:18,
    author = {Valeria Lulla and Adam M. Dinan and Myra Hosmillo and Yasmin Chaudhry and Lee Sherry and Nerea Irigoyen and Komal M. Nayak and Nicola J. Stonehouse and Matthias Zilbauer and Ian Goodfellow and Andrew E. Firth},
    title = {An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells},
    journal = {{Nat Microbiol}},
    year = {2018},
    volume = {4},
    number = {2},
    pages = {280--292},
    doi = {10.1038/s41564-018-0297-1},
    publisher = {Springer Nature},
    }
  • [DOI] F. L. Nobrega, M. Vlot, P. A. de Jonge, L. L. Dreesens, H. J. E. Beaumont, R. Lavigne, B. E. Dutilh, and S. J. J. Brouns, "Targeting mechanisms of tailed bacteriophages," Nat Rev Microbiol, vol. 16, iss. 12, p. 760–773, 2018.
    [Bibtex]
    @Article{Nobrega:18,
    author = {Franklin L. Nobrega and Marnix Vlot and Patrick A. de Jonge and Lisa L. Dreesens and Hubertus J. E. Beaumont and Rob Lavigne and Bas E. Dutilh and Stan J. J. Brouns},
    title = {Targeting mechanisms of tailed bacteriophages},
    journal = {{Nat Rev Microbiol}},
    year = {2018},
    volume = {16},
    number = {12},
    pages = {760--773},
    doi = {10.1038/s41579-018-0070-8},
    publisher = {Springer Nature},
    }
  • [DOI] J. Huerta-Cepas, D. Szklarczyk, D. Heller, A. Hernández-Plaza, S. K. Forslund, H. Cook, D. R. Mende, I. Letunic, T. Rattei, L. J. Jensen, C. von~Mering, and P. Bork, "eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses," Nucleic Acids Res, vol. 47, iss. D1, p. D309–D314, 2018.
    [Bibtex]
    @Article{Huerta-Cepas:18,
    author = {Jaime Huerta-Cepas and Damian Szklarczyk and Davide Heller and Ana Hern{\'{a}}ndez-Plaza and Sofia K Forslund and Helen Cook and Daniel R Mende and Ivica Letunic and Thomas Rattei and Lars Juhl Jensen and Christian von~Mering and Peer Bork},
    title = {{eggNOG} 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},
    journal = {{Nucleic Acids Res}},
    year = {2018},
    volume = {47},
    number = {D1},
    pages = {D309--D314},
    doi = {10.1093/nar/gky1085},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Reimering, S. Muñoz, and A. C. McHardy, "A Fréchet tree distance measure to compare phylogeographic spread paths across trees," Sci Rep, vol. 8, iss. 1, 2018.
    [Bibtex]
    @Article{Reimering:18,
    author = {Susanne Reimering and Sebastian Mu{\~{n}}oz and Alice C. McHardy},
    title = {A {F}r{\'{e}}chet tree distance measure to compare phylogeographic spread paths across trees},
    journal = {{Sci Rep}},
    year = {2018},
    volume = {8},
    number = {1},
    doi = {10.1038/s41598-018-35421-4},
    publisher = {Springer Nature},
    }
  • [DOI] S. Tu, J. Staheli, C. McClay, K. McLeod, T. Rose, and C. Upton, "Base-By-Base version 3: new comparative tools for large virus genomes," Viruses, vol. 10, iss. 11, p. 637, 2018.
    [Bibtex]
    @Article{Tu:18,
    author = {Shin-Lin Tu and Jeannette Staheli and Colum McClay and Kathleen McLeod and Timothy Rose and Chris Upton},
    title = {{Base-By-Base} Version 3: New Comparative Tools for Large Virus Genomes},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {11},
    pages = {637},
    doi = {10.3390/v10110637},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] Wasimuddin, S. D. Brändel, M. Tschapka, R. Page, A. Rasche, V. M. Corman, C. Drosten, and S. Sommer, "Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats," The ISME Journal, vol. 12, iss. 12, p. 2883–2893, 2018.
    [Bibtex]
    @Article{Wasimuddin:18,
    author = {Wasimuddin and Stefan Dominik Brändel and Marco Tschapka and Rachel Page and Andrea Rasche and Victor M. Corman and Christian Drosten and Simone Sommer},
    title = {Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats},
    journal = {{The ISME Journal}},
    year = {2018},
    volume = {12},
    number = {12},
    pages = {2883--2893},
    doi = {10.1038/s41396-018-0239-1},
    publisher = {Springer Nature},
    }
  • [DOI] E. Mittler, G. Schudt, S. Halwe, C. Rohde, and S. Becker, "A fluorescently labeled marburg virus glycoprotein as a new tool to study viral transport and assembly," J Infect Dis, vol. 218, iss. suppl{_}5, p. S318–S326, 2018.
    [Bibtex]
    @Article{Mittler:18,
    author = {Eva Mittler and Gordian Schudt and Sandro Halwe and Cornelius Rohde and Stephan Becker},
    title = {A Fluorescently Labeled Marburg Virus Glycoprotein as a New Tool to Study Viral Transport and Assembly},
    journal = {{J Infect Dis}},
    year = {2018},
    volume = {218},
    number = {suppl{\_}5},
    pages = {S318--S326},
    doi = {10.1093/infdis/jiy424},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. E. Gorbalenya, "Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank," Arch Virol, vol. 163, iss. 10, p. 2933–2936, 2018.
    [Bibtex]
    @Article{Gorbalenya:18,
    author = {Alexander E. Gorbalenya},
    title = {Increasing the number of available ranks in virus taxonomy from five to ten and adopting the {B}altimore classes as taxa at the basal rank},
    journal = {{Arch Virol}},
    year = {2018},
    volume = {163},
    number = {10},
    pages = {2933--2936},
    doi = {10.1007/s00705-018-3915-6},
    publisher = {Springer Nature},
    }
  • [DOI] R. Schmidt, L. C. Beltzig, B. Sawatsky, O. Dolnik, E. Dietzel, V. Krähling, A. Volz, G. Sutter, S. Becker, and V. von Messling, "Generation of therapeutic antisera for emerging viral infections," NPJ Vaccines, vol. 3, iss. 1, 2018.
    [Bibtex]
    @Article{Schmidt:18,
    author = {Rebecca Schmidt and Lea C. Beltzig and Bevan Sawatsky and Olga Dolnik and Erik Dietzel and Verena Krähling and Asisa Volz and Gerd Sutter and Stephan Becker and Veronika von Messling},
    title = {Generation of therapeutic antisera for emerging viral infections},
    journal = {{NPJ Vaccines}},
    year = {2018},
    volume = {3},
    number = {1},
    doi = {10.1038/s41541-018-0082-4},
    publisher = {Springer Nature},
    }
  • [DOI] S. H. Tausch, B. Strauch, A. Andrusch, T. P. Loka, M. S. Lindner, A. Nitsche, and B. Y. Renard, "LiveKraken––real-time metagenomic classification of illumina data," Bioinformatics, vol. 34, iss. 21, p. 3750–3752, 2018.
    [Bibtex]
    @Article{Tausch:18,
    author = {Simon H Tausch and Benjamin Strauch and Andreas Andrusch and Tobias P Loka and Martin S Lindner and Andreas Nitsche and Bernhard Y Renard},
    title = {{LiveKraken}{\textendash}{\textendash}real-time metagenomic classification of illumina data},
    journal = {Bioinformatics},
    year = {2018},
    volume = {34},
    number = {21},
    pages = {3750--3752},
    doi = {10.1093/bioinformatics/bty433},
    editor = {Bonnie Berger},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Kruppa, W. K. Jo, E. van der Vries, M. Ludlow, A. Osterhaus, W. Baumgaertner, and K. Jung, "Virus detection in high-throughput sequencing data without a reference genome of the host," Infect Genet Evol, vol. 66, p. 180–187, 2018.
    [Bibtex]
    @Article{Kruppa:18,
    author = {Jochen Kruppa and Wendy K. Jo and Erhard van der Vries and Martin Ludlow and Albert Osterhaus and Wolfgang Baumgaertner and Klaus Jung},
    title = {Virus detection in high-throughput sequencing data without a reference genome of the host},
    journal = {{Infect Genet Evol}},
    year = {2018},
    volume = {66},
    pages = {180--187},
    doi = {10.1016/j.meegid.2018.09.026},
    publisher = {Elsevier {BV}},
    }
  • [DOI] H. Cook, N. T. Doncheva, D. Szklarczyk, C. von Mering, and L. J. Jensen, "Viruses.STRING: a virus-host protein-protein interaction database," Viruses, vol. 10, iss. 10, p. 519, 2018.
    [Bibtex]
    @Article{Cook:18,
    author = {Helen Cook and Nadezhda Tsankova Doncheva and Damian Szklarczyk and Christian {von Mering} and Lars Juhl Jensen},
    title = {Viruses.{STRING}: A Virus-Host Protein-Protein Interaction Database},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {10},
    pages = {519},
    doi = {10.3390/v10100519},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. Saberi, A. A. Gulyaeva, J. L. Brubacher, P. A. Newmark, and A. E. Gorbalenya, "A planarian nidovirus expands the limits of RNA genome size," PLoS Pathog, vol. 14, iss. 11, p. e1007314, 2018.
    [Bibtex]
    @Article{Saberi:18,
    author = {Amir Saberi and Anastasia A. Gulyaeva and John L. Brubacher and Phillip A. Newmark and Alexander E. Gorbalenya},
    title = {A planarian nidovirus expands the limits of {RNA} genome size},
    journal = {{PLoS Pathog}},
    year = {2018},
    volume = {14},
    number = {11},
    pages = {e1007314},
    doi = {10.1371/journal.ppat.1007314},
    editor = {Stanley Perlman},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] P. J. K. Libin, K. Deforche, A. B. Abecasis, and K. Theys, "VIRULIGN: fast codon-correct alignment and annotation of viral genomes," Bioinformatics, 2018.
    [Bibtex]
    @Article{Libin:18,
    author = {Pieter J K Libin and Koen Deforche and Ana B Abecasis and Kristof Theys},
    title = {{VIRULIGN}: fast codon-correct alignment and annotation of viral genomes},
    journal = {Bioinformatics},
    year = {2018},
    doi = {10.1093/bioinformatics/bty851},
    editor = {John Hancock},
    publisher = {Oxford University Press ({OUP})},
    }
  • K. McNair, R. K. Aziz, G. D. Pusch, R. Overbeek, B. E. Dutilh, and R. Edwards, "Phage genome annotation using the RAST pipeline," in Bacteriophages, Springer, 2018, p. 231–238.
    [Bibtex]
    @InCollection{McNair:18,
    author = {McNair, Katelyn and Aziz, Ramy Karam and Pusch, Gordon D and Overbeek, Ross and Dutilh, Bas E and Edwards, Robert},
    title = {Phage genome annotation using the {RAST} pipeline},
    booktitle = {Bacteriophages},
    publisher = {Springer},
    year = {2018},
    pages = {231--238},
    }
  • M. Fareh, J. van Lopik, I. Katechis, A. W. Bronkhorst, A. C. Haagsma, R. P. van Rij, and C. Joo, "Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA," Nucleic Acids Res, vol. 46, iss. 6, p. 3187–3197, 2018.
    [Bibtex]
    @Article{Fareh:18,
    author = {Fareh, Mohamed and van Lopik, Jasper and Katechis, Iason and Bronkhorst, Alfred W and Haagsma, Anna C and van Rij, Ronald P and Joo, Chirlmin},
    title = {Viral suppressors of {RNAi} employ a rapid screening mode to discriminate viral {RNA} from cellular small {RNA}},
    journal = {{Nucleic Acids Res}},
    year = {2018},
    volume = {46},
    number = {6},
    pages = {3187--3197},
    publisher = {Oxford University Press},
    }
  • K. Eschke, J. Trimpert, N. Osterrieder, and D. Kunec, "Attenuation of a very virulent Marek's disease herpesvirus (MDV) by codon pair bias deoptimization," PLoS Pathog, vol. 14, iss. 1, p. e1006857, 2018.
    [Bibtex]
    @Article{Eschke:18,
    author = {Eschke, Kathrin and Trimpert, Jakob and Osterrieder, Nikolaus and Kunec, Dusan},
    title = {Attenuation of a very virulent {M}arek's disease herpesvirus ({MDV}) by codon pair bias deoptimization},
    journal = {{PLoS Pathog}},
    year = {2018},
    volume = {14},
    number = {1},
    pages = {e1006857},
    publisher = {Public Library of Science},
    }
  • C. Jandrasits, P. W. Dabrowski, S. Fuchs, and B. Y. Renard, "seq-seq-pan: building a computational pan-genome data structure on whole genome alignment," BMC Genomics, vol. 19, iss. 1, p. 47, 2018.
    [Bibtex]
    @Article{Jandrasits:18,
    author = {Jandrasits, Christine and Dabrowski, Piotr W and Fuchs, Stephan and Renard, Bernhard Y},
    title = {{seq-seq-pan}: Building a computational pan-genome data structure on whole genome alignment},
    journal = {{BMC Genomics}},
    year = {2018},
    volume = {19},
    number = {1},
    pages = {47},
    publisher = {BioMed Central},
    }
  • T. R. Klingen, S. Reimering, J. Loers, K. Mooren, F. Klawonn, T. Krey, G. Gabriel, and A. C. McHardy, "Sweep dynamics (SD) plots: computational identification of selective sweeps to monitor the adaptation of influenza A viruses," Sci Rep, vol. 8, iss. 1, p. 373, 2018.
    [Bibtex]
    @Article{Klingen:18a,
    author = {Klingen, Thorsten R and Reimering, Susanne and Loers, Jens and Mooren, Kyra and Klawonn, Frank and Krey, Thomas and Gabriel, G{\"u}lsah and McHardy, Alice C},
    title = {Sweep Dynamics ({SD}) plots: Computational identification of selective sweeps to monitor the adaptation of influenza {A} viruses},
    journal = {{Sci Rep}},
    year = {2018},
    volume = {8},
    number = {1},
    pages = {373},
    publisher = {Nature Publishing Group},
    }
  • K. Arkhipova, T. Skvortsov, J. P. Quinn, J. W. McGrath, C. C. Allen, B. E. Dutilh, Y. McElarney, and L. A. Kulakov, "Temporal dynamics of uncultured viruses: a new dimension in viral diversity," The ISME Journal, vol. 12, iss. 1, p. 199, 2018.
    [Bibtex]
    @Article{Arkhipova:18,
    author = {Arkhipova, Ksenia and Skvortsov, Timofey and Quinn, John P and McGrath, John W and Allen, Christopher CR and Dutilh, Bas E and McElarney, Yvonne and Kulakov, Leonid A},
    title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity},
    journal = {{The ISME Journal}},
    year = {2018},
    volume = {12},
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    @Article{Darriba:18,
    author = {Darriba, Diego and Flouri, Tom{\'a}{\v{s}} and Stamatakis, Alexandros},
    title = {The state of software for evolutionary biology},
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    title = {Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza},
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    @Article{Panasiuk:18,
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    title = {Tunneling nanotubes as a novel route of cell-to-cell spread of Herpesviruses},
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    @Article{Whitmer:18,
    author = {Whitmer, Shannon LM and Strecker, Thomas and Cadar, Daniel and Dienes, Hans-Peter and Faber, Kelly and Patel, Ketan and Brown, Shelley M and Davis, William G and Klena, John D and Rollin, Pierre E and others},
    title = {New lineage of {L}assa virus, {T}ogo, 2016},
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    @Article{Maticzka:18,
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    title = {{uvCLAP} is a fast and non-radioactive method to identify in vivo targets of {RNA}-binding proteins},
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    @Article{Rivers-Auty:18,
    author = {Rivers-Auty, Jack and Daniels, Michael JD and Colliver, Isaac and Robertson, David L and Brough, David},
    title = {Redefining the ancestral origins of the interleukin-1 superfamily},
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    @Article{Erhard:18,
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    title = {Improved {R}ibo-seq enables identification of cryptic translation events},
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    @Article{Eggenhofer:18,
    author = {Eggenhofer, Florian and Hofacker, Ivo L and Backofen, Rolf and H{\"o}ner zu Siederdissen, Christian},
    title = {{CMV}: visualization for {RNA} and protein family models and their comparisons},
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    @Article{Kupczok:18,
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    title = {Rates of mutation and recombination in {S}iphoviridae phage genome evolution over three decades},
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    @Article{Milewska:18,
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    title = {{APOBEC3}-mediated restriction of {RNA} virus replication},
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    title = {Ortervirales: new virus order unifying five families of reverse-transcribing viruses},
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    title = {Consistent prediction of mutation effect on drug binding in {HIV}-1 protease using alchemical calculations},
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    @Article{Theuns:18,
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    @Article{Mendoza:18,
    author = {Pilar Mendoza and Henning Gruell and Lilian Nogueira and Joy A. Pai and Allison L. Butler and Katrina Millard and Clara Lehmann and Isabelle Su{\'{a}}rez and Thiago Y. Oliveira and Julio C. C. Lorenzi and Yehuda Z. Cohen and Christoph Wyen and Tim Kümmerle and Theodora Karagounis and Ching-Lan Lu and Lisa Handl and Cecilia Unson-O'Brien and Roshni Patel and Carola Ruping and Maike Schlotz and Maggi Witmer-Pack and Irina Shimeliovich and Gisela Kremer and Eleonore Thomas and Kelly E. Seaton and Jill Horowitz and Anthony P. West and Pamela J. Bjorkman and Georgia D. Tomaras and Roy M. Gulick and Nico Pfeifer and Gerd Fätkenheuer and Michael S. Seaman and Florian Klein and Marina Caskey and Michel C. Nussenzweig},
    title = {Combination therapy with anti-{HIV}-1 antibodies maintains viral suppression},
    journal = {Nature},
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    @Article{Bar-On:18,
    author = {Yotam Bar-On and Henning Gruell and Till Schoofs and Joy A. Pai and Lilian Nogueira and Allison L. Butler and Katrina Millard and Clara Lehmann and Isabelle Su{\'{a}}rez and Thiago Y. Oliveira and Theodora Karagounis and Yehuda Z. Cohen and Christoph Wyen and Stefan Scholten and Lisa Handl and Shiraz Belblidia and Juan P. Dizon and Jörg J. Vehreschild and Maggi Witmer-Pack and Irina Shimeliovich and Kanika Jain and Kerstin Fiddike and Kelly E. Seaton and Nicole L. Yates and Jill Horowitz and Roy M. Gulick and Nico Pfeifer and Georgia D. Tomaras and Michael S. Seaman and Gerd Fätkenheuer and Marina Caskey and Florian Klein and Michel C. Nussenzweig},
    title = {Safety and antiviral activity of combination {HIV}-1 broadly neutralizing antibodies in viremic individuals},
    journal = {{Nat Med}},
    year = {2018},
    volume = {24},
    number = {11},
    pages = {1701--1707},
    doi = {10.1038/s41591-018-0186-4},
    publisher = {Springer Nature},
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    @Article{Stanelle-Bertram:18,
    author = {Stephanie Stanelle-Bertram and Kerstin Walendy-Gnir{\ss} and Thomas Speiseder and Swantje Thiele and Ivy Asantewaa Asante and Carola Dreier and Nancy Mounogou Kouassi and Annette Preu{\ss} and Gundula Pilnitz-Stolze and Ursula Müller and Stefanie Thanisch and Melanie Richter and Robin Scharrenberg and Vanessa Kraus and Ronja Dörk and Lynn Schau and Vanessa Herder and Ingo Gerhauser and Vanessa Maria Pfankuche and Christopher Käufer and Inken Waltl and Thais Moraes and Julie Sellau and Stefan Hoenow and Jonas Schmidt-Chanasit and Stephanie Jansen and Benjamin Schattling and Harald Ittrich and Udo Bartsch and Thomas Renn{\'{e}} and Ralf Bartenschlager and Petra Arck and Daniel Cadar and Manuel A. Friese and Olli Vapalahti and Hanna Lotter and Sany Benites and Lane Rolling and Martin Gabriel and Wolfgang Baumgärtner and Fabio Morellini and Sabine M. Hölter and Oana Amarie and Helmut Fuchs and Martin Hrabe de Angelis and Wolfgang Löscher and Froylan Calderon de Anda and Gülsah Gabriel},
    title = {Male offspring born to mildly {ZIKV}-infected mice are at risk of developing neurocognitive disorders in adulthood},
    journal = {{Nat Microbiol}},
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    @Article{Fröhlich:18,
    author = {Holger Fr\"{o}hlich and Rudi Balling and Niko Beerenwinkel and Oliver Kohlbacher and Santosh Kumar and Thomas Lengauer and Marloes H. Maathuis and Yves Moreau and Susan A. Murphy and Teresa M. Przytycka and Michael Rebhan and Hannes R\"{o}st and Andreas Schuppert and Matthias Schwab and Rainer Spang and Daniel Stekhoven and Jimeng Sun and Andreas Weber and Daniel Ziemek and Blaz Zupan},
    title = {From hype to reality: data science enabling personalized medicine},
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    @Article{Barbera:18,
    author = {Pierre Barbera and Alexey M Kozlov and Lucas Czech and Benoit Morel and Diego Darriba and Tom{\'{a}}{\v{s}} Flouri and Alexandros Stamatakis},
    title = {{EPA}-ng: Massively Parallel Evolutionary Placement of Genetic Sequences},
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    }
  • [DOI] G. Baele, S. Dellicour, M. A. Suchard, P. Lemey, and B. Vrancken, "Recent advances in computational phylodynamics," Curr Opin Virol, vol. 31, p. 24–32, 2018.
    [Bibtex]
    @Article{Baele:18,
    author = {Guy Baele and Simon Dellicour and Marc A Suchard and Philippe Lemey and Bram Vrancken},
    title = {Recent advances in computational phylodynamics},
    journal = {{Curr Opin Virol}},
    year = {2018},
    volume = {31},
    pages = {24--32},
    doi = {10.1016/j.coviro.2018.08.009},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. Wylezich, A. Papa, M. Beer, and D. Höper, "A versatile sample processing workflow for metagenomic pathogen detection," Sci Rep, vol. 8, iss. 1, 2018.
    [Bibtex]
    @Article{Wylezich:18,
    author = {Claudia Wylezich and Anna Papa and Martin Beer and Dirk H\"{o}per},
    title = {A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection},
    journal = {{Sci Rep}},
    year = {2018},
    volume = {8},
    number = {1},
    doi = {10.1038/s41598-018-31496-1},
    publisher = {Springer Nature},
    }
  • [DOI] A. Mostafa, E. Abdelwhab, T. C. Mettenleiter, and S. Pleschka, "Zoonotic potential of influenza a viruses: a comprehensive overview," Viruses, vol. 10, iss. 9, p. 497, 2018.
    [Bibtex]
    @Article{Mostafa:18,
    author = {Ahmed Mostafa and Elsayed Abdelwhab and Thomas C Mettenleiter and Stephan Pleschka},
    title = {Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {9},
    pages = {497},
    doi = {10.3390/v10090497},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Dellicour, B. Vrancken, N. S. Trovão, D. Fargette, and P. Lemey, "On the importance of negative controls in viral landscape phylogeography," Virus Evol, vol. 4, iss. 2, 2018.
    [Bibtex]
    @Article{Dellicour:18,
    author = {Simon Dellicour and Bram Vrancken and N{\'{\i}}dia S Trov{\~{a}}o and Denis Fargette and Philippe Lemey},
    title = {On the importance of negative controls in viral landscape phylogeography},
    journal = {{Virus Evol}},
    year = {2018},
    volume = {4},
    number = {2},
    doi = {10.1093/ve/vey023},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. Lamkiewicz, E. Barth, M. Marz, and B. Ibrahim, "Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis," bioRxiv, 2018.
    [Bibtex]
    @Article{Lamkiewicz:18,
    author = {Kevin Lamkiewicz and Emanuel Barth and Manja Marz and Bashar Ibrahim},
    title = {Identification of potential {microRNAs} associated with {H}erpesvirus family based on bioinformatic analysis},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/417782},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Roux, E. M. Adriaenssens, B. E. Dutilh, E. V. Koonin, A. M. Kropinski, M. Krupovic, J. H. Kuhn, R. Lavigne, R. J. Brister, A. Varsani, C. Amid, R. K. Aziz, S. R. Bordenstein, P. Bork, M. Breitbart, G. Cochrane, R. A. Daly, C. Desnues, M. B. Duhaime, J. B. Emerson, F. Enault, J. A. Fuhrman, P. Hingamp, P. Hugenholtz, B. L. Hurwitz, N. N. Ivanova, J. M. Labonté, K. Lee, R. R. Malmstrom, M. Martinez-Garcia, I. K. Mizrachi, H. Ogata, D. Páez-Espino, M. A. Petit, C. Putonti, T. Rattei, A. Reyes, F. Rodriguez-Valera, K. Rosario, L. Schriml, F. Schulz, G. F. Steward, M. B. Sullivan, S. Sunagawa, C. A. Suttle, B. Temperton, S. G. Tringe, R. V. Thurber, N. S. Webster, K. L. Whiteson, S. W. Wilhelm, E. K. Wommack, T. Woyke, K. C. Wrighton, P. Yilmaz, T. Yoshida, M. J. Young, N. Yutin, L. Z. Allen, N. C. Kyrpides, and E. A. Eloe-Fadrosh, "Minimum information about an uncultivated virus genome (MIUViG)," Nat Biotechnol, vol. 37, iss. 1, p. 29–37, 2018.
    [Bibtex]
    @Article{Roux:18,
    author = {Simon Roux and Evelien M Adriaenssens and Bas E Dutilh and Eugene V Koonin and Andrew M Kropinski and Mart Krupovic and Jens H Kuhn and Rob Lavigne and J Rodney Brister and Arvind Varsani and Clara Amid and Ramy K Aziz and Seth R Bordenstein and Peer Bork and Mya Breitbart and Guy Cochrane and Rebecca A Daly and Christelle Desnues and Melissa B Duhaime and Joanne B Emerson and Fran{\c{c}}ois Enault and Jed A Fuhrman and Pascal Hingamp and Philip Hugenholtz and Bonnie L Hurwitz and Natalia N Ivanova and Jessica M Labont{\'{e}} and Kyung-Bum Lee and Rex R Malmstrom and Manuel Martinez-Garcia and Ilene Karsch Mizrachi and Hiroyuki Ogata and David P{\'{a}}ez-Espino and Marie A Petit and Catherine Putonti and Thomas Rattei and Alejandro Reyes and Francisco Rodriguez-Valera and Karyna Rosario and Lynn Schriml and Frederik Schulz and Grieg F Steward and Matthew B Sullivan and Shinichi Sunagawa and Curtis A Suttle and Ben Temperton and Susannah G Tringe and Rebecca Vega Thurber and Nicole S Webster and Katrine L Whiteson and Steven W Wilhelm and K Eric Wommack and Tanja Woyke and Kelly C Wrighton and Pelin Yilmaz and Takashi Yoshida and Mark J Young and Natalya Yutin and Lisa Zeigler Allen and Nikos C Kyrpides and Emiley A Eloe-Fadrosh},
    title = {Minimum Information about an Uncultivated Virus Genome ({MIUViG})},
    journal = {{Nat Biotechnol}},
    year = {2018},
    volume = {37},
    number = {1},
    pages = {29--37},
    doi = {10.1038/nbt.4306},
    publisher = {Springer Nature},
    }
  • [DOI] J. Cui, F. Li, and Z. Shi, "Origin and evolution of pathogenic coronaviruses," Nat Rev Microbiol, vol. 17, iss. 3, p. 181–192, 2018.
    [Bibtex]
    @Article{Cui:18,
    author = {Jie Cui and Fang Li and Zheng-Li Shi},
    title = {Origin and evolution of pathogenic coronaviruses},
    journal = {{Nat Rev Microbiol}},
    year = {2018},
    volume = {17},
    number = {3},
    pages = {181--192},
    doi = {10.1038/s41579-018-0118-9},
    publisher = {Springer Nature},
    }
  • [DOI] N. D. Grubaugh, J. T. Ladner, P. Lemey, O. G. Pybus, A. Rambaut, E. C. Holmes, and K. G. Andersen, "Tracking virus outbreaks in the twenty-first century," Nat Microbiol, vol. 4, iss. 1, p. 10–19, 2018.
    [Bibtex]
    @Article{Grubaugh:18,
    author = {Nathan D. Grubaugh and Jason T. Ladner and Philippe Lemey and Oliver G. Pybus and Andrew Rambaut and Edward C. Holmes and Kristian G. Andersen},
    title = {Tracking virus outbreaks in the twenty-first century},
    journal = {{Nat Microbiol}},
    year = {2018},
    volume = {4},
    number = {1},
    pages = {10--19},
    doi = {10.1038/s41564-018-0296-2},
    publisher = {Springer Nature},
    }
  • [DOI] D. M. Brown, A. M. Hixon, L. M. Oldfield, Y. Zhang, M. Novotny, W. Wang, S. R. Das, R. S. Shabman, K. L. Tyler, and R. H. Scheuermann, "Contemporary circulating enterovirus d68 strains have acquired the capacity for viral entry and replication in human neuronal cells," mBio, vol. 9, iss. 5, 2018.
    [Bibtex]
    @Article{Brown:18,
    author = {David M. Brown and Alison M. Hixon and Lauren M. Oldfield and Yun Zhang and Mark Novotny and Wei Wang and Suman R. Das and Reed S. Shabman and Kenneth L. Tyler and Richard H. Scheuermann},
    title = {Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells},
    journal = {{mBio}},
    year = {2018},
    volume = {9},
    number = {5},
    doi = {10.1128/mbio.01954-18},
    editor = {Diane E. Griffin},
    publisher = {American Society for Microbiology},
    }
  • [DOI] C. E. M. Gruber, E. Giombini, M. Selleri, S. Tausch, A. Andrusch, A. Tyshaieva, G. Cardeti, R. Lorenzetti, L. D. Marco, F. Carletti, A. Nitsche, M. Capobianchi, G. Ippolito, G. Autorino, and C. Castilletti, "Whole genome characterization of orthopoxvirus (OPV) abatino, a zoonotic virus representing a putative novel clade of old world orthopoxviruses," Viruses, vol. 10, iss. 10, p. 546, 2018.
    [Bibtex]
    @Article{Gruber:18,
    author = {Cesare Ernesto Maria Gruber and Emanuela Giombini and Marina Selleri and Simon Tausch and Andreas Andrusch and Alona Tyshaieva and Giusy Cardeti and Raniero Lorenzetti and Lorenzo De Marco and Fabrizio Carletti and Andreas Nitsche and Maria Capobianchi and Giuseppe Ippolito and Gian Autorino and Concetta Castilletti},
    title = {Whole Genome Characterization of Orthopoxvirus ({OPV}) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {10},
    pages = {546},
    doi = {10.3390/v10100546},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] J. B. Singer, E. C. Thomson, J. McLauchlan, J. Hughes, and R. J. Gifford, "GLUE: a flexible software system for virus sequence data," BMC Bioinformatics, vol. 19, iss. 1, 2018.
    [Bibtex]
    @Article{Singer:18,
    author = {Joshua B. Singer and Emma C. Thomson and John McLauchlan and Joseph Hughes and Robert J. Gifford},
    title = {{GLUE}: a flexible software system for virus sequence data},
    journal = {{BMC Bioinformatics}},
    year = {2018},
    volume = {19},
    number = {1},
    doi = {10.1186/s12859-018-2459-9},
    publisher = {Springer Nature},
    }
  • [DOI] Y. Zhang, C. Zmasek, G. Sun, C. N. Larsen, and R. H. Scheuermann, "Hepatitis C virus database and bioinformatics analysis tools in the virus pathogen resource (ViPR)," in Methods Mol Biol, Springer new york, 2018, p. 47–69.
    [Bibtex]
    @InCollection{Zhang:18,
    author = {Yun Zhang and Christian Zmasek and Guangyu Sun and Christopher N. Larsen and Richard H. Scheuermann},
    title = {Hepatitis {C} Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource ({ViPR})},
    booktitle = {{Methods Mol Biol}},
    publisher = {Springer New York},
    year = {2018},
    pages = {47--69},
    doi = {10.1007/978-1-4939-8976-8_3},
    }
  • [DOI] A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, "Nanopore direct RNA sequencing reveals modification in full-length coronavirus genomes," bioRxiv, 2018.
    [Bibtex]
    @Article{Viehweger:18,
    author = {Adrian Viehweger and Sebastian Krautwurst and Kevin Lamkiewicz and Ramakanth Madhugiri and John Ziebuhr and Martin Hölzer and Manja Marz},
    title = {Nanopore direct {RNA} sequencing reveals modification in full-length coronavirus genomes},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/483693},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. Zhu, T. Dennis, J. Hughes, and R. J. Gifford, "Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database.," bioRxiv, 2018.
    [Bibtex]
    @Article{Zhu:18,
    author = {Henan Zhu and Tristan Dennis and Joseph Hughes and Robert J Gifford},
    title = {Database-integrated genome screening ({DIGS}): exploring genomes heuristically using sequence similarity search tools and a relational database.},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/246835},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. F. Löchel, M. Riemenschneider, D. Frishman, and D. Heider, "SCOTCH: subtype a coreceptor tropism classification in HIV-1," Bioinformatics, vol. 34, iss. 15, p. 2575–2580, 2018.
    [Bibtex]
    @Article{Löchel:18,
    author = {Hannah F Löchel and Mona Riemenschneider and Dmitrij Frishman and Dominik Heider},
    title = {{SCOTCH}: subtype A coreceptor tropism classification in {HIV}-1},
    journal = {Bioinformatics},
    year = {2018},
    volume = {34},
    number = {15},
    pages = {2575--2580},
    doi = {10.1093/bioinformatics/bty170},
    editor = {John Hancock},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Riemenschneider, J. Wienbeck, A. Scherag, and D. Heider, "Data science for molecular diagnostics applications: from academia to clinic to industry," Syst Med, vol. 1, iss. 1, p. 13–17, 2018.
    [Bibtex]
    @Article{Riemenschneider:18,
    author = {Mona Riemenschneider and Joachim Wienbeck and Andr{\'{e}} Scherag and Dominik Heider},
    title = {Data Science for Molecular Diagnostics Applications: From Academia to Clinic to Industry},
    journal = {{Syst Med}},
    year = {2018},
    volume = {1},
    number = {1},
    pages = {13--17},
    doi = {10.1089/sysm.2018.0002},
    publisher = {Mary Ann Liebert Inc},
    }
  • [DOI] J. Schwarz and D. Heider, "GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making," Bioinformatics, 2018.
    [Bibtex]
    @Article{Schwarz:18,
    author = {Johanna Schwarz and Dominik Heider},
    title = {{GUESS}: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making},
    journal = {Bioinformatics},
    year = {2018},
    doi = {10.1093/bioinformatics/bty984},
    editor = {Jonathan Wren},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Döring, J. Büch, G. Friedrich, A. Pironti, P. Kalaghatgi, E. Knops, E. Heger, M. Obermeier, M. Däumer, A. Thielen, R. Kaiser, T. Lengauer, and N. Pfeifer, "Geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.," Nucleic Acids Res, vol. 46, p. W271–W277, 2018.
    [Bibtex]
    @Article{Doering:18,
    author = {Döring, Matthias and Büch, Joachim and Friedrich, Georg and Pironti, Alejandro and Kalaghatgi, Prabhav and Knops, Elena and Heger, Eva and Obermeier, Martin and Däumer, Martin and Thielen, Alexander and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico},
    title = {geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.},
    journal = {{Nucleic Acids Res}},
    year = {2018},
    volume = {46},
    pages = {W271--W277},
    abstract = {Identifying resistance to antiretroviral drugs is crucial for ensuring the successful treatment of patients infected with viruses such as human immunodeficiency virus (HIV) or hepatitis C virus (HCV). In contrast to Sanger sequencing, next-generation sequencing (NGS) can detect resistance mutations in minority populations. Thus, genotypic resistance testing based on NGS data can offer novel, treatment-relevant insights. Since existing web services for analyzing resistance in NGS samples are subject to long processing times and follow strictly rules-based approaches, we developed geno2pheno[ngs-freq], a web service for rapidly identifying drug resistance in HIV-1 and HCV samples. By relying on frequency files that provide the read counts of nucleotides or codons along a viral genome, the time-intensive step of processing raw NGS data is eliminated. Once a frequency file has been uploaded, consensus sequences are generated for a set of user-defined prevalence cutoffs, such that the constructed sequences contain only those nucleotides whose codon prevalence exceeds a given cutoff. After locally aligning the sequences to a set of references, resistance is predicted using the well-established approaches of geno2pheno[resistance] and geno2pheno[hcv]. geno2pheno[ngs-freq] can assist clinical decision making by enabling users to explore resistance in viral populations with different abundances and is freely available at http://ngs.geno2pheno.org.},
    doi = {10.1093/nar/gky349},
    issue = {W1},
    pmid = {29718426},
    }
  • [DOI] B. Ibrahim, K. Arkhipova, A. C. Andeweg, S. Posada-Céspedes, F. Enault, A. Gruber, E. Koonin, A. Kupczok, P. Lemey, A. McHardy, D. McMahon, B. Pickett, D. Robertson, R. Scheuermann, A. Zhernakova, M. Zwart, A. Schönhuth, B. Dutilh, and M. Marz, "Bioinformatics meets virology: the European Virus Bioinformatics Center's second annual meeting," Viruses, vol. 10, iss. 5, p. 256, 2018.
    [Bibtex]
    @Article{Ibrahim:18a,
    author = {Bashar Ibrahim and Ksenia Arkhipova and Arno C. Andeweg and Susana Posada-C{\'{e}}spedes and Fran{\c{c}}ois Enault and Arthur Gruber and Eugene Koonin and Anne Kupczok and Philippe Lemey and Alice McHardy and Dino McMahon and Brett Pickett and David Robertson and Richard Scheuermann and Alexandra Zhernakova and Mark Zwart and Alexander Schönhuth and Bas Dutilh and Manja Marz},
    title = {Bioinformatics Meets Virology: The {E}uropean {V}irus {B}ioinformatics {C}enter's Second Annual Meeting},
    journal = {Viruses},
    year = {2018},
    volume = {10},
    number = {5},
    pages = {256},
    doi = {10.3390/v10050256},
    publisher = {{MDPI} {AG}},
    }

2017

  • [DOI] J. Fuchs, M. Hölzer, M. Schilling, C. Patzina, A. Schoen, T. Hoenen, G. Zimmer, M. Marz, F. Weber, M. A. Müller, and G. Kochs, "Evolution and antiviral specificities of interferon-induced mx proteins of bats against Ebola, Influenza, and other RNA viruses," J Virol, vol. 91, iss. 15, 2017.
    [Bibtex]
    @Article{Fuchs:17,
    author = {Jonas Fuchs and Martin H\"{o}lzer and Mirjam Schilling and Corinna Patzina and Andreas Schoen and Thomas Hoenen and Gert Zimmer and Manja Marz and Friedemann Weber and Marcel A. M\"{u}ller and Georg Kochs},
    title = {Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against {E}bola, {I}nfluenza, and Other {RNA} Viruses},
    journal = {{J Virol}},
    year = {2017},
    volume = {91},
    number = {15},
    doi = {10.1128/jvi.00361-17},
    editor = {Bryan R. G. Williams},
    publisher = {American Society for Microbiology},
    }
  • [DOI] A. Brinkmann, K. Ergünay, A. Radonić, Z. Kocak Tufan, C. Domingo, and A. Nitsche, "Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics," PLoS Negl Trop Dis, vol. 11, p. e0006075, 2017.
    [Bibtex]
    @Article{Brinkmann:17,
    author = {Brinkmann, Annika and Erg\"{u}nay, Koray and Radonić, Aleksandar and Kocak Tufan, Zeliha and Domingo, Cristina and Nitsche, Andreas},
    title = {Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics},
    journal = {{PLoS Negl Trop Dis}},
    year = {2017},
    volume = {11},
    pages = {e0006075},
    abstract = {We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.},
    doi = {10.1371/journal.pntd.0006075},
    issue = {11},
    keywords = {Adult; Chikungunya virus, genetics, isolation & purification; DNA, Viral, genetics; Ebolavirus, genetics, isolation & purification; Hemorrhagic Fever Virus, Crimean-Congo, genetics, isolation & purification; Hemorrhagic Fevers, Viral, diagnosis, virology; High-Throughput Nucleotide Sequencing, methods; Humans; Junin virus, genetics, isolation & purification; Nucleic Acid Amplification Techniques, methods; Rift Valley fever virus, genetics, isolation & purification; Sensitivity and Specificity; Sequence Analysis, DNA; Yellow fever virus, genetics, isolation & purification},
    pmid = {29155823},
    }
  • [DOI] J. Trimpert, N. Groenke, M. Jenckel, S. He, D. Kunec, M. L. Szpara, S. J. Spatz, N. Osterrieder, and D. P. McMahon, "A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America," Evol Appl, vol. 10, p. 1091–1101, 2017.
    [Bibtex]
    @Article{Trimpert:17,
    author = {Trimpert, Jakob and Groenke, Nicole and Jenckel, Maria and He, Shulin and Kunec, Dusan and Szpara, Moriah L and Spatz, Stephen J and Osterrieder, Nikolaus and McMahon, Dino P},
    title = {A phylogenomic analysis of {M}arek's disease virus reveals independent paths to virulence in {E}urasia and {N}orth {A}merica},
    journal = {{Evol Appl}},
    year = {2017},
    volume = {10},
    pages = {1091--1101},
    abstract = {Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek's disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens has been rising steadily since the adoption of intensive farming techniques and vaccination programs in the 1950s and 1970s, respectively. It has remained uncertain, however, which of these factors is causally more responsible for the observed increase in virulence of circulating viruses. We conducted a phylogenomic study to understand the evolution of MDV in the context of dramatic changes to poultry farming and disease control. Our analysis reveals evidence of geographical structuring of MDV strains, with reconstructions supporting the emergence of virulent viruses independently in North America and Eurasia. Of note, the emergence of virulent viruses appears to coincide approximately with the introduction of comprehensive vaccination on both continents. The time-dated phylogeny also indicated that MDV has a mean evolutionary rate of ~1.6 × 10 substitutions per site per year. An examination of gene-linked mutations did not identify a strong association between mutational variation and virulence phenotypes, indicating that MDV may evolve readily and rapidly under strong selective pressures and that multiple genotypic pathways may underlie virulence adaptation in MDV.},
    doi = {10.1111/eva.12515},
    issue = {10},
    keywords = {disease; emergence; evolution; resistance; virulence},
    pmid = {29151863},
    }
  • [DOI] W. Wan, L. Kolesnikova, M. Clarke, A. Koehler, T. Noda, S. Becker, and J. A. G. Briggs, "Structure and assembly of the Ebola virus nucleocapsid," Nature, vol. 551, p. 394–397, 2017.
    [Bibtex]
    @Article{Wan:17,
    author = {Wan, William and Kolesnikova, Larissa and Clarke, Mairi and Koehler, Alexander and Noda, Takeshi and Becker, Stephan and Briggs, John A G},
    title = {Structure and assembly of the {E}bola virus nucleocapsid},
    journal = {Nature},
    year = {2017},
    volume = {551},
    pages = {394--397},
    abstract = {Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.},
    doi = {10.1038/nature24490},
    issue = {7680},
    keywords = {Animals; Cercopithecus aethiops; Cryoelectron Microscopy; Ebolavirus, chemistry, ultrastructure; Electron Microscope Tomography; HEK293 Cells; Humans; Marburgvirus, chemistry; Models, Molecular; Molecular Conformation; Nucleocapsid, chemistry, ultrastructure; Nucleocapsid Proteins, chemistry, ultrastructure; RNA, Viral, chemistry, ultrastructure; Vero Cells},
    pmid = {29144446},
    }
  • [DOI] M. Grossegesse, J. Doellinger, A. Tyshaieva, L. Schaade, and A. Nitsche, "Combined proteomics/genomics approach reveals proteomic changes of mature virions as a novel poxvirus adaptation mechanism," Viruses, vol. 9, 2017.
    [Bibtex]
    @Article{Grossegesse:17,
    author = {Grossegesse, Marica and Doellinger, Joerg and Tyshaieva, Alona and Schaade, Lars and Nitsche, Andreas},
    title = {Combined Proteomics/Genomics Approach Reveals Proteomic Changes of Mature Virions as a Novel Poxvirus Adaptation Mechanism},
    journal = {Viruses},
    year = {2017},
    volume = {9},
    abstract = {DNA viruses, like poxviruses, possess a highly stable genome, suggesting that adaptation of virus particles to specific cell types is not restricted to genomic changes. Cowpox viruses are zoonotic poxviruses with an extraordinarily broad host range, demonstrating their adaptive potential in vivo. To elucidate adaptation mechanisms of poxviruses, we isolated cowpox virus particles from a rat and passaged them five times in a human and a rat cell line. Subsequently, we analyzed the proteome and genome of the non-passaged virions and each passage. While the overall viral genome sequence was stable during passaging, proteomics revealed multiple changes in the virion composition. Interestingly, an increased viral fitness in human cells was observed in the presence of increased immunomodulatory protein amounts. As the only minor variant with increasing frequency during passaging was located in a viral RNA polymerase subunit and, moreover, most minor variants were found in transcription-associated genes, protein amounts were presumably regulated at transcription level. This study is the first comparative proteome analysis of virus particles before and after cell culture propagation, revealing proteomic changes as a novel poxvirus adaptation mechanism.},
    doi = {10.3390/v9110337},
    issue = {11},
    keywords = {Adaptation, Physiological, genetics; Amino Acid Sequence; Animals; Cell Line; Cowpox virus, chemistry, genetics; DNA-Directed RNA Polymerases; Gene Expression Regulation; Genetic Fitness; Genome, Viral, genetics; High-Throughput Nucleotide Sequencing; Host Specificity; Immunomodulation; Proteome, genetics; Rats; Rats, Wistar; Sequence Analysis, DNA; Viral Proteins, analysis, genetics; Virion, chemistry; Virus Cultivation; Virus Replication; adaptation; cell culture; cowpox virus; genomics; passaging; poxvirus; proteomics},
    pmid = {29125539},
    }
  • [DOI] S. Giese, K. Ciminski, H. Bolte, É. A. Moreira, S. Lakdawala, Z. Hu, Q. David, L. Kolesnikova, V. Götz, Y. Zhao, J. Dengjel, E. Y. Chin, K. Xu, and M. Schwemmle, "Role of influenza A virus NP acetylation on viral growth and replication," Nat Commun, vol. 8, p. 1259, 2017.
    [Bibtex]
    @Article{Giese:17,
    author = {Giese, Sebastian and Ciminski, Kevin and Bolte, Hardin and Moreira, \'{E}tori Aguiar and Lakdawala, Seema and Hu, Zehan and David, Quinnlan and Kolesnikova, Larissa and G\"{o}tz, Veronika and Zhao, Yongxu and Dengjel, J\"{o}rn and Chin, Y Eugene and Xu, Ke and Schwemmle, Martin},
    title = {Role of influenza {A} virus {NP} acetylation on viral growth and replication},
    journal = {{Nat Commun}},
    year = {2017},
    volume = {8},
    pages = {1259},
    abstract = {Lysine acetylation is a post-translational modification known to regulate protein functions. Here we identify several acetylation sites of the influenza A virus nucleoprotein (NP), including the lysine residues K77, K113 and K229. Viral growth of mutant virus encoding K229R, mimicking a non-acetylated NP lysine residue, is severely impaired compared to wildtype or the mutant viruses encoding K77R or K113R. This attenuation is not the result of decreased polymerase activity, altered protein expression or disordered vRNP co-segregation but rather caused by impaired particle release. Interestingly, release deficiency is also observed mimicking constant acetylation at this site (K229Q), whereas virus encoding NP-K113Q could not be generated. However, mimicking NP hyper-acetylation at K77 and K229 severely diminishes viral polymerase activity, while mimicking NP hypo-acetylation at these sites has no effect on viral replication. These results suggest that NP acetylation at K77, K113 and K229 impacts multiple steps in viral replication of influenza A viruses.},
    doi = {10.1038/s41467-017-01112-3},
    issue = {1},
    keywords = {Acetylation; Animals; Dogs; HEK293 Cells; Humans; Influenza A virus, genetics, growth & development, metabolism; Lysine, metabolism; Madin Darby Canine Kidney Cells; Mutation; RNA-Binding Proteins, genetics, metabolism; Viral Core Proteins, genetics, metabolism; Virus Replication, genetics},
    pmid = {29097654},
    }
  • [DOI] E. Wyler, J. Menegatti, V. Franke, C. Kocks, A. Boltengagen, T. Hennig, K. Theil, A. Rutkowski, C. Ferrai, L. Baer, L. Kermas, C. C. Friedel, N. Rajewsky, A. Akalin, L. Dölken, F. Grässer, and M. Landthaler, "Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection," Genome Biol, vol. 18, p. 209, 2017.
    [Bibtex]
    @Article{Wyler:17,
    author = {Wyler, Emanuel and Menegatti, Jennifer and Franke, Vedran and Kocks, Christine and Boltengagen, Anastasiya and Hennig, Thomas and Theil, Kathrin and Rutkowski, Andrzej and Ferrai, Carmelo and Baer, Laura and Kermas, Lisa and Friedel, Caroline C and Rajewsky, Nikolaus and Akalin, Altuna and Dölken, Lars and Grässer, Friedrich and Landthaler, Markus},
    title = {Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection},
    journal = {{Genome Biol}},
    year = {2017},
    volume = {18},
    pages = {209},
    abstract = {Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ways to adapt the infected cells to their needs, but knowledge about these transcriptional and post-transcriptional modifications is sparse. Here, we show that HSV-1 induces the expression of about 1000 antisense transcripts from the human host cell genome. A subset of these is also activated by the closely related varicella zoster virus. Antisense transcripts originate either at gene promoters or within the gene body, and they show different susceptibility to the inhibition of early and immediate early viral gene expression. Overexpression of the major viral transcription factor ICP4 is sufficient to turn on a subset of antisense transcripts. Histone marks around transcription start sites of HSV-1-induced and constitutively transcribed antisense transcripts are highly similar, indicating that the genetic loci are already poised to transcribe these novel RNAs. Furthermore, an antisense transcript overlapping with the BBC3 gene (also known as PUMA) transcriptionally silences this potent inducer of apoptosis in cis. We show for the first time that a virus induces widespread antisense transcription of the host cell genome. We provide evidence that HSV-1 uses this to downregulate a strong inducer of apoptosis. Our findings open new perspectives on global and specific alterations of host cell transcription by viruses.},
    doi = {10.1186/s13059-017-1329-5},
    issue = {1},
    keywords = {Apoptosis Regulatory Proteins, genetics, metabolism; Gene Expression Regulation, Viral, drug effects; Genome, Human; HeLa Cells; Herpes Simplex, virology; Herpesvirus 1, Human, physiology; Histone Code; Host-Pathogen Interactions, drug effects, genetics; Humans; Lipopolysaccharides, pharmacology; Monocytes, drug effects, metabolism; NF-kappa B, metabolism; Promoter Regions, Genetic, genetics; Proto-Oncogene Proteins, genetics, metabolism; RNA, Antisense, genetics, metabolism; RNA, Messenger, genetics, metabolism; Reproducibility of Results; Sequence Analysis, RNA; Transcription, Genetic, drug effects; Viral Proteins, metabolism; Antisense; BBC3; Herpes; ICP4; NFKB; Transcription; Virus; lncRNA},
    pmid = {29089033},
    }
  • [DOI] A. Hake and N. Pfeifer, "Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time," PLoS Comput Biol, vol. 13, p. e1005789, 2017.
    [Bibtex]
    @Article{Hake:17,
    author = {Hake, Anna and Pfeifer, Nico},
    title = {Prediction of {HIV}-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time},
    journal = {{PLoS Comput Biol}},
    year = {2017},
    volume = {13},
    pages = {e1005789},
    abstract = {Treatment with broadly neutralizing antibodies (bNAbs) has proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. Due to the high mutation rate of HIV-1, resistance testing of the patient's viral strains to the bNAbs is still inevitable. So far, bNAb resistance can only be tested in expensive and time-consuming neutralization experiments. Here, we introduce well-performing computational models that predict the neutralization response of HIV-1 to bNAbs given only the envelope sequence of the virus. Using non-linear support vector machines based on a string kernel, the models learnt even the important binding sites of bNAbs with more complex epitopes, i.e., the CD4 binding site targeting bNAbs, proving thereby the biological relevance of the models. To increase the interpretability of the models, we additionally provide a new kind of motif logo for each query sequence, visualizing those residues of the test sequence that influenced the prediction outcome the most. Moreover, we predicted the neutralization sensitivity of around 34,000 HIV-1 samples from different time points to a broad range of bNAbs, enabling the first analysis of HIV resistance to bNAbs on a global scale. The analysis showed for many of the bNAbs a trend towards antibody resistance over time, which had previously only been discovered for a small non-representative subset of the global HIV-1 population.},
    doi = {10.1371/journal.pcbi.1005789},
    issue = {10},
    keywords = {Antibodies, Neutralizing, chemistry, immunology; Binding Sites; CD4 Antigens; Drug Resistance, Viral, immunology; Epitope Mapping, methods; HIV Antibodies, chemistry, immunology; HIV-1, chemistry, immunology; Humans; Protein Binding; Protein Interaction Mapping, methods; Sequence Analysis, Protein, methods; Time Factors},
    pmid = {29065122},
    }
  • [DOI] B. Vrancken, M. A. Suchard, and P. Lemey, "Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling," Virus Evol, vol. 3, p. vex028, 2017.
    [Bibtex]
    @Article{Vrancken:17,
    author = {Vrancken, Bram and Suchard, Marc A and Lemey, Philippe},
    title = {Accurate quantification of within- and between-host {HBV} evolutionary rates requires explicit transmission chain modelling},
    journal = {{Virus Evol}},
    year = {2017},
    volume = {3},
    pages = {vex028},
    abstract = {Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, , 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state b