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:

2020

  • [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] 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] F. Mock, A. Viehweger, E. Barth, and M. Marz, “Viral host prediction with deep learning,” bioRxiv, p. 575571, 2019.
    [Bibtex]
    @Article{Mock:19,
    author = {Florian Mock and Adrian Viehweger and Emanuel Barth and Manja Marz},
    title = {Viral host prediction with Deep Learning},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {575571},
    doi = {10.1101/575571},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [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. Gifford, D. 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 Gifford and David 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] A. W. Whisnant, C. S. Jürges, T. Hennig, E. Wyler, B. Prusty, A. J. Rutkowski, A. L’hernault, M. Göbel, K. Döring, J. Menegatti, R. Antrobus, N. J. Matheson, F. W. H. Künzig, G. Mastrobuoni, C. Bielow, S. Kempa, L. Chunguang, T. Dandekar, R. Zimmer, M. Landthaler, F. Grässer, P. J. Lehner, C. C. Friedel, F. Erhard, and L. Dölken, “Integrative functional genomics decodes herpes simplex virus 1,” bioRxiv, p. 603654, 2019.
    [Bibtex]
    @Article{Whisnant:19,
    author = {Adam W. Whisnant and Christopher S. Jürges and Thomas Hennig and Emanuel Wyler and Bhupesh Prusty and Andrzej J Rutkowski and Anne L'hernault and Margarete Göbel and Kristina Döring and Jennifer Menegatti and Robin Antrobus and Nicholas J. Matheson and Florian W.H. Künzig and Guido Mastrobuoni and Chris Bielow and Stefan Kempa and Liang Chunguang and Thomas Dandekar and Ralf Zimmer and Markus Landthaler and Friedrich Grässer and Paul J. Lehner and Caroline C. Friedel and Florian Erhard and Lars Dölken},
    title = {Integrative functional genomics decodes herpes simplex virus 1},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {603654},
    doi = {10.1101/603654},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [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. 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 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. 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 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. 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 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] M. Kuhring, J. Doellinger, A. Nitsche, T. Muth, and B. Y. Renard, "An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples," bioRxiv, 2019.
    [Bibtex]
    @Article{Kuhring:19,
    author = {Mathias Kuhring and Joerg Doellinger and Andreas Nitsche and Thilo Muth and Bernhard Y. Renard},
    title = {An iterative and automated computational pipeline for untargeted strain-level identification using {MS}/{MS} spectra from pathogenic samples},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/812313},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Duchene, P. Lemey, T. Stadler, S. Y. Ho, D. A. Duchene, V. Dhanasekaran, and G. Baele, "Bayesian evaluation of temporal signal in measurably evolving populations," bioRxiv, 2019.
    [Bibtex]
    @Article{Duchene:19,
    author = {Sebastian Duchene and Philippe Lemey and Tanja Stadler and Simon YW Ho and David A Duchene and Vijaykrishna Dhanasekaran and Guy Baele},
    title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations},
    journal = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/810697},
    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] 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," bioRxiv, 2019.
    [Bibtex]
    @Article{Kreer:19,
    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 = {{bioRxiv}},
    year = {2019},
    doi = {10.1101/847574},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [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] C. Whitten-Bauer, J. Chung, A. Gómez-Moreno, P. Gomollón-Zueco, M. D. Huber, L. Gerace, and U. Garaigorta, "The host factor erlin-1 is required for efficient Hepatitis C Virus infection.," Cells, vol. 8, 2019.
    [Bibtex]
    @Article{Whitten-Bauer:19,
    author = {Whitten-Bauer, Christina and Chung, Josan and Gómez-Moreno, Andoni and Gomollón-Zueco, Pilar and Huber, Michael D and Gerace, Larry and Garaigorta, Urtzi},
    title = {The Host Factor Erlin-1 is Required for Efficient {H}epatitis {C} {V}irus Infection.},
    journal = {{Cells}},
    year = {2019},
    volume = {8},
    abstract = {Development of hepatitis C virus (HCV) infection cell culture systems has permitted the identification of cellular factors that regulate the HCV life cycle. Some of these cellular factors affect steps in the viral life cycle that are tightly associated with intracellular membranes derived from the endoplasmic reticulum (ER). Here, we describe the discovery of erlin-1 protein as a cellular factor that regulates HCV infection. Erlin-1 is a cholesterol-binding protein located in detergent-resistant membranes within the ER. It is implicated in cholesterol homeostasis and the ER-associated degradation pathway. Silencing of erlin-1 protein expression by siRNA led to decreased infection efficiency characterized by reduction in intracellular RNA accumulation, HCV protein expression and virus production. Mechanistic studies revealed that erlin-1 protein is required early in the infection, downstream of cell entry and primary translation, specifically to initiate RNA replication, and later in the infection to support infectious virus production. This study identifies erlin-1 protein as an important cellular factor regulating HCV infection.},
    doi = {10.3390/cells8121555},
    issue = {12},
    keywords = {HCV; RNA replication; endoplasmic reticulum; erlin-1; erlin-2; hepatitis C virus; host factor; lipid droplet; protein production; virus production},
    pmid = {31810281},
    }
  • [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},
    }

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},
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    title = {Safety and antiviral activity of combination {HIV}-1 broadly neutralizing antibodies in viremic individuals},
    journal = {{Nat Med}},
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    [Bibtex]
    @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}},
    year = {2018},
    volume = {3},
    number = {10},
    pages = {1161--1174},
    doi = {10.1038/s41564-018-0236-1},
    publisher = {Springer Nature},
    }
  • [DOI] H. Fröhlich, R. Balling, N. Beerenwinkel, O. Kohlbacher, S. Kumar, T. Lengauer, M. H. Maathuis, Y. Moreau, S. A. Murphy, T. M. Przytycka, M. Rebhan, H. Röst, A. Schuppert, M. Schwab, R. Spang, D. Stekhoven, J. Sun, A. Weber, D. Ziemek, and B. Zupan, "From hype to reality: data science enabling personalized medicine," BMC Medicine, vol. 16, iss. 1, 2018.
    [Bibtex]
    @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},
    journal = {{BMC Medicine}},
    year = {2018},
    volume = {16},
    number = {1},
    doi = {10.1186/s12916-018-1122-7},
    publisher = {Springer Nature},
    }
  • [DOI] P. Barbera, A. M. Kozlov, L. Czech, B. Morel, D. Darriba, T. Flouri, and A. Stamatakis, "EPA-ng: massively parallel evolutionary placement of genetic sequences," Syst Biol, vol. 68, iss. 2, p. 365–369, 2018.
    [Bibtex]
    @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},
    journal = {{Syst Biol}},
    year = {2018},
    volume = {68},
    number = {2},
    pages = {365--369},
    doi = {10.1093/sysbio/syy054},
    editor = {David Posada},
    publisher = {Oxford University Press ({OUP})},
    }
  • [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. 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 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},
    }

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 Radoni\'{c}, 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. 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 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 between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.},
    doi = {10.1093/ve/vex028},
    issue = {2},
    keywords = {BEAST; hepatitis B virus; statistical phylogenetics; substitution rate; transmission chain},
    pmid = {29026650},
    }
  • [DOI] A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Dröge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. S. Jørgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, M. Balvočiūtė, L. H. Hansen, S. J. Sørensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. Don Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. D. Barton, T. Lingner, H. Lin, Y. Liao, G. G. Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H. Klenk, M. Göker, N. C. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, and A. C. McHardy, "Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software," Nat Methods, vol. 14, p. 1063–1071, 2017.
    [Bibtex]
    @Article{Sczyrba:17,
    author = {Sczyrba, Alexander and Hofmann, Peter and Belmann, Peter and Koslicki, David and Janssen, Stefan and Dröge, Johannes and Gregor, Ivan and Majda, Stephan and Fiedler, Jessika and Dahms, Eik and Bremges, Andreas and Fritz, Adrian and Garrido-Oter, Ruben and Jørgensen, Tue Sparholt and Shapiro, Nicole and Blood, Philip D and Gurevich, Alexey and Bai, Yang and Turaev, Dmitrij and DeMaere, Matthew Z and Chikhi, Rayan and Nagarajan, Niranjan and Quince, Christopher and Meyer, Fernando and Balvočiūtė, Monika and Hansen, Lars Hestbjerg and Sørensen, Søren J and Chia, Burton K H and Denis, Bertrand and Froula, Jeff L and Wang, Zhong and Egan, Robert and Don Kang, Dongwan and Cook, Jeffrey J and Deltel, Charles and Beckstette, Michael and Lemaitre, Claire and Peterlongo, Pierre and Rizk, Guillaume and Lavenier, Dominique and Wu, Yu-Wei and Singer, Steven W and Jain, Chirag and Strous, Marc and Klingenberg, Heiner and Meinicke, Peter and Barton, Michael D and Lingner, Thomas and Lin, Hsin-Hung and Liao, Yu-Chieh and Silva, Genivaldo Gueiros Z and Cuevas, Daniel A and Edwards, Robert A and Saha, Surya and Piro, Vitor C and Renard, Bernhard Y and Pop, Mihai and Klenk, Hans-Peter and Göker, Markus and Kyrpides, Nikos C and Woyke, Tanja and Vorholt, Julia A and Schulze-Lefert, Paul and Rubin, Edward M and Darling, Aaron E and Rattei, Thomas and McHardy, Alice C},
    title = {{C}ritical {A}ssessment of {M}etagenome {I}nterpretation-a benchmark of metagenomics software},
    journal = {{Nat Methods}},
    year = {2017},
    volume = {14},
    pages = {1063--1071},
    abstract = {Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.},
    doi = {10.1038/nmeth.4458},
    issue = {11},
    keywords = {Algorithms; Benchmarking; Metagenomics; Sequence Analysis, DNA; Software},
    pmid = {28967888},
    }
  • [DOI] M. Kiening, F. Weber, and D. Frishman, "Conserved RNA structures in the intergenic regions of ambisense viruses," Sci Rep, vol. 7, p. 16625, 2017.
    [Bibtex]
    @Article{Kiening:17,
    author = {Kiening, Michael and Weber, Friedemann and Frishman, Dmitrij},
    title = {Conserved {RNA} structures in the intergenic regions of ambisense viruses},
    journal = {{Sci Rep}},
    year = {2017},
    volume = {7},
    pages = {16625},
    abstract = {Ambisense viruses are negative-sense single-stranded RNA viruses that use a unique expression strategy. Their genome contains at least one ambisense RNA segment that carries two oppositely oriented reading frames separated by an intergenic region. It is believed that a structural RNA element within the intergenic region is involved in transcription termination. However, a general overview over the structural repertoire of ambisense intergenic regions is currently lacking. In this study we investigated the structural potential of the intergenic regions of all known ambisense viruses and compared their structural repertoire by structure-guided clustering. Intergenic regions of most ambisense viruses possess a high potential to build stable secondary structures and many viruses share common structural motifs in the intergenic regions of their ambisense segments. We demonstrate that (i) within the phylogenetic virus groups sets of conserved functional structures are present, but that (ii) between the groups conservation is low to non-existent. These results reflect a high degree of freedom to regulate ambisense transcription termination and also imply that the genetic strategy of having an ambisense RNA genome has evolved several times independently.},
    doi = {10.1038/s41598-017-16875-4},
    issue = {1},
    pmid = {29192224},
    }
  • K. Meixenberger, K. P. Yousef, M. R. Smith, S. Somogyi, S. Fiedler, B. Bartmeyer, O. Hamouda, N. Bannert, M. von Kleist, and C. Kücherer, "Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors," Virol J, vol. 14, iss. 1, p. 223, 2017.
    [Bibtex]
    @Article{Meixenberger:17,
    author = {Meixenberger, Karolin and Yousef, Kaveh Pouran and Smith, Maureen Rebecca and Somogyi, Sybille and Fiedler, Stefan and Bartmeyer, Barbara and Hamouda, Osamah and Bannert, Norbert and von Kleist, Max and K{\"u}cherer, Claudia},
    title = {Molecular evolution of {HIV}-1 integrase during the 20 years prior to the first approval of integrase inhibitors},
    journal = {{Virol J}},
    year = {2017},
    volume = {14},
    number = {1},
    pages = {223},
    publisher = {BioMed Central},
    }
  • A. E. Shaw, J. Hughes, Q. Gu, A. Behdenna, J. B. Singer, T. Dennis, R. J. Orton, M. Varela, R. J. Gifford, S. J. Wilson, and others, "Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type i interferon responses," PLoS Biol, vol. 15, iss. 12, p. e2004086, 2017.
    [Bibtex]
    @Article{Shaw:17,
    author = {Shaw, Andrew E and Hughes, Joseph and Gu, Quan and Behdenna, Abdelkader and Singer, Joshua B and Dennis, Tristan and Orton, Richard J and Varela, Mariana and Gifford, Robert J and Wilson, Sam J and others},
    title = {Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses},
    journal = {{PLoS Biol}},
    year = {2017},
    volume = {15},
    number = {12},
    pages = {e2004086},
    publisher = {Public Library of Science},
    }