Event Calendar » viruses in silico | the EVBC lecture series

To keep you up to date with the latest developments in virus bioinformatics, especially new tools that might help you in your research, the European Virus Bioinformatics Center is organising a monthly lecture series entitled viruses in silico.

The lecture will take place online as a Zoom Meeting. Participation is free. Use the registration form to receive the login details. Registration is possible until 1 hour before the start of the event.

Please note that the lectures are not recorded. Exceptions can be requested in advance.

If you want a lecture to be recorded, please contact us beforehand.


Computational investigation of phage sequences in MetaSUB data
27. May 2024 | 4 pm CET
João Carlos Setubal, University of São Paulo, Brazil

The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics. In this work, we searched MetaSUB metagenomic data for bacteriophage genomes. We recovered and analyzed 1,714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. One driving interest in phage sequence data analysis is host prediction. For this, we used three methods, one of which was the program vHULK, developed by our group. We were able to predict hosts (at the genus or species level) for 48% of the phage genomes, and observed general agreement between phage abundance and the respective predicted bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. This work has been recently published as Flores et al., Scientific Reports, doi: 10.1038/s41598-024-58226-0.


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