Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Mateus Bernabe Fiamenghi, Antônio Pedro Camargo, Iro N Chasapi, Fotis A. Baltoumas, Simon Roux, Artyom A. Egorov, Eleni Aplakidou, Éric Olo Ndela, Yumary M. Vasquez, I-Min A. Chen, Krishna Palaniappan, T. B. K. Reddy, Supratim Mukherjee, Natalia Ivanova, Frederik Schulz, Tanja Woyke, Emiley A. Eloe‐Fadrosh, Georgios A. Pavlopoulos, Nikos C. Kyrpides
Abstract
Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.