Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms. Together, these data cover roughly a quarter of mammal diversity, a 10th of bird diversity, and ∼6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution and make suggestions for best practices that address the unique mix of evidence that coexists in these data. IMPORTANCE Animals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in different levels of detail. VIRION is a new database that combines several of these existing data sources, reconciles taxonomy to a single consistent backbone, and reports metadata in a format designed by and for virologists. Researchers can use VIRION to easily answer questions like “Can any fish viruses infect humans?” or “Which bats host coronaviruses?” or to build more advanced predictive models, making it an unprecedented step toward a full inventory of the global virome.
Digital Object Identifier (DOI)
Published in mBio, Volume 13, Issue 2, 2022.
© 2022 Carlson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Carlson, C. J., Gibb, R. J., Albery, G. F., Brierley, L., Connor, R. P., Dallas, T. A., Eskew, E. A., Fagre, A. C., Farrell, M. J., Frank, H. K., Muylaert, R. L., Poisot, T., Rasmussen, A. L., Ryan, S. J., & Seifert, S. N. (2022). The global virome in One Network (virion): An atlas of vertebrate-virus associations. mBio, 13(2). https://doi.org/10.1128/mbio.02985-21