{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T07:30:59Z","timestamp":1776238259146,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"D1","funder":[{"name":"U.S. Department of Energy Joint Genome Institute"},{"name":"Office of Science of the U.S. Department of Energy","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG\/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and\/or sequence similarity. Here, we present the fourth version of IMG\/VR, composed of &amp;gt;15 million virus genomes and genome fragments, a\u00a0\u22486-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG\/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG\/VR v4 is available at https:\/\/img.jgi.doe.gov\/vr, and the underlying data are available to download at https:\/\/genome.jgi.doe.gov\/portal\/IMG_VR.<\/jats:p>","DOI":"10.1093\/nar\/gkac1037","type":"journal-article","created":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T18:34:07Z","timestamp":1668796447000},"page":"D733-D743","source":"Crossref","is-referenced-by-count":405,"title":["IMG\/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3913-2484","authenticated-orcid":false,"given":"Antonio Pedro","family":"Camargo","sequence":"first","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Stephen","family":"Nayfach","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2026-9798","authenticated-orcid":false,"given":"I-Min A","family":"Chen","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Krishnaveni","family":"Palaniappan","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Anna","family":"Ratner","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Ken","family":"Chu","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Stephan\u00a0J","family":"Ritter","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0871-5567","authenticated-orcid":false,"given":"T B K","family":"Reddy","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6322-2271","authenticated-orcid":false,"given":"Supratim","family":"Mukherjee","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Frederik","family":"Schulz","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Lee","family":"Call","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Russell\u00a0Y","family":"Neches","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Tanja","family":"Woyke","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Natalia\u00a0N","family":"Ivanova","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8162-1276","authenticated-orcid":false,"given":"Emiley\u00a0A","family":"Eloe-Fadrosh","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"given":"Nikos\u00a0C","family":"Kyrpides","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5831-5895","authenticated-orcid":false,"given":"Simon","family":"Roux","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA"}]}],"member":"286","published-online":{"date-parts":[[2022,11,18]]},"reference":[{"key":"2023010804303220300_B1","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.tim.2005.04.003","article-title":"Here a virus, there a virus, everywhere the same virus?","volume":"13","author":"Breitbart","year":"2005","journal-title":"Trends Microbiol."},{"key":"2023010804303220300_B2","doi-asserted-by":"crossref","first-page":"e00193-20","DOI":"10.1128\/MMBR.00193-20","article-title":"Viruses defined by the position of the virosphere within the replicator space","volume":"85","author":"Koonin","year":"2021","journal-title":"Microbiol. 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Virol."},{"key":"2023010804303220300_B5","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.virusres.2017.10.014","article-title":"A decade of RNA virus metagenomics is (not) enough","volume":"244","author":"Greninger","year":"2018","journal-title":"Virus Res."},{"key":"2023010804303220300_B6","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/nbt.4306","article-title":"Minimum information about an uncultivated virus genome (MIUViG)","volume":"37","author":"Roux","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2023010804303220300_B7","doi-asserted-by":"crossref","first-page":"e2023202118","DOI":"10.1073\/pnas.2023202118","article-title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases","volume":"118","author":"Tisza","year":"2021","journal-title":"Proc. Natl. Acad. Sci. 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