{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T03:31:31Z","timestamp":1762918291430,"version":"3.41.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","funder":[{"DOI":"10.13039\/100000092","name":"U.S. National Library of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Rapid response to the current coronavirus disease 2019 (COVID-19) pandemic requires fast dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data in order to align diagnostic tests and vaccines with the natural evolution of the virus as it spreads through the world. To facilitate this, the National Library of Medicine\u2019s National Center for Biotechnology Information developed an automated pipeline for the deposition and quick processing of SARS-CoV-2 genome assemblies into GenBank for the user community. The pipeline ensures the collection of contextual information about the virus source, assesses sequence quality and annotates descriptive biological features, such as protein-coding regions and mature peptides. The process promotes standardized nomenclature and creates and publishes fully processed GenBank files within minutes of deposition. The software has processed and published 982\u2009454 annotated SARS-CoV-2 sequences, as of 21 October 2021. This development addresses the needs of the scientific community as the sequencing of SARS-CoV-2 genomes increases and will facilitate unrestricted access to and usability of SARS-CoV-2 genomic sequence data, providing important reagents for scientific and public health activities in response to the COVID-19 pandemic. Database URL https:\/\/submit.ncbi.nlm.nih.gov\/sarscov2\/genbank\/<\/jats:p>","DOI":"10.1093\/database\/baac006","type":"journal-article","created":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T12:13:29Z","timestamp":1643976809000},"source":"Crossref","is-referenced-by-count":4,"title":["Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank"],"prefix":"10.1093","volume":"2022","author":[{"given":"Beverly A","family":"Underwood","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda","family":"Yankie","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric P","family":"Nawrocki","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasuki","family":"Palanigobu","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergiy","family":"Gotvyanskyy","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent C","family":"Calhoun","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Kornbluh","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas G","family":"Smith","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lydia","family":"Fleischmann","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denis","family":"Sinyakov","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colleen J","family":"Bollin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0289-7101","authenticated-orcid":false,"given":"Ilene","family":"Karsch-Mizrachi","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,1]]},"reference":[{"key":"2022031007350207400_R1","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"2022031007350207400_R2","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"2022031007350207400_R3","first-page":"1843","article-title":"Detection of SARS-CoV-2 in different types of clinical specimens","volume":"323","author":"Wang","year":"2020","journal-title":"JAMA"},{"key":"2022031007350207400_R4","doi-asserted-by":"crossref","first-page":"9241","DOI":"10.1073\/pnas.2004999117","article-title":"Phylogenetic network analysis of SARS-CoV-2 genomes","volume":"117","author":"Forster","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022031007350207400_R5","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0241535","article-title":"Variant analysis of 1,040 SARS-CoV-2 genomes","volume":"15","author":"Rouchka","year":"2020","journal-title":"PLoS One"},{"key":"2022031007350207400_R6","doi-asserted-by":"crossref","first-page":"D9","DOI":"10.1093\/nar\/gkz899","article-title":"Database resources of the national center for biotechnology information","volume":"48","author":"Sayers","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022031007350207400_R7","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gkaa967","article-title":"The international nucleotide sequence database collaboration","volume":"49","author":"Arita","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022031007350207400_R8","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2022031007350207400_R9","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-020-3537-3","article-title":"VADR: validation and annotation of virus sequence submissions to GenBank","volume":"21","author":"Schaffer","year":"2020","journal-title":"BMC Bioinform."},{"key":"2022031007350207400_R10","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41564-020-0695-z","article-title":"The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2","volume":"5","author":"Coronaviridae Study Group of the International Committee on Taxonomy of Viruses","year":"2020","journal-title":"Nat. Microbiol."},{"key":"2022031007350207400_R11","doi-asserted-by":"crossref","first-page":"D57","DOI":"10.1093\/nar\/gkr1163","article-title":"BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata","volume":"40","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac006\/42793431\/baac006.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac006\/42793431\/baac006.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T07:35:24Z","timestamp":1646897724000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baac006\/6540156"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":11,"URL":"https:\/\/doi.org\/10.1093\/database\/baac006","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2022,1,1]]},"article-number":"baac006"}}