{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T15:00:22Z","timestamp":1768748422509,"version":"3.49.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,11]],"date-time":"2021-10-11T00:00:00Z","timestamp":1633910400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research Program of China","award":["2021YFC0863300"],"award-info":[{"award-number":["2021YFC0863300"]}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDA19050301"],"award-info":[{"award-number":["XDA19050301"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["WX145XQ07-01"],"award-info":[{"award-number":["WX145XQ07-01"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["KFZD-SW-219"],"award-info":[{"award-number":["KFZD-SW-219"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["82161148010"],"award-info":[{"award-number":["82161148010"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn\/ncovn.<\/jats:p>","DOI":"10.1093\/nar\/gkab921","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T20:48:32Z","timestamp":1633034912000},"page":"D888-D897","source":"Crossref","is-referenced-by-count":28,"title":["VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes"],"prefix":"10.1093","volume":"50","author":[{"given":"Qinglan","family":"Sun","sequence":"first","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Chang","family":"Shu","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Wenyu","family":"Shi","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Yingfeng","family":"Luo","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Guomei","family":"Fan","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Jingyi","family":"Nie","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Yuhai","family":"Bi","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Qihui","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Jianxun","family":"Qi","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4409-1667","authenticated-orcid":false,"given":"Jian","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China"}]},{"given":"Yuanchun","family":"Zhou","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"Zhihong","family":"Shen","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"Zhen","family":"Meng","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"}]},{"given":"Xinjiao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Zhengfei","family":"Yu","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Shenghan","family":"Gao","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5255-1846","authenticated-orcid":false,"given":"Linhuan","family":"Wu","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Juncai","family":"Ma","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"Chinese National Microbiology Data Center (NMDC), Beijing 100101, China"}]},{"given":"Songnian","family":"Hu","sequence":"additional","affiliation":[{"name":"Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,11]]},"reference":[{"key":"2022010507405560900_B1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.chom.2021.02.017","article-title":"One year of SARS-CoV-2 evolution","volume":"29","author":"Wu","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2022010507405560900_B2","doi-asserted-by":"crossref","first-page":"104351","DOI":"10.1016\/j.meegid.2020.104351","article-title":"Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection","volume":"83","author":"van\u00a0Dorp","year":"2020","journal-title":"Genetics Evol."},{"key":"2022010507405560900_B3","doi-asserted-by":"crossref","first-page":"e00496","DOI":"10.1128\/JVI.00496-21","article-title":"Genomewide variation in betacoronaviruses","volume":"95","author":"LaTourrette","year":"2021","journal-title":"Virol"},{"key":"2022010507405560900_B4","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1016\/j.cell.2020.09.032","article-title":"Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant","volume":"3","author":"Yurkovetskiy","year":"2020","journal-title":"Cell"},{"key":"2022010507405560900_B5","doi-asserted-by":"crossref","first-page":"6929","DOI":"10.1021\/acsnano.0c10833","article-title":"Computational mutagenesis at the SARS-CoV-2 spike protein\/angiotensin-converting enzyme 2 binding interface: comparison with experimental evidence","volume":"15","author":"Laurini","year":"2021","journal-title":"ACS Nano"},{"key":"2022010507405560900_B6","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.jpha.2021.03.006","article-title":"Molecular detection of SARS-CoV-2 being challenged by virus variation and asymptomatic infection","volume":"11","author":"Jiang","year":"2021","journal-title":"J. Pharm. Analysis"},{"key":"2022010507405560900_B7","doi-asserted-by":"crossref","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: A fast and versatile genome alignment system","volume":"14","author":"Marcais","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"2022010507405560900_B8","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.abi7994","article-title":"SARS-CoV-2 immune evasion by the B.1.427\/B.1.429 variant of concern","volume":"373","author":"McCallum","year":"2021","journal-title":"Science"},{"key":"2022010507405560900_B9","doi-asserted-by":"crossref","first-page":"5212","DOI":"10.1016\/j.jmb.2020.07.009","article-title":"Mutations strengthened SARS-CoV-2 infectivity","volume":"432","author":"Chen","year":"2020","journal-title":"J. Mol. Biol."},{"key":"2022010507405560900_B10","doi-asserted-by":"crossref","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"EuroSurveillance"},{"key":"2022010507405560900_B11","doi-asserted-by":"crossref","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the National Center for Biotechnology Information","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507405560900_B12","doi-asserted-by":"crossref","first-page":"2563","DOI":"10.3390\/ijms21072563","article-title":"SAAMBE-3D: predicting effect of mutations on protein\u2013protein interactions","volume":"21","author":"Pahari","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"2022010507405560900_B13","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1126\/science.abc5881","article-title":"Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody","volume":"369","author":"Lv","year":"2020","journal-title":"Science"},{"key":"2022010507405560900_B14","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.abd0827","article-title":"Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail","volume":"369","author":"Hansen","year":"2020","journal-title":"Science"},{"key":"2022010507405560900_B15","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1016\/j.cell.2020.09.049","article-title":"A therapeutic Non-self-reactive SARS-CoV-2 antibody protects from lung pathology in a COVID-19 hamster model","volume":"183","author":"Kreye","year":"2020","journal-title":"Cell"},{"key":"2022010507405560900_B16","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.chom.2020.06.010","article-title":"Neutralization of SARS-CoV-2 by destruction of the prefusion spike","volume":"28","author":"Huo","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2022010507405560900_B17","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1038\/s41594-020-0480-y","article-title":"Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient","volume":"27","author":"Zhou","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2022010507405560900_B18","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/s41586-020-2852-1","article-title":"SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies","volume":"588","author":"Barnes","year":"2020","journal-title":"Nature"},{"key":"2022010507405560900_B19","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1016\/j.cell.2020.09.037","article-title":"Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology","volume":"183","author":"Piccoli","year":"2020","journal-title":"Cell"},{"key":"2022010507405560900_B20","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1016\/j.cell.2021.02.033","article-title":"Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera","volume":"184","author":"Supasa","year":"2021","journal-title":"Cell"},{"key":"2022010507405560900_B21","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-020-2381-y","article-title":"A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2","volume":"584","author":"Shi","year":"2020","journal-title":"Nature"},{"key":"2022010507405560900_B22","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/s41467-020-20602-5","article-title":"A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein","volume":"12","author":"Kim","year":"2021","journal-title":"Nat. Commun."},{"key":"2022010507405560900_B23","doi-asserted-by":"crossref","first-page":"eabf1906","DOI":"10.1126\/scitranslmed.abf1906","article-title":"The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates","volume":"13","author":"Jones","year":"2021","journal-title":"Sci. Transl. Med."},{"key":"2022010507405560900_B24","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/s41586-021-03807-6","article-title":"SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape","volume":"597","author":"Starr","year":"2021","journal-title":"Nature"},{"key":"2022010507405560900_B25","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1016\/j.molcel.2021.01.035","article-title":"Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication","volume":"81","author":"Bravo","year":"2021","journal-title":"Mol. Cell"},{"key":"2022010507405560900_B26","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1038\/s41594-020-0469-6","article-title":"Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2","volume":"27","author":"Huo","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2022010507405560900_B27","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1038\/s41467-020-20501-9","article-title":"Antibody neutralization of SARS-CoV-2 through ACE2 receptor mimicry","volume":"12","author":"Ge","year":"2021","journal-title":"Nat. Commun."},{"key":"2022010507405560900_B28","first-page":"e15280","article-title":"Emergent inpatient administration of casirivimab and imdevimab antibody cocktail for the treatment of COVID-19 pneumonia","volume":"13","author":"Phan","year":"2021","journal-title":"Cureus"},{"key":"2022010507405560900_B29","first-page":"49","article-title":"An EUA for bamlanivimab and etesevimab for COVID-19","volume":"63","year":"2021","journal-title":"Med. Lett. Drugs Ther."},{"key":"2022010507405560900_B30","first-page":"97","article-title":"An EUA for sotrovimab for treatment of COVID-19","volume":"63","year":"2021","journal-title":"Med. Lett. Drugs Ther."},{"key":"2022010507405560900_B31","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1111\/j.1420-9101.2009.01698.x","article-title":"SNP deserts of Asian cultivated rice: genomic regions under domestication","volume":"22","author":"Wang","year":"2009","journal-title":"J. Evol. Biol."},{"key":"2022010507405560900_B32","first-page":"434","article-title":"On the PAM matrix model of protein evolution","volume":"2","author":"Wilbur","year":"1985","journal-title":"Mol. Biol. Evol."},{"key":"2022010507405560900_B33","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/prot.340170108","article-title":"Performance evaluation of amino acid substitution matrices","volume":"17","author":"Henikoff","year":"1993","journal-title":"Proteins"},{"key":"2022010507405560900_B34","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/bioinformatics\/btv195","article-title":"PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels","volume":"31","author":"Choi","year":"2015","journal-title":"Bioinformatics"},{"key":"2022010507405560900_B35","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic. Acids. Res."},{"key":"2022010507405560900_B36","first-page":"514","article-title":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","volume":"9","author":"Ponomarenko","year":"2008","journal-title":"BioMed Central"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D888\/42058507\/gkab921.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D888\/42058507\/gkab921.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:20:59Z","timestamp":1641370859000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D888\/6389500"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,11]]},"references-count":36,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,10,11]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab921","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,10,11]]}}}