{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:11Z","timestamp":1772138471140,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T00:00:00Z","timestamp":1706832000000},"content-version":"vor","delay-in-days":28,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP17K08682"],"award-info":[{"award-number":["JP17K08682"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP19K22647"],"award-info":[{"award-number":["JP19K22647"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP20K07316"],"award-info":[{"award-number":["JP20K07316"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>SARS-CoV-2 is the cause of the current worldwide pandemic of severe acute respiratory syndrome. The change of nucleotide composition of the SARS-CoV-2 genome is crucial for understanding the spread and transmission dynamics of the virus because viral nucleotide sequences are essential in identifying viral strains. Recent studies have shown that cytosine (C) to uracil (U) substitutions are overrepresented in SARS-CoV-2 genome sequences. These asymmetric substitutions between C and U indicate that traditional time-reversible substitution models cannot be applied to the evolution of SARS-CoV-2 sequences. Thus, we develop a new time-irreversible model of nucleotide substitutions to estimate the substitution rates in SARS-CoV-2 genomes. We investigated the number of nucleotide substitutions among the 7862 genomic sequences of SARS-CoV-2 registered in the Global Initiative on Sharing All Influenza Data (GISAID) that have been sampled from all over the world. Using the new method, the substitution rates in SARS-CoV-2 genomes were estimated. The C-to-U substitution rates of SARS-CoV-2 were estimated to be 1.95\u00a0\u00d7\u00a010\u22123\u00a0\u00b1\u00a04.88\u00a0\u00d7\u00a010\u22124 per site per year, compared with 1.48\u00a0\u00d7\u00a010\u22124\u00a0\u00b1\u00a07.42\u00a0\u00d7\u00a010\u22125 per site per year for all other types of substitutions.<\/jats:p>","DOI":"10.1093\/nargab\/lqae009","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T23:45:57Z","timestamp":1705448757000},"source":"Crossref","is-referenced-by-count":0,"title":["A simple method for estimating time-irreversible nucleotide substitution rates in the SARS-CoV-2 genome"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6277-4330","authenticated-orcid":false,"given":"Kazuharu","family":"Misawa","sequence":"first","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine , 3-9 Fukuura, Kanazawa-ku , Yokohama 236-0004 , Japan"},{"name":"RIKEN Center for Advanced Intelligence Project , 1-4-1 Nihonbashi, Chuo-ku , Tokyo\u00a0 103-0027 , Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2186-568X","authenticated-orcid":false,"given":"Ryo","family":"Ootsuki","sequence":"additional","affiliation":[{"name":"Department of Natural Sciences, Faculty of Arts and Sciences , 1-23-1 Komazawa, Setagaya-ku , Tokyo\u00a0 154-8525 , Japan"},{"name":"Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University , 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,2]]},"reference":[{"key":"2024020221430393700_B1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1001\/jama.2020.1585","article-title":"Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China","volume":"323","author":"Wang","year":"2020","journal-title":"JAMA"},{"key":"2024020221430393700_B2","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":"2024020221430393700_B3","doi-asserted-by":"crossref","first-page":"e00408-20","DOI":"10.1128\/mSphere.00408-20","article-title":"Rampant C\u2192U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: causes and consequences for their short- and long-term evolutionary trajectories","volume":"5","author":"Simmonds","year":"2020","journal-title":"mSphere"},{"key":"2024020221430393700_B4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/s12866-021-02158-6","article-title":"Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes","volume":"21","author":"Iwasaki","year":"2021","journal-title":"BMC Microbiol."},{"key":"2024020221430393700_B5","doi-asserted-by":"crossref","first-page":"14972","DOI":"10.1038\/s41598-022-19067-x","article-title":"The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness","volume":"12","author":"Kim","year":"2022","journal-title":"Sci. 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