{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T18:46:00Z","timestamp":1775760360998,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","funder":[{"name":"Intramural Research Program of the National Human Genome Research Institute"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1ZIAHG200401"],"award-info":[{"award-number":["1ZIAHG200401"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The genome of the seasonal acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has a 12-nucleotide insertion that produced a furin cleavage site at the S1\/S2 junction of its spike protein. It has been noted that compared to related coronavirus genomes, the insertion aligns best in the middle of a codon. However, a precise placement of the insertion would require an understanding of the S1\/S2 junction sequence in the ancestor of SARS-CoV-2 in which the insertion occurred, whose genome sequence we do not have. Leveraging ancestral sequence reconstruction, we find that the genome of the most recent common ancestor of SARS-CoV-2 and other published coronaviruses very likely shared its S1\/S2 junction sequence with coronaviruses like RaTG13 and BANAL-20-52. The insertion occurred in a descendant of this ancestor; we considered whether mutations could have occurred along the SARS-CoV-2 lineage that would have allowed the insertion to fall cleanly between codons, and found that such mutations were unlikely. Thus, the insertion likely interrupted a codon.<\/jats:p>","DOI":"10.1093\/ve\/veag015","type":"journal-article","created":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T12:41:02Z","timestamp":1773492062000},"source":"Crossref","is-referenced-by-count":0,"title":["Ancestral sequence reconstruction analysis indicates the S1\/S2 insertion in the SARS-CoV-2 spike gene likely interrupted a codon"],"prefix":"10.1093","volume":"12","author":[{"given":"Michael James","family":"Chambers","sequence":"first","affiliation":[{"name":"Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health , 49 Convent Drive, Bethesda, MD 20892 ,","place":["United States"]},{"name":"Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mudabir","family":"Abdullah","sequence":"additional","affiliation":[{"name":"Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health , 49 Convent Drive, Bethesda, MD 20892 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8636-9102","authenticated-orcid":false,"given":"Meru J","family":"Sadhu","sequence":"additional","affiliation":[{"name":"Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health , 49 Convent Drive, Bethesda, MD 20892 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"2026040913464787800_ref1","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1186\/s12859-017-1793-7","article-title":"A new and updated resource for codon usage tables","volume":"18","author":"Athey","year":"2017","journal-title":"BMC Bioinform"},{"key":"2026040913464787800_ref2","doi-asserted-by":"publisher","first-page":"msad085","DOI":"10.1093\/molbev\/msad085","article-title":"Evolution of the SARS-CoV-2 mutational spectrum","volume":"40","author":"Bloom","year":"2023","journal-title":"Mol Biol Evol"},{"key":"2026040913464787800_ref3","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1038\/s41564-020-0771-4","article-title":"Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic","volume":"5","author":"Boni","year":"2020","journal-title":"Nat Microbiol"},{"key":"2026040913464787800_ref4a","doi-asserted-by":"publisher","author":"Dor","DOI":"10.1093\/ve\/veag016"},{"key":"2026040913464787800_ref5","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1038\/s41589-022-01059-7","article-title":"Structure and activity of human TMPRSS2 protease implicated in SARS-CoV-2 activation","volume":"18","author":"Fraser","year":"2022","journal-title":"Nat Chem Biol"},{"key":"2026040913464787800_ref6","doi-asserted-by":"publisher","first-page":"2341","DOI":"10.1007\/s00705-020-04750-z","article-title":"A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-COV-2","volume":"165","author":"Gallaher","year":"2020","journal-title":"Arch Virol"},{"key":"2026040913464787800_ref7","doi-asserted-by":"publisher","first-page":"e2211107119","DOI":"10.1073\/pnas.2211107119","article-title":"SARS-CoV-2 furin cleavage site was not engineered","volume":"119","author":"Garry","year":"2022","journal-title":"Proc Natl Acad Sci"},{"key":"2026040913464787800_ref8","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1038\/s42003-021-02858-9","article-title":"Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring","volume":"4","author":"Garushyants","year":"2021","journal-title":"Commun Biol"},{"key":"2026040913464787800_ref9","doi-asserted-by":"publisher","first-page":"198674","DOI":"10.1016\/j.virusres.2022.198674","article-title":"Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein","volume":"310","author":"Gerdol","year":"2022","journal-title":"Virus Res"},{"key":"2026040913464787800_ref10","doi-asserted-by":"publisher","first-page":"gkaf503","DOI":"10.1093\/nar\/gkaf503","article-title":"The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure","volume":"53","author":"Haddox","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026040913464787800_ref11","doi-asserted-by":"publisher","first-page":"e17486","DOI":"10.1111\/mec.17486","article-title":"Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. 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