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Article: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

TitleEvolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Authors
Issue Date2020
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nmicrobiol/
Citation
Nature Microbiology, 2020, v. 5 n. 11, p. 1408-1417 How to Cite?
AbstractThere are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses—the viral subgenus containing SARS-CoV and SARS-CoV-2—undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
Persistent Identifierhttp://hdl.handle.net/10722/289537
ISSN
2023 Impact Factor: 20.5
2023 SCImago Journal Rankings: 7.982
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorBoni, MF-
dc.contributor.authorLemey, P-
dc.contributor.authorJiang, X-
dc.contributor.authorLam, TTY-
dc.contributor.authorPerry, BW-
dc.contributor.authorCastoe, TA-
dc.contributor.authorRambaut, A-
dc.contributor.authorRobertson, DL-
dc.date.accessioned2020-10-22T08:14:02Z-
dc.date.available2020-10-22T08:14:02Z-
dc.date.issued2020-
dc.identifier.citationNature Microbiology, 2020, v. 5 n. 11, p. 1408-1417-
dc.identifier.issn2058-5276-
dc.identifier.urihttp://hdl.handle.net/10722/289537-
dc.description.abstractThere are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses—the viral subgenus containing SARS-CoV and SARS-CoV-2—undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.-
dc.languageeng-
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nmicrobiol/-
dc.relation.ispartofNature Microbiology-
dc.rightsThis is a post-peer-review, pre-copyedit version of an article published in [insert journal title]. The final authenticated version is available online at: https://doi.org/[insert DOI]-
dc.titleEvolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic-
dc.typeArticle-
dc.identifier.emailLam, TTY: ttylam@hku.hk-
dc.identifier.authorityLam, TTY=rp01733-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1038/s41564-020-0771-4-
dc.identifier.pmid32724171-
dc.identifier.scopuseid_2-s2.0-85088964983-
dc.identifier.hkuros316838-
dc.identifier.volume5-
dc.identifier.issue11-
dc.identifier.spage1408-
dc.identifier.epage1417-
dc.identifier.isiWOS:000553342400001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl2058-5276-

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