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dc.creatorLytras, Spyros
dc.creatorHughes, Joseph
dc.creatorMartin, Darren P.
dc.creatorSwanepoel, Phillip
dc.creatorde Klerk, Arne
dc.creatorLourens, Rentia
dc.creatorPond, Sergei
dc.creatorXia, Wei
dc.creatorJiang, Xiaowei
dc.creatorRobertson, David L.
dc.date.accessioned2022-04-22T20:27:48Z
dc.date.available2022-04-22T20:27:48Z
dc.date.issued2022-02-08
dc.identifier.citationSpyros Lytras, Joseph Hughes, Darren Martin, Phillip Swanepoel, Arné de Klerk, Rentia Lourens, Sergei L Kosakovsky Pond, Wei Xia, Xiaowei Jiang, David L Robertson, Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination, Genome Biology and Evolution, Volume 14, Issue 2, February 2022, evac018, https://doi.org/10.1093/gbe/evac018
dc.identifier.issn1759-6653
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/7544
dc.identifier.urihttp://hdl.handle.net/20.500.12613/7566
dc.description.abstractThe lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses’ ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses’ phylogeny that present high risk for future spillovers.
dc.format.extent14 pages
dc.languageEnglish
dc.language.isoeng
dc.relation.ispartofCOVID-19 Research
dc.relation.haspartGenome Biology and Evolution, Vol. 14, No. 2
dc.relation.isreferencedbyOxford University Press
dc.rightsAttribution CC BY
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectSARS-CoV-2
dc.subjectSarbecoviruses
dc.subjectBats
dc.subjectOrigin
dc.subjectCOVID-19
dc.subjectHost range
dc.subjectCoronaviruses
dc.subjectRecombination
dc.subjectRhinolophus
dc.subjectPangolins
dc.titleExploring the Natural Origins of SARS-CoV-2 in the Light of Recombination
dc.typeText
dc.type.genreJournal article
dc.contributor.groupInstitute for Genomics and Evolutionary Medicine (Temple University)
dc.description.departmentBiology
dc.relation.doihttps://doi.org/10.1093/gbe/evac018
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.description.schoolcollegeTemple University. College of Science and Technology
dc.creator.orcidKosakovsky Pond|0000-0003-4817-4029
dc.temple.creatorKosakovsky Pond, Sergei L.
refterms.dateFOA2022-04-22T20:27:48Z


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