Lytras, S., Hughes, J. , Martin, D., Swanepoel, P., de Klerk, A., Lourens, R., Kosakovsky Pond, S. L., Xia, W., Jiang, X. and Robertson, D. L. (2022) Exploring the natural origins of SARS-CoV-2 in the light of recombination. Genome Biology and Evolution, 14(2), evac018. (doi: 10.1093/gbe/evac018) (PMID:35137080) (PMCID:PMC8882382)
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Abstract
The 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 fuelling 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 non-random 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 co-circulation 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 (i) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, (ii) the intermediate species that facilitated transmission from bats to humans (if there is one), and (iii) survey the extent of the diversity in the related sarbecoviruses’ phylogeny that present high risk for future spillovers.
| Item Type: | Articles |
|---|---|
| Additional Information: | DLR and JH are funded by the MRC (MC_UU_1201412) and DLR by the WT (220977/Z/20/Z). SL is funded by an MRC studentship. DPM is funded by the Wellcome Trust (222574/Z/21/Z). SLKP was supported in part by a grant from the NIH (R01 AI134384 (NIH/NIAID)). XJ is funded by the Jiangsu Province High-level Innovation and Entrepreneurship Talent Programme. |
| Keywords: | SARS-CoV-2, Sarbecoviruses, bats, origin, COVID-19, host range, coronaviruses, recombination, Rhinolophus, pangolins. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Robertson, Professor David and Hughes, Dr Joseph and Lytras, Spyros |
| Authors: | Lytras, S., Hughes, J., Martin, D., Swanepoel, P., de Klerk, A., Lourens, R., Kosakovsky Pond, S. L., Xia, W., Jiang, X., and Robertson, D. L. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Genome Biology and Evolution |
| Publisher: | Oxford University Press |
| ISSN: | 1759-6653 |
| ISSN (Online): | 1759-6653 |
| Published Online: | 08 February 2022 |
| Copyright Holders: | Copyright © 2022 The Authors |
| First Published: | First published in Genome Biology and Evolution 14(2):evac018 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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