Cited by 1,014SARS-CoV-2 and COVID-19 ResearchAnimal Virus Infections StudiesEvolution and Genetic Dynamics

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

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Boni, Maciej F., Lemey, Philippe, Jiang, Xiaowei, Lam, Tommy Tsan-Yuk, Perry, Blair W., Castoe, Todd A., Rambaut, Andrew, Robertson, David L.·2020·Nature Microbiology

DOI 10.1038/s41564-020-0771-4

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Abstract

There 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.

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BackgroundMethodInfluential
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Method
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BackgroundInfluential
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BackgroundInfluential
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BackgroundMethodInfluential
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Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v18
WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v17
Recommendation: Ultrafast Enzymatic Digestion of Deoxyribonucleic Acid in Aqueous Microdroplets for Sequence Discrimination and Identification — R0/PR4
(2021) · QRB Discovery · doi:10.1017/qrd.2021.2.pr4
WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v29
WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v22
WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v27
WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v23
Recommendation: Ultrafast Enzymatic Digestion of Deoxyribonucleic Acid in Aqueous Microdroplets for Sequence Discrimination and Identification — R2/PR6
(2021) · QRB Discovery · doi:10.1017/qrd.2021.2.pr6
Recommendation: Ultrafast Enzymatic Digestion of Deoxyribonucleic Acid in Aqueous Microdroplets for Sequence Discrimination and Identification — R1/PR5
(2021) · QRB Discovery · doi:10.1017/qrd.2021.2.pr5
Respiratory Diseases
Tomsic, J. A., Ashrafi, A., English, R., & Brown, K. (2020) · Springer eBooks · doi:10.1007/978-3-030-48880-2_14
Sucul Hayvanlarında ve Su Ürünlerinde SARS-CoV-2 (COVID-19) Virüsünün Varlığı
Ajmi, N., & Duman, M. (2022) · Journal of Anatolian Environmental and Animal Sciences · doi:10.35229/jaes.1062753
EDITORIAL : Coronaviruses, bats, and museums
Lim, B. K. (2022) · TAPROBANICA The Journal of Asian Biodiversity · doi:10.47605/tapro.v11i1.271
3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules
de Souza, C., de Oliveira, M. D. L., Bessa, J. A., Mota, K., & de Freitas, R. (2022) · CLEI electronic journal · doi:10.19153/cleiej.25.2.9
“Within a few weeks the disease spread to China, reaching other countries and continents, taking on the proportions of a pandemic, as enacted by the World Health Organization (WHO) on March 11, 2020 [4].”
Background
Coronaviruses
Louten, J. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90565-7.00014-9
Les dangers du SARS-CoV-2 pour les écosystèmes aquatiques
Ferchichi, S., Fatnassi, N., Dhaouadi, A., & Hili, H. A. E. (2022) · Médecine tropicale et santé internationale · doi:10.48327/mtsi.v2i1.2022.228
“D’après l’étude de Zhou et al en 2020, le virus présente 96 % d’identité nucléotidique avec celle d’un virus de chauve-souris (Bat CoV RaTG13) du genre Rhinolophus suggérant que l’un des ancêtres de l’agent de la COVID-19 aurait été hébergé chez une espèce de chauvesouris [11].”
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Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentationPreprint
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The Evolution of SARS-CoV-2
Bailey, S. F., & Akter, M. (2022) · Springer eBooks · doi:10.1007/978-981-19-1356-3_5
Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentationPreprint
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References
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How Do Arab and Moslem Countries and Communities Act in Dealing with the Impacts of the COVID-19 Pandemic?
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Prediction of RNA secondary structures in SARS-CoV-2 and comparison with contemporary predictionsPreprint
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“The most recent common ancestor of RaTG13 and SARS-CoV-2 may have existed as little as fifty years ago [67].”
Background
İNSANLARDAKİ COVID-19 YABAN HAYVANLARINDA RİSK OLUŞTURUYOR MU?
Hanedan, B., BİLGİLİ, A., & ABBASOVA, N. (2022) · Izmir Democracy University Health Sciences Journal · doi:10.52538/iduhes.1162455
Perspective Chapter: Real-Time Genomic Surveillance for SARS-CoV-2 on Center Stage
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Sequence evidence that the D614G clade of SARS-CoV-2 was already circulating in northern Italy in the fall of 2019Preprint
Xia, X. (2022) · doi:10.32388/7u3ht7

Authors: Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A., & Robertson, D. L.
Affiliations: Pennsylvania State University (US)
KU Leuven (BE)
Xi’an Jiaotong-Liverpool University (CN)
University of Hong Kong (HK)
The University of Texas at Arlington (US)
University of Edinburgh (GB)
MRC University of Glasgow Centre for Virus Research (GB)
Corresponding author: Boni, Maciej F.
Lemey, Philippe
Rambaut, Andrew
Robertson, David L.
ORCID: Boni, Maciej F.
Lemey, Philippe
Jiang, Xiaowei
Lam, Tommy Tsan-Yuk
Perry, Blair W.
Castoe, Todd A.
Rambaut, Andrew
Robertson, David L.
Venue: Nature Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2020-07-28
Volume: 5
Issue: 11
Pages: 1408-1417
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-020-0771-4
OpenAlex: W3046218112
Cited by: 1,014
References: 69
Citations by year: 2026: 23 · 2025: 46 · 2024: 79 · 2023: 118 · 2022: 240 · 2021: 327 · 2020: 178
FWCI: 28.54
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Microbiology (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
PubMed (publishedVersion)
ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion, cc-by-sa)
Lirias (KU Leuven) (submittedVersion)
Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
Funders: Fonds Wetenschappelijk Onderzoek (G0D5117N, G0B9317N)
Wellcome Trust (206298/Z/17/Z)
RCUK | Medical Research Council (MC_UU_1201412)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: SARS-CoV-2, sarbecoviruses, COVID-19 pandemic, viral recombination, bat reservoirs, pangolins, divergence time estimation, receptor-binding motif, ACE2 receptor, phylogenetic dating, viral emergence, genetic diversity, SARS-CoV
MeSH terms: Betacoronavirus, Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, Animals, Bayes Theorem, China, Chiroptera, Humans, Peptidyl-Dipeptidase A, Phylogeny, Pneumonia, Viral, Recombination, Genetic, Genetic Variation, Genome, Viral, Coronavirus Infections, Evolution, Molecular, Pandemics

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

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