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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BackgroundMethodInfluential
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BackgroundInfluential
A new coronavirus associated with human respiratory disease in China
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BackgroundMethodInfluential
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BackgroundMethod
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Additional file 9 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 6 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 7 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 3 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 10 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 4 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 8 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 2 of Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants
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Additional file 11 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Additional file 1 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
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Molecular mechanisms of RaTG13 and SARS ‐ CoV ‐2 RBD bound to Rhinolophus affinis bat ACE2
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“A bioinformatic study indicated that the divergence time estimate for RaTG13 and SARS-CoV-2 was 40 – 70 years ago, most probably in Rhinolophus affinis bats and the PCoVs might also be acquired from bat viruses (Boni et al. 2020).”
Structural insights into the receptor-binding domain of bat coronavirus ZXC21
Wang, C., Xu, N., Deng, Y., Fan, S., Li, X., & Lan, J. (2025) · Structure · doi:10.1016/j.str.2025.04.004
Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon
Cruz, A. M. S., Cardoso, J. F., Pinheiro, K. D. C., Ferreira, J. A., Barbagelata, L. S., da Silva, S. P., das Chagas, W. D., Lobo, P. D. S., Teixeira, D. M., Junior, W. A., et al. (2025) · Microorganisms · doi:10.3390/microorganisms13051088
“…after the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and subsequent coronavirus disease pandemic 2019 (COVID-19) [1], global scientific efforts have been directed towards understanding viral biology [2,3], epidemiology, and pathophysiology of these infections [4].”
On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching
Xia, X. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf134
Binding of an N protein peptide to M protein of a bat coronavirus
Wang, X., Yang, S., Yang, P., Sun, Z., & Zhou, X. (2025) · Journal of Structural Biology · doi:10.1016/j.jsb.2025.108234
Evolutionary Insights From the COVID Pandemic: Genomic Diversity and Origins of SARS-CoV-2
Cosentino, M. A. C., Moreira, F. R. R., D’arc, M., & Santos, A. F. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15750-9.00151-8
Coronavirus: where do new viruses come from?
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Here’s how scientists know the coronavirus came from bats and wasn’t made in a lab
Hayes, P. M. (2020) · doi:10.64628/ab.xt3vp6w6r
In 2010, a virus similar to SARS-CoV-2 was already present in Cambodia
Hassanin, A. (2021) · doi:10.64628/aak.nj6q5squ3
Pada 2010, virus menyerupai SARS-CoV-2 sudah ada di Kamboja
Hassanin, A. (2021) · doi:10.64628/aan.tsq3gjvc3
Il y a 10 ans, un virus proche du SARS-CoV-2 circulait déjà au Cambodge
Hassanin, A. (2021) · doi:10.64628/aak.kw6gtf6eq
From Pandemic to Persistence: Obesity, Immunity, and Next-Gen COVID-19 Vaccines
Mondal, K. K., Uddin, M. S., & Mahmud, T. (2025) · doi:10.38124/ijisrt/25aug1400
Mating behaviour and connectivity drive sporadic European bat lyssavirus 2 infections in Myotis myotisPreprint
Touzalin, F., Wasniewski, M., Meyer, E. P., Farcy, O., Bris, Y. L., Lehouedec, A., LeFloch, C., Griffiths, M. E., Puechmaille, S. J., Teeling, E. C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.22.677820
“Despite increased attention to bats as reservoirs of zoonotic viruses [4–7], mechanistic models are still rarely used to elucidate pathogen persistence and transmission within bat populations [3,8–12], particularly for bat-borne viruses with seasonal shedding patterns [13].”
Detection of SARS-CoV-2 virus by reverse transcription Loop-mediated isothermal amplification (RT-LAMP) assay
Ruíz, E., Muñoz, A. L., Torres, O., Ortiz, F. J. V., & Villamil, J. P. S. (2024) · REVISTA SAYWA · doi:10.54104/saywa.v5n6.1506
Effects of genomic recombination on SARS-CoV-2 evolution and the growth of the recombinant variant XFG in GermanyPreprint
Yi, B. (2025) · medRxiv · doi:10.1101/2025.11.17.25339653
Rodent Origins and Human-Mediated Evolutionary Dynamics of PRRSVPreprint
Novosel, D., Jungić, A., Rota‐Stabelli, O., Cortey, M., Čurik, I., & Mateu, E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.25.690366
“This concordance underscores how methodological choices - especially the genomic regions analysed - critically influence molecular clock estimates 25,26 .”
Nanotechnology-based drug delivery for combating SARS-CoV-2 variants
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Additional file 5 of Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Wang, D., Yang, X. Y. X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26704608
Additional file 1 of Phytoconstituents of Artemisia annua as potential inhibitors of SARS CoV2 main protease: an in silico study
Irfan, E., Dilshad, E., Ahmad, F., Almajhdi, F. N., Hussain, T., Abdi, G., & Waheed, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26721030
Additional file 1 of Indels in SARS-CoV-2 occur at template-switching hotspots
Chrisman, B., Paskov, K. M., Stockham, N., Tabatabaei, K., Jung, J.-Y., Washington, P. Y., Varma, M., Sun, M., Maleki, S., & Wall, D. P. (2021) · Figshare · doi:10.6084/m9.figshare.14253984
Additional file 2 of Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2
Patiño-Galindo, J. Á., Filip, I., Chowdhury, R., Maranas, C. D., Sorger, P. K., AlQuraishi, M., & Rabadan, R. (2021) · Figshare · doi:10.6084/m9.figshare.15128115
Additional file 2 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
Bhattacharjee, M. J., Bhattacharya, A., Kashyap, B., Taw, M. J., Li, W., Mukherjee, A. K., & Khan, M. R. (2023) · Figshare · doi:10.6084/m9.figshare.24077078
Additional file 1 of Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants
Yi, C., Sun, X., Lin, Y., Gu, C., Ding, L., Lu, X., Yang, Z., Zhang, Y., Ma, L., Gu, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16815699
Additional file 3 of Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Wang, D., Yang, X. Y. X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26704602
Additional file 1 of Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Wang, D., Yang, X. Y. X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25583895
Additional file 5 of Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations
Bhattacharjee, M. J., Bhattacharya, A., Kashyap, B., Taw, M. J., Li, W., Mukherjee, A. K., & Khan, M. R. (2023) · Figshare · doi:10.6084/m9.figshare.24077090
Additional file 2 of Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Wang, D., Yang, X. Y. X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25584013
Additional file 1 of Reinfection in patients with COVID-19: a systematic review
Ren, X., Zhou, J., Guo, J., Hao, C., Zheng, M., Zhang, R., Huang, Q., Yao, X., Li, R., & Jin, Y. (2022) · Figshare · doi:10.6084/m9.figshare.19687129
Additional file 4 of Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Wang, D., Yang, X. Y. X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26704605
Genetic Diversity of SARS-CoV-2 in Kazakhstan from 2020 to 2022
Sagymbay, A., Komissarov, A. B., Mutaliyeva, A. S., Usserbayev, A., Karamendin, K., Perederiy, A. A., Fadeev, A. V., Kuatbayeva, A. M., Jussupova, D. B., Abdaliyev, A., et al. (2026) · Viruses · doi:10.3390/v18010138
“Overall, SARS-CoV-2 shares approximately 79.5% and 96% genomic sequence identity with previously identified SARS-CoV and bat coronavirus, SL-CoV-RaTG13, respectively [5,6].”
Influential

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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