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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“Most recent evidence suggests that SARSCoV-2, the coronavirus that causes COVID-19, came from bats in the Yunnan province in China [2].”
Background
History and Global Status of the New Coronavirus Covid-2019 and Aspects of Previous Infections of SARS-CoV and MERS-CoV: A Systematic Review
da Costa, A. P. A., da Rocha, V. L., Ramos, R. R., Neto, J. M. P., da Silva, W. R., Pereira, L. L. V., Ramos, K., Marques, T. C. N., Filho, I. J. Z., & Lozano, A. W. (2021) · Coronaviruses · doi:10.2174/2666796702666210118153843 · Cited by 2
A year after the start of COVID-19
Camacho-Ortíz, A. (2021) · Medicina Universitaria · doi:10.24875/rmu.m21000056 · Cited by 2
COVID-19 and Preparing for Future Ecological Crises: Hopes from Metagenomics in Facing Current and Future Viral Pandemic Challenges
Fulci, V., Carissimi, C., & Laudadio, I. (2021) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2021.0058 · Cited by 3
“No-tably, both H1N1 and SARS-CoV-2 viral infections have a zoonotic origin (Andersen et al., 2020; Boni et al., 2020; Smith et al., 2009), have indeed been transmitted to humans from wild or domestic animals through direct contacts or indirectly through exposure to the urine or feces of infected…”
Favipiravir: A Critical Review of Pharmacology, Pre-Clinical Data, and Emerging Clinical Uses in COVID-19
Motule, A. S. (2021) · International Journal for Research in Applied Science and Engineering Technology · doi:10.22214/ijraset.2021.37739 · Cited by 2
Los murciélagos y la COVID-19, una injusta historia
Galindo-González, J. R., & Medellín, R. A. (2021) · CIENCIA ergo sum · doi:10.30878/ces.v28n2a11 · Cited by 2
Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptorPreprint
Brintnell, E., Gupta, M., & Anderson, D. W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.22.165787 · Cited by 2
Structural Variants in SARS-CoV-2 Occur at Template-Switching HotspotsPreprint
Chrisman, B., Paskov, K. M., Stockham, N., Tabatabaei, K., Jung, J.-Y., Washington, P. Y., Varma, M., Sun, M., Maleki, S., & Wall, D. P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.01.278952 · Cited by 2
“Analysis on the sarbecovirus recombinant origins of SARS-CoV-2 identified possible recombination breakpoints at 1684, 3046, 9237, 11885, 21753, 22773 and 24628.(3).”
Background
A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platformPreprint
Farah, I., Lalli, G., Baker, D. J., & Schumacher, A. (2020) · medRxiv · doi:10.1101/2020.09.28.20203257 · Cited by 2
The Anomalous Nature of the Fecal Swab Data, Receptor Binding Domain and Other Questions in RaTG13 GenomePreprint
Rahalkar, M. C., & Bahulikar, R. A. (2020) · Preprints.org · doi:10.20944/preprints202008.0205.v3 · Cited by 2
SARS-CoV-2 and Zoonotic Preparedness: Unknown Knowns?
Irving, A. T., & Welburn, S. C. (2021) · Infectious Microbes & Diseases · doi:10.1097/im9.0000000000000051 · Cited by 2
“While most CoVs exist in animals, SARS-CoV-2 is one of seven CoVs known to actively infect humans, all having likely derived from animal hosts.(2,3) The majority of CoV infections result in mild infection (eg, 229E) though MERS-CoV, SARS-CoV and SARSCoV-2 may result in severe morbidity and mortality.”
Background
Human endemic coronavirus emergence in the context of past and recent zoonotic outbreaksPreprint
Forni, D., Cagliani, R., Arrigoni, F., Benvenuti, M., Pontremoli, C., Pozzoli, U., Clerici, M., GIOIA, L. D., & Sironi, M. (2021) · Research Square · doi:10.21203/rs.3.rs-134999/v1 · Cited by 2
Unlocking capacities of viral genomics for the COVID-19 pandemic responsePreprint
Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Comarova, Z., Lu, A., Porozov, Y. B., et al. (2021) · PubMed · doi:10.48550/arxiv.2104.14005 · Cited by 2
Self-citation
Evolutionary trajectory of SARS-CoV-2 genomePreprint
Wang, A. (2021) · Research Square · doi:10.21203/rs.3.rs-1009010/v1 · Cited by 2
Considerations for an ethic of One Health : Towards a socially responsible zoonotic disease control
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Microbicidal actives with virucidal efficacy against SARS-CoV-2 and other beta- and alpha-coronaviruses: implications for future emerging coronaviruses and other enveloped virusesPreprint
Ijaz, M. K., Nims, R. W., Zhou, S. S., Whitehead, K., Sriniva, V., Kapes, T., Fanuel, S., Epstein, J. H., Daszak, P., Rubino, J. R., et al. (2020) · doi:10.21203/rs.3.rs-75158/v1 · Cited by 2
Comprehensive Mapping of Binding Hot Spots of SARS-CoV-2 RBD-specific Neutralizing Antibodies for Tracking Immune Escape VariantsPreprint
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Chances of finding COVID-virus ancestor ‘almost nil’, say virologists
Mallapaty, S. (2022) · Nature · doi:10.1038/d41586-022-03611-w · Cited by 2
Epidemiological modeling of SARS-CoV-2 in white-tailed deer ( Odocoileus virginianus ) reveals conditions for introduction and widespread transmissionPreprint
Rosenblatt, E., Cook, J. D., DiRenzo, G. V., Grant, E. H. C., Arce, F., Pepin, K. M., Rudolph, F. J., Runge, M. C., Shriner, S. A., Walsh, D. P., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.30.555493 · Cited by 2
The Omicron XBB.1 Variant and its Descendants: Genomic Mutations, Rapid Dissemination and Notable CharacteristicsPreprint
Veltri, P., Giancotti, R., Lomoio, U., Puccio, B., Tradigo, G., Guzzi, P. H., Vizza, P., & Torti, C. (2023) · doi:10.22541/au.169570833.31408402/v1 · Cited by 2
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirsPreprint
Hetland, M. A. K., Winkler, M. A., Kaspersen, H. P., Håkonsholm, F., Bakksjø, R., Bernhoff, E., Delgado‐Blas, J. F., Brisse, S., Correia, A., Fostervold, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.11.612360 · Cited by 2
On the Controversies Surrounding the Lab-Leak Theory of COVID-19
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Protecting half of the planet is the best way to fight climate change and biodiversity loss – we’ve mapped the key places to do it
Asner, G. P. (2020) · The Conversation · doi:10.64628/aai.cfsp7grfj · Cited by 2
Exploring People’s Perception on Pros and Cons of Human-Bat Coexistence in Urban Environs in Southwestern Nigeria
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“12,13 This report has aggravated bitterness against bats despite findings identifying man as the main cause of his own public health challenges.”
Background
Timeline of the pandemic: epidemiology, global spread, variants and waves
Liu, Y.-X., Luo, J.-Y., Liu, R., Li, Y., & Guan, W. (2024) · European Respiratory Society eBooks · doi:10.1183/2312508x.10018823 · Cited by 1
Analysis of Extinction Spectra of a Plasmonic Ag/Air/Ag Square Nanostructure to Design a Highly Sensitive Plasmonic Biosensor for Detection of PSA and SARS-CoV-2
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Virology Applications to the COVID-19 Pandemic
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Advancing viral genome classification: assesing the efficiency and accuracy of the alignment-free k-mer method in emerging pandemics
Paiva, D. D. A., Yotoko, K. S. C., Zarzar, C. A., de Paiva, J. T., Siqueira, D. P., Rodrigues, G., de Souza, L. P. M., & Sáfadi, T. (2025) · Caderno Pedagógico · doi:10.54033/cadpedv22n8-177 · Cited by 1
In vivo antibody diversification targeting a conserved coronavirus epitope
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“Coronaviruses' envelope spike (S) protein facilitates virus entry into host cells by binding to the cellular receptor angiotensin-converting enzyme 2 (ACE2) in humans [41–43].”
Superior RdRp Function Drives the Dominance of Prevalent GI.3 Norovirus Lineages
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Self-citation
SARS-CoV-2 and Emerging Foodborne Pathogens: Intriguing Commonalities and Obvious Differences
Abdelhamid, A. G., Faraone, J. N., Evans, J. P., Liu, S., & Yousef, A. E. (2022) · Pathogens · doi:10.3390/pathogens11080837 · Cited by 1
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BackgroundResultInfluential
Advances in Diagnosis and Treatment for SARS-CoV-2 Variants
Akhter, N., Sana, S., Ahsan, M. A., Siddique, Z., Huraira, A., & Sana, S. (2023) · Infectious diseases · doi:10.5772/intechopen.107846 · Cited by 1
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An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families
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Influential
Reduction of extracellular vimentin in blood provides protection against SARS-CoV-2 infection
Kim, H.-M., Wang, M., Zhai, C., Kim, S., Park, J., & Hong, S. (2025) · Virulence · doi:10.1080/21505594.2025.2568052 · Cited by 5
“However, none of these zoonotic virus genomes exhibit more than 98% similarity to that of SARS-CoV-2 [6–8], suggesting that these SARS-CoV-2-related coronaviruses are not direct ancestor of SARS-CoV-2.”
Пандемия COVID-19. SARS-Cov-2, пути передачи, особенности распространения и индивидуальной восприимчивости
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Background
ORIGIN OF SARS-COV-2:NATURAL O SELECTION OR ADAPTATIVE SELECTION?
Martínez, P. M. (2021) · REBIOL · doi:10.17268/rebiol.2020.40.02.14

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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