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Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Open accessPublished version of a preprint
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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“Although the proximal origins are unknown, SARS-CoV-2 is thought to derive from a bat SARS-CoV-related coronavirus with a furin cleavage site that enhances the capacity of the virus to infect human cells.48, 49”
From The Lancet Commission on lessons for the future from the COVID-19 pandemic (2022) · cites this paper as [48]
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Cites
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · cited 2×
“2.8 (Stamatakis, 2014, 2006), GTR+Γ model, 100 bootstrap replicates – was inferred for each BFR longer than 500nt.”
BackgroundMethodInfluentialIQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046 · cited 1×
“The latter was reconstructed using IQTREE (Nguyen et al., 2014 ) under a General-Time Reversible (GTR) model with a discrete gamma distribution to model among-site rate variation.”
MethodA pneumonia outbreak associated with a new coronavirus of probable bat origin
Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., et al. (2020) · Nature · doi:10.1038/s41586-020-2012-7 · Cited by 21,969 · cited 11×
“…thought to be instrumental to SARS-CoV-2’s ability to infect humans – a polybasic cleavage site insertion in the Spike protein – has been seen in another close bat relative of the SARS-CoV-2 virus (Zhou et al., 2020a); however, the sequence is different and it is likely an independent event.”
BackgroundInfluentialEarly transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia
Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001316 · Cited by 16,575 · cited 8×
“In December 2019, a cluster of pneumonia cases epidemiologically linked to an open-air wet market in city of Wuhan (Hubei Province), China (Li et al., 2020a; Zhou et al., 2020b) led local health officials to issue an epidemiological alert to the Chinese Center for Disease Control and Prevention…”
BackgroundMethodInfluentialSelf-citationRAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582 · cited 2×
“2.8 (Stamatakis, 2014, 2006), GTR+Γ model, 100 bootstrap replicates – was inferred for each BFR longer than 500nt.”
BackgroundMethodInfluentialLu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30251-8 · Cited by 11,907 · cited 4×
“Across a large region of its genome, corresponding approximately to ORF1b , it did not cluster with any of the known bat coronaviruses indicating that recombination likely played a role in the evolutionary history of these viruses (Lu et al., 2020; Wu et al.”
BackgroundInfluentialA new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688 · cited 4×
“When the first genome sequence of SARS-CoV-2, Wuhan-Hu-1, was released on January 10 2020 on Virological.org by a consortium led by Yong-Zhen Zhang (Wu et al., 2020a) it enabled the immediate analyses of its ancestry.”
BackgroundMethodInfluentialGorbalenya, A. E., Baker, S. C., Baric, R. S., de Groot, R. J., Drosten, C., Gulyaeva, A. A., Haagmans, B. L., Lauber, C., Leontovich, A. M., Neuman, B. W., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0695-z · Cited by 8,745 · cited 3×
“Next, we (1) collected all breakpoints into a single set, (2) complemented this set to generate a set of non-breakpoints, (3) grouped non-breakpoints into contiguous BFRs and (4) sorted these regions by length.”
BackgroundMethodThe proximal origin of SARS-CoV-2
Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020) · Nature Medicine · doi:10.1038/s41591-020-0820-9 · Cited by 5,081 · cited 3×
“Influenza viruses reassort (Webster et al., 1992) but they do not undergo homologous recombination within RNA segments (Boni et al., 2008, 2010), meaning that ‘origins’ questions for influenza outbreaks can always be reduced to origins questions for each of influenza’s eight RNA segments.”
BackgroundMethodSelf-citationEvolution and ecology of influenza A viruses
Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M., & Kawaoka, Y. (1992) · Microbiological Reviews · doi:10.1128/mr.56.1.152-179.1992 · Cited by 4,739
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Wang, X., Yang, Y., Sun, Z., & Zhou, X. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad021 · Cited by 9
Giancotti, R., Lomoio, U., Puccio, B., Tradigo, G., Vizza, P., Torti, C., Veltri, P., & Guzzi, P. H. (2024) · Biology · doi:10.3390/biology13020090 · Cited by 9
Lerm, M. (2020) · Journal of Internal Medicine · doi:10.1111/joim.13198 · Cited by 9
“The disease, termed coronavirus disease-19 (COVID-19), emerged in 2019 in Wuhan, China, possibly through a species jump of coronavirus with origin in bats [1].”
BackgroundDaron, J., & Bravo, I. G. (2021) · Viruses · doi:10.3390/v13091800 · Cited by 9
“Before the 2019 zoonotic spillover, viruses closely related to SARS-CoV-2 had circulated probably for decades in bats as well as in other intermediate hosts, such as the Sunda pangolin Manis javanica [2].”
BackgroundDavies‐Bolorunduro, O. F., Fowora, M. A., Amoo, O. S., Adeniji, E., Osuolale, K. A., Oladele, O. E., Onuigbo, T. I., Chioma, J., Oraegbu, J. I., Ogundepo, O., et al. (2022) · Bulletin of the National Research Centre/Bulletin of the National Research Center · doi:10.1186/s42269-022-00811-2 · Cited by 9
Animal models for studying COVID-19, prevention, and therapy: Pathology and disease phenotypes
Choudhary, S., Kanevsky, I., & Tomlinson, L. (2022) · Veterinary Pathology · doi:10.1177/03009858221092015 · Cited by 9
Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses
Escalera‐Zamudio, M., Pond, S. L. K., de la Viña, N. M., Gutiérrez, B., Inward, R. P. D., Thézé, J., van Dorp, L., Castelán-Sánchez, H. G., Bowden, T. A., Pybus, O. G., et al. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad076 · Cited by 6
Infection Dynamics, Pathogenesis, and Immunity to SARS-CoV-2 in Naturally Susceptible Animal Species
Nooruzzaman, M., & Diel, D. G. (2023) · The Journal of Immunology · doi:10.4049/jimmunol.2300378 · Cited by 9
Host genetic factors and susceptibility to SARS‐CoV ‐2 infection
Schurr, T. G. (2020) · American Journal of Human Biology · doi:10.1002/ajhb.23497 · Cited by 9
FIRST DESCRIPTION OF SEROLOGICAL EVIDENCE FOR SARS-CoV-2 IN CATTLEPreprint
Fiorito, F., Iovane, V., Pagnini, U., Cerracchio, C., Brandi, S., Levante, M., Marati, L., Ferrara, G., Tammaro, V., Carlo, E. D., et al. (2022) · doi:10.22541/au.164927303.35296083/v1 · Cited by 9
“Coronaviruses (CoVs), such as SARS-CoV-2, can emerge from wildlife hosts and infect humans and domestic and/or livestock animals (Dhama et al., 2020; Shi et al., 2020; Hu et al., 2021).”
BackgroundA comprehensive dataset of animal-associated sarbecoviruses
Liu, B., Zhao, P., Xu, P., Han, Y., Wang, Y., Chen, L., Wú, Z., & Yang, J. (2023) · Scientific Data · doi:10.1038/s41597-023-02558-5 · Cited by 9
A spike virosome vaccine induces pan-sarbecovirus antibody responses in mice
Brinkkemper, M., Poniman, M., Rijnstra, E. S.-V., Iddouch, W. A., Bijl, T. P. L., Guerra, D., Tejjani, K., Grobben, M., Bhoelan, F., Bemelman, D., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109719 · Cited by 8
The cytokine storm—An appropriate, over‐reactive response to SARS‐CoV‐2 or the wrong immune pathway?
Bellgrau, D., & Modiano, J. F. (2020) · Scandinavian Journal of Immunology · doi:10.1111/sji.12979 · Cited by 8
Bousali, M., Dimadi, A., Kostaki, E. G., Tsiodras, S., Nikolopoulos, G. K., Sgouras, D. N., Magiorkinis, G., Papatheodoridis, G., Pogka, V., Lourida, P., et al. (2021) · Life · doi:10.3390/life11030219 · Cited by 8
Impact of COVID-19 Vaccination Status and Confidence on Dietary Practices among Chinese Residents
Li, Z., Ma, Y., Huo, S., Ke, Y., & Zhao, A. (2022) · Foods · doi:10.3390/foods11091365 · Cited by 9
Sbarigia, C., Vardanyan, D., Buccini, L., Tacconi, S., & Dini, L. (2022) · Frontiers in Nanotechnology · doi:10.3389/fnano.2022.987034 · Cited by 8
“The vaccination campaign helped to counteract severe clinical outcomes, but the ability of SARSCoV-2 to mutate and evade immune responses still implies the need to find new intervention strategies, requiring in turn a deeper understanding of SARS-CoV-2 biology (Boni et al., 2020).”
BackgroundHuman Coronavirus Cell Receptors Provide Challenging Therapeutic Targets
López-Cortés, G. I., Palacios-Pérez, M., Hernández-Aguilar, M. M., Veledíaz, H. F., & José, M. V. (2023) · Vaccines · doi:10.3390/vaccines11010174 · Cited by 10
“Adipose tissue may also act as a virus reservoir [120,121].”
BackgroundPatarca, R., & Haseltine, W. A. (2023) · Virology Journal · doi:10.1186/s12985-023-01998-0 · Cited by 8
The evolution of SARS-CoV-2 and the COVID-19 pandemic
Si, Y., Wu, W., Xue, X., Sun, X., Qin, Y., Li, Y., Qiu, C., Li, Y., Zhuo, Z., Mi, Y., et al. (2023) · PeerJ · doi:10.7717/peerj.15990 · Cited by 8
“The evolutionary origin of SARS-CoV-2 remains controversial, however, scientists believe that the virus possibly originated in bats before being transmitted to an intermediate host, likely a pangolin, where it mutated and then transferred to humans ( Boni et al., 2020 ).”
BackgroundHeckley, A. M., Lock, L. R., & Becker, D. J. (2023) · Ecography · doi:10.1111/ecog.07041 · Cited by 7
Corona- and Paramyxoviruses in Bats from Brazil: A Matter of Concern?
Weber, M. N., & da Silva, M. S. (2023) · Animals · doi:10.3390/ani14010088 · Cited by 8
“SARS-CoV, SARS-CoV-2 and MERS-CoV β -CoVs are strongly associated with severe respiratory diseases in humans and present their origin in bat bridge hosts [12,30,31].”
BackgroundGenetic drift promotes and recombination hinders speciation on holey fitness landscapes
Kalirad, A., Burch, C. L., & Azevedo, R. B. R. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011126 · Cited by 9
Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics
Pardo‐Seco, J., Gómez‐Carballa, A., Bello, X., Martinón‐Torres, F., & Salas, A. (2021) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2020.364 · Cited by 7
“… sequences available in these resources to make inferences about SARS-CoV-2 genetic variation and its phylogenetic roots, natural selection, and phylodynamics (Boni et al., 2020; Forster et al., 2020; Gómez-Carballa et al., 2020a, 2020b; Gudbjartsson et al., 2020; …”
Tyshkovskiy, A., & Panchin, A. Y. (2021) · BioEssays · doi:10.1002/bies.202000325 · Cited by 8
“that the ancestors of SARS-CoV-2 have been circulating unnoticed for decades.[3] If the RaTG13 genome had been used as the backbone for the creation of SARS-CoV-2, the Wuhan Institute of Virology (WIV) group would have needed to passage it in cells or animals for years to accumulate 3.”
BackgroundMethodInfluentialExploration of hosts and transmission traits for SARS-CoV-2 based on the k-mer natural vector
Zhang, Y., Wen, J., Li, X., & Li, G. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104933 · Cited by 8
Prediction of two novel overlapping ORFs in the genome of SARS-CoV-2
Pavesi, A. (2021) · Virology · doi:10.1016/j.virol.2021.07.011 · Cited by 8
Jumping a Moving Train: SARS-CoV-2 Evolution in Real Time
Moustafa, A. M., & Planet, P. J. (2021) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piab051 · Cited by 8
“There are many arguments against this including convincing and careful analyses about the relationship with viruses from bats [8, 13, 22, 36] and, that despite these close relationships, the virus sequence is still substantially different, with variable positions distributed throughout its genome, from any virus known…”
BackgroundInfluentialA collective statement in support of saving pangolins
Choo, S. W., Chong, J. L., Gaubert, P., Hughes, A. C., O’Brien, S. J., Chaber, A., Antunes, A., Platto, S., Sun, N. C., Yu, L., et al. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.153666 · Cited by 8
Kirichenko, A. D., Poroshina, A. A., Sherbakov, D. Y., Sadovsky, M. G., & Krutovsky, K. V. (2022) · PLoS ONE · doi:10.1371/journal.pone.0264640 · Cited by 8
Rana, R., Ranjan, V., Kumar, N., Chugh, P., Khillan, K., Gogia, A., Rana, D. S., & Ganguly, N. K. (2022) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-022-04485-2 · Cited by 8
“Coronavirus disease 2019 (COVID-19) emerged from Wuhan, China in December 2019 is one of the biggest threats that the entire humankind is facing today [1, 2].”
BackgroundMacdonald, P. J., Schaub, J. M., Ruan, Q., Williams, C. L., Prostko, J. C., & Tetin, S. Y. (2022) · Communications Medicine · doi:10.1038/s43856-022-00174-9 · Cited by 8
Emergence of Genomic Diversity in the Spike Protein of the “Omicron” Variant
Basak, S., Kayet, P., Ghosh, M., Chatterjee, J., & Dutta, S. (2023) · Viruses · doi:10.3390/v15102132 · Cited by 8
“The SARS-CoV-2 genome can actually be thought of as a collection of several “recombination blocks”, or areas between predicted breakpoints for recombination events [16].”
BackgroundPotential Immunotherapy against SARS-CoV-2: Strategy and Status
Banday, A. H., Shah, S. A., & Ajaz, S. J. (2020) · Coronaviruses · doi:10.2174/2666796701999200625212040 · Cited by 8
“The family consists of two subfamilies: Letovirinae and Orthocorovirinae, with the latter consisting of four genera, Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus [3].”
BackgroundUnique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan
Abe, H., Ushijima, Y., Amano, M., Sakurai, Y., Yoshikawa, R., Kinoshita, T., Kurosaki, Y., Yanagihara, K., Izumikawa, K., Morita, K., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10010099 · Cited by 8
Patial, S., Nazim, M., Khan, A. A. P., Raizada, P., Singh, P., Hussain, C. M., & Asiri, A. M. (2022) · Journal of Hazardous Materials Advances · doi:10.1016/j.hazadv.2022.100097 · Cited by 8
Exploring the natural origins of SARS-CoV-2 in the light of recombination
(2021) · TUScholarShare (Temple University) · doi:10.34944/dspace/7030 · Cited by 8
Evolving Infection Paradox of SARS-CoV-2: Fitness Costs Virulence?Preprint
Alam, A. S. M. R. U., Islam, O. K., Hasan, S., Al‐Emran, H. M., Jahid, I. K., & Hossain, M. A. (2020) · OSF Preprints (OSF Preprints) · doi:10.31219/osf.io/y36ve · Cited by 8
A Critical Analysis of the Evidence for the SARS-CoV-2 Origin Hypotheses
Alwine, J. C., Casadevall, A., Enquist, L. W., Goodrum, F. D., & Imperiale, M. J. (2023) · mBio · doi:10.1128/mbio.00583-23 · Cited by 10
“Recombination within the Sarbecovirus subgenus to which SARS-CoV-2 belongs is exceedingly common (18, 22, 23).”
BackgroundIntegrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS‐CoV‐2
Wang, A. (2024) · Journal of Medical Virology · doi:10.1002/jmv.29557 · Cited by 6
“The evolutionary trajectory of the SARS ‐ CoV ‐ 2 genome has been widely regarded as one of the most crucial topics in SARS ‐ CoV ‐ 2 studies, 5,6,8,34 yet it remains undisclosed.”
BackgroundA tale of endurance: bats, viruses and immune dynamics
Apoorva, & Singh, S. K. (2024) · Future Microbiology · doi:10.2217/fmb-2023-0233 · Cited by 7
Co-designing zoonotic diseases prevention practices when people depend on wild meat
Tomo, N. E., Pouliquen, A., Mapeyi, G. A. B., Makouloutou-Nzassi, P., N’dilimabaka, N., Ngoubangoye, B., Cornélis, D., Lebel, S., Peyre, M., Olive, M., et al. (2025) · One Health · doi:10.1016/j.onehlt.2025.101074 · Cited by 7
“These diseases pose significant threats to human health world-wide, as demonstrated by the Ebola outbreaks in Africa [4 – 6] and the recent SARS-CoV-2 pandemic [7,8].”
The Role of Probiotics and Their Postbiotic Metabolites in Post-COVID-19 Syndrome
Jach, M. E., Sajnaga, E., Bumbul, M., Serefko, A., Borowicz, K. K., Golczyk, H., Kieliszek, M., & Wiater, A. (2025) · Molecules · doi:10.3390/molecules30204130 · Cited by 8
“The COVID-19 (Coronavirus disease 2019) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has had a significant impact on global public health, healthcare, and social structures, with more than 259 million cases of the illness worldwide [1–4].”
Inside China’s response to COVID
Murphy, F. (2020) · Nature · doi:10.1038/d41586-020-03361-7 · Cited by 7
Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data
Bondaryuk, A. N., Peretolchina, T. E., Романова, Е. В., Yudinceva, A. V., Andaev, E. I., & Bukin, Y. (2021) · Biology · doi:10.3390/biology10121282 · Cited by 7
dos Santos, F. A. A., Dalton, K. P., Carvalho, C. L., Casero, M., Álvarez, Á. L., Parra, F., & Duarte, M. D. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14540 · Cited by 7
Sources of Ambivalence, Contagion, and Sympathy
Laugrand, F. B., Laugrand, A., & Simon, L. (2023) · Current Anthropology · doi:10.1086/725081 · Cited by 7
“The closest-known virus to SARS-Cov-2 is the coronavirus RaTwhich is found in the horseshoe bats of Yunnan (Boni et al. 2020). nt Anthropology, volume 64, number 3, June 2023. q 2023 The Wenner-Gr niversity of Chicago Press for The Wenner‐Gren Foundation for Anthropologi Ever since the pandemic…”
BackgroundInfluentialRosenblatt, 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. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012263 · Cited by 8
A vector representation for phylogenetic trees
Chauve, C., Colijn, C., & Zhang, L. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2024.0226 · Cited by 7
“…have many applications, facilitating the study of gene, genome and species evolution [2,3], conservation and biodiversity research [4], mapping human migration patterns [5,6] and investigations into the transmission dynamics of infectious diseases such as HIV, COVID-19 and influenza [7,8].”
Analyses génomiques et phylodynamiques du Sars-CoV-2
Elie, B., & Alizon, S. (2020) · Revue Francophone des Laboratoires · doi:10.1016/s1773-035x(20)30314-2 · Cited by 7
War der Coronavirus-Lockdown notwendig?
Richter, D. (2021) · transcript Verlag eBooks · doi:10.14361/9783839455456 · Cited by 7
David, D., Davidson, I., Karniely, S., Edery, N., Rosenzweig, A., & Sol, A. (2021) · Viruses · doi:10.3390/v13030407 · Cited by 7
“In fact, bats are considered the natural reservoir of a large variety of zoonotic viruses including henipaviruses [4], filoviruses [5], some lyssaviruses [6], SARS-CoV [7], Middle East Respiratory Syndrome [8] and SARS-CoV-2 [9].”
BackgroundHost Community Interfaces: The Wildlife-Livestock
VerCauteren, K. C., Gortázar, C., Beltrán‐Alcrudo, D., & Vicente, J. (2021) · Wildlife research monographs · doi:10.1007/978-3-030-65365-1_1 · Cited by 10
The zoonotic and natural foci characteristics of SARS-CoV-2
Li, Z., Jiang, J.-F., Ruan, X., Tong, Y., Xu, S., Han, L., & Xu, J. (2021) · Journal of Biosafety and Biosecurity · doi:10.1016/j.jobb.2021.06.002 · Cited by 7
“SARS-CoV-2-related coronavirus undergoes frequent recombination and exhibits spatially structured genetic diversity on a regional scale, which makes it difficult to determine the origin of SARS-CoV-2.”
InfluentialHighly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences
Ortuño, F. M., Loucera, C., Casimiro‐Soriguer, C. S., Lepe, J. A., Camacho‐Martínez, P., Díaz, L. M., de Salazar, A., Chueca, N., García, F., Pérez-Florido, J., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab078 · Cited by 9
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MethodLi, T., Cui, Z., Jia, Y., Liang, Z., Nie, J., Zhang, L., Wang, M., Li, Q., Wu, J., Xu, N., et al. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27596 · Cited by 8
“SARS‐CoV‐2 not only is transmissible between humans but also shows some infectious ability in animals such as minks,(32) bats, and pangolins were probably wildlife hosts of SARS‐CoV‐2.(33,34) We thereby investigated whether combinations of mutated possible variants cause changes in infectivity in different species to…”
BackgroundInfluentialBentum, K. E., Shaddox, S., Ware, C., Reddy, G., Abebe, W., Folitse, R. D., Martin, P., & Samuel, T. (2022) · BMC Veterinary Research · doi:10.1186/s12917-022-03217-4 · Cited by 7
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Labandeira, C. M., Pedrosa, M. A., Suárez-Quintanilla, J. A., Cortes-Ayaso, M., Labandeira-García, J. L., & Rodriguez-Perez, A. I. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.840662 · Cited by 7
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BackgroundMethodLang, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1008792 · Cited by 8
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BackgroundRavi, V., Swaminathan, A., Yadav, S. K., Arya, H., & Pandey, R. (2022) · Viruses · doi:10.3390/v14112499 · Cited by 7
Hassanin, A., & Rambaud, O. (2023) · Viruses · doi:10.3390/v15020406 · Cited by 7
“As discussed previously [9,10], most conflicting phylogenetic signals in different genomic regions of our Sarbecovirus alignment can be explained by multiple past events of recombination at different periods of time and involving viruses circulating in several reservoir species of horseshoe bats (genus Rhinolophus).”
BackgroundSARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works
Cassari, L., Pavan, A., Zoia, G., Chinellato, M., Zeni, E., Grinzato, A., Rothenberger, S., Cendron, L., Dettin, M., & Pasquato, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054791 · Cited by 8
“SARS‐CoV‐2 is thought to have emerged from bats, possibly via a secondary host [2].”
BackgroundLomoio, U., Puccio, B., Tradigo, G., Guzzi, P. H., & Veltri, P. (2023) · PLoS ONE · doi:10.1371/journal.pone.0283400 · Cited by 7
Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models
Tay, J. H., Baele, G., & Duchêne, S. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad212 · Cited by 7
Ravi, V., Shamim, U., Khan, M. A., Swaminathan, A., Mishra, P., Rajender, S., Bharali, P., Chauhan, N. S., & Pandey, R. (2024) · Frontiers in Medicine · doi:10.3389/fmed.2023.1294699 · Cited by 7
“Understanding the virus’s evolution can be crucial in predicting future paths, public health preparedness, and developing prevention/treatment strategies (6).”
BackgroundHeinz, F. X., & Stiasny, K. (2020) · Wiener klinische Wochenschrift · doi:10.1007/s00508-020-01763-1 · Cited by 8
“mately 96% identity in almost all genomic regions [31, 32]; however, RaTG13 is unable to recognize human”
BackgroundSubramanian, S. (2021) · Biology · doi:10.3390/biology10010052 · Cited by 7
Melnick, M., Gonzales, P. K., LaRocca, T. J., Song, Y., Wuu, J., Benatar, M. G., Oskarsson, B., Petrucelli, L., Dowell, R. D., Link, C. D., et al. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab141 · Cited by 8
“To simulate a novel virus, we ran Mystery Miner on versions of the BLASTN and BLASTX databases obtained before SARS-CoV-2 was discovered and were able to properly identify SARS-CoV-2 as a bat related coronavirus (Boni et al., 2020) (Figure S1) (File S7).”
MethodThe Impact of SARS-COVID-19 Outbreak on European Cities Urban Mobility
Vitello, P., Fiandrino, C., Capponi, A., Klopp, P., Connors, R. D., & Viti, F. (2021) · Frontiers in Future Transportation · doi:10.3389/ffutr.2021.666212 · Cited by 9
“The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) (Boni et al., 2020) was declared as a global emergency by the World Health Organisation (WHO) as of January 30, 2020.”
BackgroundYan, D. D., Hyuk, O. H. S., & Yan, B. (2021) · Animal Diseases · doi:10.1186/s44149-021-00017-5 · Cited by 8
Brintnell, E., Gupta, M., & Anderson, D. W. (2021) · Journal of Molecular Evolution · doi:10.1007/s00239-021-10034-0 · Cited by 8
Lawley, B., Grant, J., Harfoot, R., Treece, J. M., Day, R. C., Hernández, L. C., Stanton, J. L., Ussher, J. E., & Quiñones‐Mateu, M. E. (2021) · Viruses · doi:10.3390/v13112222 · Cited by 7
“This massive amount of information has been extremely valuable in understanding the evolution and epidemiology of the virus [7,32,33], leading to the classification of SARSCoV-2 genetic diversity into clades or lineages [34].”
BackgroundLuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples
Stahl, E. C., Gopez, A., Tsuchida, C. A., Fan, V. B., Moehle, E. A., Witkowsky, L. B., Hamilton, J. R., Lin-Shiao, E., McElroy, M. T., McDevitt, S. L., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0258263 · Cited by 7
Tsai, S. J., Ai, Y., Guo, C., & Gould, S. J. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101846 · Cited by 8
Maiti, A. K. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198712 · Cited by 6
“10.4 package (Drummond and Rambaut, 2007; Drummond et al., 2012; Rambaut et al., 2018).”
InfluentialRecombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein SPreprint
Tagliamonte, M. S., Abid, N., Ostrov, D. A., Chillemi, G., Pond, S. L. K., Salemi, M., & Mavian, C. N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.30.015685 · Cited by 7
Barrett, C. T., Neal, H. E., Edmonds, K. L., Moncman, C. L., Thompson, R., Branttie, J. M., Boggs, K. B., Wu, C., Leung, D. W., & Dutch, R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.24.428007 · Cited by 7
“62 Similar to several other CoVs, SARS-CoV-2 likely utilizes bats as a reservoir 63 species, specifically Rhinolophus affinis or horseshoe bats [11, 22-25].”
InfluentialGarushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.23.441209 · Cited by 8
Isolation and comparative analysis of antibodies that broadly neutralize sarbecovirusesPreprint
Liu, L., Iketani, S., Guo, Y., Casner, R. G., Reddem, E. R., Nair, M. S., Yu, J., Chan, J. F., Wang, M., Cerutti, G., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.11.472236 · Cited by 7
“that do not use human ACE2 as receptor (16, 18).”
BackgroundHussain, B., & Wu, C. (2024) · Viruses · doi:10.3390/v16060907 · Cited by 6
Paulino-Ramírez, R., López, P. L., Mueses, S., Cuevas, P., Jabier, M., & Rivera‐Amill, V. (2023) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph20085503 · Cited by 6
Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2
Gomez, L. R. E., Weber, A., Kocher, A., & Kühnert, D. (2024) · Scientific Reports · doi:10.1038/s41598-023-50952-1 · Cited by 6
“Lastly a uniform distribution between 0 and 15,000 years was also set as the prior for the age of the root of the clonal frame, considering the results of a previous dating analysis of Sarbecoviruses 10 .”
Figueiroa, T., Bueno, M. G., Moura, P. E. B., de Oliveira, M. B., Cordeiro, J. L. P., Santos-Cavalcante, N. M. D. C., Mazzarotto, G. A. C. A., Wallau, G. L., Junior, L. C. D. S., Resende, P. C., et al. (2025) · Animals · doi:10.3390/ani15030332 · Cited by 6
Ndzouboukou, J. B., Kamara, A. A., Ullah, N., Lei, Q., & Fan, X. (2025) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2411.11059 · Cited by 7
“SARS-CoV-2 is evolutionarily related to other potentially deadly respiratory viruses, including the SARS-CoV-1 and Middle East respiratory coronavirus virus (MERS-CoV), both from the beta-CoV genus and Coronaviridae family [2].”
Viral syncytia evolve to resist interferon
Li, T., Kang, I., Ye, J., Hu, Z., Gibbs, J. S., Ye, C., Takeda, K., Košík, I., Shi, G., Hollý, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74676-8 · Cited by 6
“1a) 12,13 .”
Pontes, C. F. T., Ruiz‐Serra, V., Lepore, R., & Valencia, A. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.006 · Cited by 6
“Like in SARS-CoV, horseshoe bats represent the most likely candidate animal source for SARS-CoV-2 so far [11].”
La pandemia de la COVID-19 como debate público: el caso español
Cuello, J. M. A. (2021) · Anuario electrónico de estudios en Comunicación Social Disertaciones · doi:10.12804/revistas.urosario.edu.co/disertaciones/a.10334 · Cited by 6
Jolma, E. R., Gibson, L., Suu‐Ire, R., Fleischer, G., Asumah, S., Languon, S., Restif, O., Wood, J. L. N., & Cunningham, A. A. (2021) · Viruses · doi:10.3390/v13081654 · Cited by 6
“Bats (order Chiroptera) host a huge number and diversity of viruses and have been identified as the source of a range of recently emerged viruses of public health significance, including Hendra virus, Nipah virus, MERS coronavirus and probably SARS-CoV-2, the causative agent of COVID-19 [1,2].”
BackgroundA novel predictor of ACE2-binding ability among betacoronaviruses
Dixson, J. D., & Azad, R. K. (2021) · Evolution Medicine and Public Health · doi:10.1093/emph/eoab032 · Cited by 6
Fumagalli, M. J., de Castro-Jorge, L. A., de Souza, W. M., de Azevedo, P. O., Hansen, A. W., Gazzinelli, R. T., da Fonseca, B. A. L., Spilki, F. R., & Figueiredo, L. T. M. (2022) · Viruses · doi:10.3390/v14020305 · Cited by 6
Hassanin, A. (2021) · Gene · doi:10.1016/j.gene.2022.146641 · Cited by 6
Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview
Hadizadeh, N., Naderi, M., Khezri, J., Yazdani, M., Shamsara, M., & Hashemi, E. (2022) · Journal of Diabetes & Metabolic Disorders · doi:10.1007/s40200-022-01002-6 · Cited by 7
“However, the highest genomic similarity of the first Covid-19 sequence was detected in the bat-CoV (RaTG13) strain which further elucidates the possible origins of this virus [60].”
BackgroundLeak or Leap? Evidence and Cognition Surrounding the Origins of the SARS-CoV-2 Virus
Lewandowsky, S., Jacobs, P., & Neil, S. J. D. (2023) · Routledge eBooks · doi:10.4324/9781003330769-5 · Cited by 6
A linear SARS-CoV-2 DNA vaccine candidate reduces virus shedding in ferrets
Martins, M., do Nascimento, G. M., Conforti, A., Noll, J. C. G., Impellizeri, J. A., Sanchez, E., Wagner, B., Lione, L., Salvatori, E., Pinto, E., et al. (2023) · Archives of Virology · doi:10.1007/s00705-023-05746-1 · Cited by 6
“However, the genetic distance of approximately 4% (~1,150 54 mutations) between RaTG13 and SARS-CoV-2 isolate Wuhan-Hu-1 indicate that transmission 55 likely did not occur directly from bats to humans and further suggest that a yet unidentified 56 animal species may have served as an intermediate host prior to spillov…”
BackgroundThe species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
Yang, J., Skaro, M. F., Chen, J., Zhan, D., Lyu, L., Gay, S., Kandeil, A., Ali, M. A., Kayali, G., Stoianova, K., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-32622-4 · Cited by 6
Oral non-viral gene delivery platforms for therapeutic applications
Ghaemi, A., Azghandi, M. V., Abnous, K., Taghdisi, S. M., Ramezani, M., & Alibolandi, M. (2023) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2023.123198 · Cited by 6
Xenotransplantation Literature Update January/February 2021
Rao, J. S., Matson, A. W., Taylor, R. T., & Burlak, C. (2021) · Xenotransplantation · doi:10.1111/xen.12685 · Cited by 6
Zhong, X., Chen, H., & Zare, R. N. (2021) · QRB Discovery · doi:10.1017/qrd.2021.2 · Cited by 6
Khan, A. H., Ema, N. T., Rakhi, N. N., Saha, O., Ahamed, T., & Rahaman, M. M. (2021) · COVID · doi:10.3390/covid1010017 · Cited by 6
Okeke, E. S., Olovo, C. V., Nkwoemeka, N. E., Okoye, C. O., Nwankwo, C. E. I., & Onu, C. (2022) · Heliyon · doi:10.1016/j.heliyon.2022.e09449 · Cited by 6
“The sarbecoviruses, which are the subgenus of the beta-coronaviruses to which SARS-CoV and SARS-CoV-2 belong, undergo frequent genetic recombination across host-species boundaries (Boni et al., 2020; Singh and Yi, 2021).”
Yang, H., Wang, J.-H., Yang, C.-T., Lin, Y.-C., Hsieh, H., Chen, P.-W., Liao, H.-C., Chen, C., & Liao, J. C. (2022) · PNAS Nexus · doi:10.1093/pnasnexus/pgac181 · Cited by 6
Metadata
- 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
- Venue
- Nature Microbiology
- Published
- 2020-07-28
- Volume
- 5
- Issue
- 11
- Pages
- 1408-1417
- ISSN
- 2058-5276 (ISSN-L)
- 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
- 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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