The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Cited by
Sorted by citations
Coronavirus biology and replication: implications for SARS-CoV-2
V’kovski, P., Kratzel, A., Steiner, S., Stalder, H., & Thiel, V. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00468-6 · Cited by 3,371
Mechanisms of SARS-CoV-2 entry into cells
Jackson, C. B., Farzan, M., Chen, B., & Choe, H. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00418-x · Cited by 3,022
Starr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956
“There is a dizzying diversity of RBD genotypes and phenotypes among sarbecoviruses within bat reservoirs (Boni et al., 2020; Demogines et al., 2012; Frank et al., 2020; Hu et al., 2017; Latinne et al., 2020; Letko et al., 2020; MacLean et al., 2020).”
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04411-y · Cited by 1,678
Self-citationMarkov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025
“Its receptor-binding motif, important for human ACE2 receptor-binding specificity, appears to be an ancestral trait shared with multiple bat viruses (Boni et al., 2020).”
Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans
Munnink, B. B. O., Sikkema, R. S., Nieuwenhuijse, D. F., Molenaar, R. J., Münger, E., Molenkamp, R., van der Spek, A. N., Tolsma, P., Rietveld, A., Brouwer, M., et al. (2020) · Science · doi:10.1126/science.abe5901 · Cited by 1,116
“bat sequence is estimated somewhere between 1948-1982 (9).”
BackgroundThe biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009
The Lancet Commission on lessons for the future from the COVID-19 pandemic
Sachs, J. D., Karim, S. S. A., Aknin, L., Allen, J., Brosbøl, K., Colombo, F., Barron, G. C., Espinosa, M. F., Gaspar, V., Gaviria, A., et al. (2022) · The Lancet · doi:10.1016/s0140-6736(22)01585-9 · Cited by 842
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets
Peacock, T. P., Goldhill, D. H., Zhou, J., Baillon, L., Frise, R., Swann, O. C., Kugathasan, R., Penn, R., Brown, J. C., Sanchez-David, R. Y., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00908-w · Cited by 802
Emerging Pandemic Diseases: How We Got to COVID-19
Morens, D. M., & Fauci, A. S. (2020) · Cell · doi:10.1016/j.cell.2020.08.021 · Cited by 780
“, 2020a, 2020b) indicates that SARS-CoV-2 probably emerged from an as-yet-unidentified bat reservoir either directly or after infection of an intermediate host such as a pangolin (Boni et al., 2020; Letko et al., 2020; Li et al., 2020; Zhou et al., 2020a, 2020b).”
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Self-citationRecurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P. (2021) · Science · doi:10.1126/science.abf6950 · Cited by 535
The origins of SARS-CoV-2: A critical review
Holmes, E. C., Goldstein, S. A., Rasmussen, A. L., Robertson, D. L., Crits‐Christoph, A., Wertheim, J. O., Anthony, S. J., Barclay, W., Boni, M. F., Doherty, P. C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.017 · Cited by 553
“…the spike protein, including N501Y, K417N/T, L452R, and E484K/Q—constituent mutations of the variants of concern—similarly enhance viral infectivity (Cai et al., 2021; Khan et al., 2021; Kuzmina et al., 2021) and ACE2 binding (Liu et al., 2021; Starr et al., 2020; Zhu et al., 2021a), refuting…”
BackgroundSelf-citationThe emergence, genomic diversity and global spread of SARS-CoV-2
Li, J., Lai, S., Gao, G. F., & Shi, W. (2021) · Nature · doi:10.1038/s41586-021-04188-6 · Cited by 427
SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801
Wahl, A. R., Gralinski, L. E., Johnson, C. E., Yao, W., Kovářová, M., Dinnon, K. H., Liu, H., Madden, V. J., Krzystek, H. M., De, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03312-w · Cited by 412
Tali, S. H. S., LeBlanc, J. J., Sadiq, Z., Oyewunmi, O. D., Camargo, C., Nikpour, B., Armanfard, N., Sagan, S. M., & Jahanshahi‐Anbuhi, S. (2021) · Clinical Microbiology Reviews · doi:10.1128/cmr.00228-20 · Cited by 430
Jones, D. L., Quintela‐Baluja, M., Graham, D. W., Corbishley, A., McDonald, J. E., Malham, S. K., Hillary, L. S., Connor, T. R., Gaze, W. H., Moura, I. B., et al. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.141364 · Cited by 404
“The direct ancestor of SARS-CoV-2 appears to have been circulating unnoticed for decades in bats and subsequently transmitted to pangolins and then humans (Boni et al., 2020).”
BackgroundDetection of Viral Infections by Innate Immunity
Carty, M., Guy, C., & Bowie, A. (2020) · Biochemical Pharmacology · doi:10.1016/j.bcp.2020.114316 · Cited by 427
From People to Panthera : Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo
McAloose, D., Laverack, M. A., Wang, L., Killian, M. L., Caserta, L. C., Yuan, F., Mitchell, P. K., Queen, K. J., Mauldin, M. R., Cronk, B. D., et al. (2020) · mBio · doi:10.1128/mbio.02220-20 · Cited by 409
“However, a recent study suggests the virus may have been circulating in bats for several decades (7), and an early cluster of human COVID-19 cases had an epidemiological link to the Huanan Seafood Wholesale market in Wuhan where a variety of live wild animals were sold (4).”
BackgroundLessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic
To, K. K., Sridhar, S., Chiu, K. H., Hung, D. L. L., Li, X., Hung, I. F., Tam, A. R., Chung, T. W., Chan, J. F., Zhang, J., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1898291 · Cited by 359
“sarbecovirus has been estimated to be 1948 [57].”
BackgroundOn the origin and evolution of SARS-CoV-2
Singh, D., & Yi, S. V. (2021) · Experimental & Molecular Medicine · doi:10.1038/s12276-021-00604-z · Cited by 281
“For example, upon comparing the genome sequences of 68 Sarbecovirus strains, including SARS-CoV-2, Boni et al.28 detected numerous recombination breakpoints in the data.”
BackgroundMethodResultInfluentialEcology, evolution and spillover of coronaviruses from bats
Ruiz‐Aravena, M., McKee, C., Gamble, A., Lunn, T. J., Morris, A. L., Snedden, C. E., Yinda, C. K., Port, J. R., Buchholz, D. W., Yeo, Y. Y., et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00652-2 · Cited by 303
“Additional SARS-related corona-viruses (SARSr-CoVs) have been detected in hippo-siderid and molossid bats in Africa, Asia and Europe (Supplementary Table 1), and it is widely accepted that bats are the natural reservoir of SARSr-CoVs 18–20 .”
InfluentialDivergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
Pickering, B., Lung, O., Maguire, F., Kruczkiewicz, P., Kotwa, J. D., Buchanan, T., Gagnier, M., Guthrie, J. L., Jardine, C. M., Marchand‐Austin, A., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01268-9 · Cited by 266
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1101/2021.12.19.21268028 · Cited by 253
Self-citationZoonotic spillover: Understanding basic aspects for better prevention
Ellwanger, J. H., & Chies, J. A. B. (2021) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2020-0355 · Cited by 284
“On the other hand, some data support that the viral strain that originated SARS-CoV-2 may have been circulating in bat populations for many years (maybe since the 1940s or before that) and subsequently been transmitted to humans without necessarily the participation of an intermediary host (Boni et al., 2020).”
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
Pekar, J. E., Magee, A. F., Parker, E., Moshiri, N., Izhikevich, K., Havens, J. L., Gangavarapu, K., Serrano, L. M. M., Crits‐Christoph, A., Matteson, N. L., et al. (2022) · Science · doi:10.1126/science.abp8337 · Cited by 277
Self-citationDhama, K., Patel, S. K., Sharun, K., Pathak, M., Tiwari, R., Yatoo, M. I., Malik, Y. S., Sah, R., Rabaan, A. A., Panwar, P. K., et al. (2020) · Travel Medicine and Infectious Disease · doi:10.1016/j.tmaid.2020.101830 · Cited by 256
“transmission [27] and later it was disapproved by other researchers [163,164].”
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R., Darby, A. C., Haldenby, S. T., Hill, V., Lucaci, A. O., McCrone, J. T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.014 · Cited by 229
Self-citationTso, F. Y., Lidenge, S. J., Peña, P. B., Clegg, A. A., Ngowi, J. R., Mwaiselage, J. D., Ngalamika, O., Julius, P., West, J. T., & Wood, C. A. (2020) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2020.10.104 · Cited by 228
“In addition, HCoV-NL63 s the only other HCoV that uses angiotensin-converting enzyme 2, hich is the same receptor used by SARS and SARS-CoV-2 (Abdulbioinformatics study also suggested that SARS-CoV-2 evolved from a bat coronavirus and bats may be a primary reservoir (Boni et al., 2020).”
The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
Munnink, B. B. O., Worp, N., Nieuwenhuijse, D. F., Sikkema, R. S., Haagmans, B. L., Fouchier, R. A. M., & Koopmans, M. (2021) · Nature Medicine · doi:10.1038/s41591-021-01472-w · Cited by 238
Immunological imprinting of the antibody response in COVID-19 patients
Aydillo, T., Rombauts, A., Stadlbauer, D., Aslam, S., Abelenda-Alonso, G., Escalera, A., Amanat, F., Jiang, K., Krammer, F., Carratala, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23977-1 · Cited by 223
The evolutionary consequences of human–wildlife conflict in cities
Schell, C. J., Stanton, L. A., Young, J. K., Angeloni, L. M., Lambert, J. E., Breck, S. W., & Murray, M. H. (2020) · Evolutionary Applications · doi:10.1111/eva.13131 · Cited by 244
“Evidence suggests bats are a natural reservoir host for the novel coronavirus, SARSCoV-2 (Boni et al., 2020; MacFarlane & Rocha, 2020).”
BackgroundSARS‐CoV‐2 sensing by RIG‐I and MDA5 links epithelial infection to macrophage inflammation
Thorne, L., Reuschl, A., Zuliani‐Alvarez, L., Whelan, M. V. X., Turner, J. L. E., Noursadeghi, M., Jolly, C. L., & Towers, G. J. (2021) · The EMBO Journal · doi:10.15252/embj.2021107826 · Cited by 223
Gutiérrez‐Castrellón, P., Gandara-Martí, T., y Abreu, A. T. A., Nieto-Rufino, C. D., López-Orduña, E., Jiménez–Escobar, I., Jiménez-Gutiérrez, C., López‐Velázquez, G., & Espadaler, J. (2022) · Gut Microbes · doi:10.1080/19490976.2021.2018899 · Cited by 220
“Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is the causative agent of Coronavirus Disease 2019 (Covid19) global pandemic.(1) SARSCoV2 infection can range from asymptomatic to death, but most symptomatic patients typically display mild to moderate symptoms, even despite significant viral loads,(2) and t…”
BackgroundOu, J., Lan, W., Wu, X., Zhao, T., Duan, B., Yang, P., Ren, Y., Quan, L., Zhao, W., Seto, D., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00992-2 · Cited by 211
Evidence for SARS-CoV-2 Infection of Animal Hosts
Abdel-Moneim, A. S., & Abdelwhab, E. M. (2020) · Pathogens · doi:10.3390/pathogens9070529 · Cited by 209
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
Chiara, M., D’Erchia, A. M., Gissi, C., Manzari, C., Parisi, A., Resta, N., Zambelli, F., Picardi, E., Pavesi, G., Horner, D. S., et al. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa297 · Cited by 214
“In just a few months, genome sequence data have allowed reconstruction of the probable time of spillover of SARS-CoV2 into the human population [140–142], the development of systems for the classification of viral strains which have been fundamental for monitoring the spread of the virus [41, 140, 142], and for the id…”
BackgroundACE2 binding is an ancestral and evolvable trait of sarbecoviruses
Starr, T. N., Zepeda, S. K., Walls, A. C., Greaney, A. J., Alkhovsky, S. V., Veesler, D., & Bloom, J. D. (2022) · Nature · doi:10.1038/s41586-022-04464-z · Cited by 207
On the evolutionary epidemiology of SARS-CoV-2
Day, T., Gandon, S., Lion, S., & Otto, S. P. (2020) · Current Biology · doi:10.1016/j.cub.2020.06.031 · Cited by 208
“In the long run, deleterious mutations are expected to be eliminated, as seen in genetic comparisons between more distantly related coronavirus lineages [6].”
BackgroundMacLean, O. A., Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Pond, S. L. K., & Robertson, D. L. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001115 · Cited by 227
“We use an array of selection detection methods (summarised in S2 Fig) on a set of (i) 133,741 SARS-CoV-2 genomes sampled from December 2019 to October 2020 and on (ii) 69 Sarbecovirus genomes (including a representative of SARS-CoV-1 and SARS-CoV-2 sequences) separated into phylogenetically congruent regions based on…”
BackgroundMethodInfluentialSelf-citationComparison of transgenic and adenovirus hACE2 mouse models for SARS-CoV-2 infection
Rathnasinghe, R., Strohmeier, S., Amanat, F., Gillespie, V., Krammer, F., García‐Sastre, A., Coughlan, L., Schotsaert, M., & Uccellini, M. B. (2020) · Emerging Microbes & Infections · doi:10.1080/22221751.2020.1838955 · Cited by 198
“The virus likely originated in bats (5, 6), 45 before potentially jumping to an intermediate host and then to humans.”
A novel SARS-CoV-2 related coronavirus in bats from Cambodia
Delaune, D., Hul, V., Karlsson, E. A., Hassanin, A., Ou, T. P., Baidaliuk, A., Gámbaro, F., Prot, M., Tú, V. T., Chea, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26809-4 · Cited by 227
The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines
McLean, G. R., Kamil, J. P., Lee, B., Moore, P. L., Schulz, T. F., Muik, A., Şahin, U., Türeci, Ö., & Pather, S. (2022) · mBio · doi:10.1128/mbio.02979-21 · Cited by 195
“SARS-CoV-2 is assumed to be of zoonotic origin, although the exact zoonotic source of the parental virus and the circumstances behind its emergence in humans in late 2019 remain unknown (25, 26).”
BackgroundOne year update on the COVID-19 pandemic: Where are we now?
Mishra, S. K., & Tripathi, T. (2020) · Acta Tropica · doi:10.1016/j.actatropica.2020.105778 · Cited by 196
“the primary reservoir of the SARS-CoV-2 lineage (Boni et al., 2020).”
COVID-19—Zoonosis or Emerging Infectious Disease?
Haider, N., Rothman-Ostrow, P., Osman, A. Y., Arruda, L. B., Macfarlane-Berry, L., Elton, L., Thomason, M. J., Yeboah‐Manu, D., Ansumana, R., Kapata, N., et al. (2020) · Frontiers in Public Health · doi:10.3389/fpubh.2020.596944 · Cited by 209
SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights
Kadam, S. B., Sukhramani, G. S., Bishnoi, P., Pable, A. A., & Barvkar, V. T. (2021) · Journal of Basic Microbiology · doi:10.1002/jobm.202000537 · Cited by 206
“The RBD, which is important for binding with human ACE2 receptor, is an ancestral trait from bat viruses rather than recent recombination [106].”
BackgroundAnimal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic
Xiao, X., Newman, C., Buesching, C. D., Macdonald, D. W., & Zhou, Z.-M. (2021) · Scientific Reports · doi:10.1038/s41598-021-91470-2 · Cited by 180
The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study
Townsend, J. P., Hassler, H. B., Wang, Z., Miura, S., Singh, J., Kumar, S., Ruddle, N. H., Galvani, A. P., & Dornburg, A. (2021) · The Lancet Microbe · doi:10.1016/s2666-5247(21)00219-6 · Cited by 186
The COVID-19 pandemic is intricately linked to biodiversity loss and ecosystem health
Lawler, O. K., Allan, H., Baxter, P. W. J., Castagnino, R., Tor, M. C., Dann, L. E., Hungerford, J., Karmacharya, D. B., Lloyd, T. J., López, M. J., et al. (2021) · The Lancet Planetary Health · doi:10.1016/s2542-5196(21)00258-8 · Cited by 204
“14,16 Direct spillover of SARS-CoV-2 or its progenitor to humans from a bat host has also been proposed as a possibility (appendix pp 1–2).”
BackgroundThe Evolution and Biology of SARS-CoV-2 VariantsPreprint
Telenti, A., Hodcroft, E. B., & Robertson, D. L. (2022) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041390 · Cited by 191
Self-citationTriggle, C. R., Bansal, D., Ding, H., Islam, M. M., Farag, E., Hadi, H. A., & Sultan, A. A. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.631139 · Cited by 187
“Genetic sequence data reveals that SARS-CoV-2 is a close relative of other species of coronaviruses found to be circulating in Rhinolophus bat (Horseshoe Bat) populations (9, 16).”
BackgroundExploring the Natural Origins of SARS-CoV-2 in the Light of Recombination
Lytras, S., Hughes, J., Martin, D. P., Swanepoel, P., de Klerk, A., Lourens, R., Pond, S. L. K., Xia, W., Jiang, X., & Robertson, D. L. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac018 · Cited by 174
Self-citationAnimal and translational models of SARS-CoV-2 infection and COVID-19
Johansen, M. D., Irving, A. T., Montagutelli, X., Tate, M. D., Rudloff, I., Nold, M. F., Hansbro, N. G., Kim, R., Donovan, C., Liu, G., et al. (2020) · Mucosal Immunology · doi:10.1038/s41385-020-00340-z · Cited by 173
“OTHER INFECTED ANIMALS Bats While SARS-CoV-2 is clearly a suitable human virus, its origins remains elusive with a common ancestor of bat SARS-Like CoVs and SARS-CoV-2 existing ~40–70 years prior to emergence.(155) Scientists are now searching for further evidence in wild bats and have performed infection studies with…”
BackgroundPolymeric nanoparticle vaccines to combat emerging and pandemic threats
Wibowo, D., Jorritsma, S. H. T., Gonzaga, Z. J., Evert, B. J., Chen, S., & Rehm, B. H. A. (2020) · Biomaterials · doi:10.1016/j.biomaterials.2020.120597 · Cited by 177
“A notable example is the ongoing pandemic coronavirus disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) originated from bats [4].”
Timing the SARS-CoV-2 index case in Hubei Province
Pekar, J., Worobey, M., Moshiri, N., Scheffler, K., & Wertheim, J. O. (2021) · Science · doi:10.1126/science.abf8003 · Cited by 156
Olival, K. J., Cryan, P. M., Amman, B. R., Baric, R. S., Blehert, D. S., Brook, C. E., Calisher, C. H., Castle, K. T., Coleman, J. T. H., Daszak, P., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008758 · Cited by 172
“Third, if SARS-CoV-2 infection persists in North American bats of one or more species, it could potentially evolve or recombine with endemic viruses [19, 21] to become more pathogenic or infectious to humans or other animals.”
BackgroundHigh-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants
Fontenele, R. S., Kraberger, S. J., Hadfield, J., Driver, E. M., Bowes, D. A., Holland, L. A., Faleye, T. O. C., Adhikari, S., Kumar, R., Inchausti, R., et al. (2021) · Water Research · doi:10.1016/j.watres.2021.117710 · Cited by 167
Self-citationControl and prevention of infectious diseases from a One Health perspective
Ellwanger, J. H., da Veiga, A. B. G., Kaminski, V. D. L., Valverde-Villegas, J. M., de Freitas, A. W. Q., & Chies, J. A. B. (2021) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2020-0256 · Cited by 200
Profile of a killer: the complex biology powering the coronavirus pandemic
Cyranoski, D. (2020) · Nature · doi:10.1038/d41586-020-01315-7 · Cited by 170
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Chan, K. K., Tan, T. J. C., Narayanan, K. K., & Procko, E. (2021) · Science Advances · doi:10.1126/sciadv.abf1738 · Cited by 152
“In addition, large changes in coronavirus genomes have frequently occurred in nature from recombination events, especially in bats where coinfection levels can be high (15, 16).”
BackgroundNchioua, R., Kmiec, D., Müller, J. A., Conzelmann, C., Groß, R., Swanson, C. M., Neil, S. J. D., Stenger, S., Sauter, D., Münch, J., et al. (2020) · mBio · doi:10.1128/mbio.01930-20 · Cited by 146
“In this part of the genome, SARS-CoV-2 shows substantially higher similarity in sequence and CpG numbers to bat RaTG13 and pangolin Pang Guangdong CoV strains than to RmYN02 (20, 54).”
BackgroundInfluentialTransmission of SARS-CoV-2 from humans to animals and potential host adaptation
Tan, C. C. S., Lam, S. D., Richard, D., Owen, C. J., Berchtold, D., Orengo, C. A., Nair, M. S., Kuchipudi, S. V., Kapur, V., van Dorp, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30698-6 · Cited by 154
“Evolutionary analyses of SARS-CoV-2 and close relatives suggest that both ef fi cient human-to-human transmission and ACE2 usage were not acquired recently, but may already have been present in ancestral bat-associated lineages 4,5 .”
Evolutionary trajectory of SARS-CoV-2 and emerging variants
Singh, J., Pandit, P., McArthur, A. G., Banerjee, A., & Mossman, K. L. (2021) · Virology Journal · doi:10.1186/s12985-021-01633-w · Cited by 150
Fagre, A. C., Lewis, J., Eckley, M., Zhan, S., Rocha, S. M., Sexton, N. R., Burke, B. E., Geiss, B. J., Peersen, O. B., Bass, T. A., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009585 · Cited by 145
SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective
Sironi, M., Hasnain, S. E., Rosenthal, B. M., Phan, T. G., Luciani, F., Shaw, M., Sallum, M. A. M., Mirhashemi, M. E., Morand, S., & Gónzález‐Candelas, F. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104384 · Cited by 145
Lost in deletion: The enigmatic ORF8 protein of SARS-CoV-2
Zinzula, L. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.10.045 · Cited by 136
“117 this well correlates with the proposed theory of SARS-CoV-2 originating from recombination events between horseshoe bat coronaviruses, as well as with the plausible role of pangolins as intermediate hosts that preceded SARS-CoV-2 spillover into human population [4,17].”
Binding and molecular basis of the bat coronavirus RaTG13 virus to ACE2 in humans and other species
Liu, K., Pan, X., Li, L., Yu, F., Zheng, A., Du, P., Han, P., Meng, Y., Zhang, Y., Wu, L., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.031 · Cited by 136
“3% amino acid identity in the receptor binding domain (RBD) (Boni et al., 2020; Wu et al., 2020a; Zhou et al., 2020b).”
InfluentialTang, T., Jaimes, J. A., Bidon, M. K., Straus, M. R., Daniel, S., & Whittaker, G. R. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.0c00701 · Cited by 136
SARS-CoV-2 Infects Neurons and Induces Neuroinflammation in a Non-Human Primate Model of COVID-19
Beckman, D., Bonillas, A. C., Diniz, G. B., Ott, S. P., Roh, J. W., Elizaldi, S. R., Schmidt, B., Sammak, R. L., Rompay, K. K. A. V., Iyer, S. S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111573 · Cited by 132
Thompson, C. W., Phelps, K. L., Allard, M. W., Cook, J. A., Dunnum, J. L., Ferguson, A. W., Gelang, M., Khan, F. A. A., Paul, D. L., Reeder, D. M., et al. (2021) · mBio · doi:10.1128/mbio.02698-20 · Cited by 133
“SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) (3), the causative agent of COVID-19, has demonstrated that a previously unknown pathogen can emerge from wildlife species and threaten public health on a global scale within months.”
BackgroundInfluentialThe Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19
Schreiber, G. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.595739 · Cited by 136
“Similar virus strains that circulate in bats in Hubei province in China may in the future cause further new zoonotic outbreaks (29).”
BackgroundAssessing the risks of SARS-CoV-2 in wildlife
Delahay, R. J., de la Fuente, J., Smith, G. C., Sharun, K., Snary, E., Giron, L. F., Nziza, J., Fooks, A. R., Brookes, S. M., Lean, F. Z. X., et al. (2021) · One Health Outlook · doi:10.1186/s42522-021-00039-6 · Cited by 128
Zoonotic disease and virome diversity in bats
Brussel, K. V., & Holmes, E. C. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.12.008 · Cited by 128
Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19
Zhang, J., Ejikemeuwa, A., Gerzanich, V., Nasr, M., Tang, Q., Simard, J. M., & Zhao, Y. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.854567 · Cited by 138
Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene
Pereira, F. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104525 · Cited by 123
“After the S gene, ORF8 stands out as being the most divergent gene when SARS-CoV-2 is compared with bat and pangolin coronaviruses (Boni et al., 2020).”
Recent advances in mRNA cancer vaccines: meeting challenges and embracing opportunities
Wang, B., Pei, J., Xu, S., Liu, J., & Yu, J. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1246682 · Cited by 131
“Recently, the successful applications of COVID-19 global pandemic offered a great opportunity for messenger RNA (mRNA)vaccines in antitumor therapy (8 – 10).”
BackgroundLam, S. D., Bordin, N., Waman, V., Scholes, H. M., Ashford, P., Sen, N., van Dorp, L., Rauer, C., Dawson, N. L., Pang, C., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-71936-5 · Cited by 109
A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways
Lorenzo-Redondo, R., Nam, H. H., Roberts, S. C., Simons, L. M., Jennings, L. J., Qi, C., Achenbach, C. J., Hauser, A. R., Ison, M. G., Hultquist, J. F., et al. (2020) · EBioMedicine · doi:10.1016/j.ebiom.2020.103112 · Cited by 110
“6 £ 10 4 for the global tree, consistent with other studies [12,33].”
Reinfection in patients with COVID-19: a systematic review
Ren, X., Zhou, J., Guo, J., Hao, C., Zheng, M., Zhang, R., Huang, Q. Y., Yao, X., Li, R., & Jin, Y. (2022) · Global Health Research and Policy · doi:10.1186/s41256-022-00245-3 · Cited by 104
“Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is a single-stranded positive-strand RNA virus that belongs to the Coronaviridae family [2, 3].”
BackgroundRisk of human‐to‐wildlife transmission of SARS‐CoV‐2
Gryseels, S., Bruyn, L. D., Gyselings, R., Calvignac‐Spencer, S., Leendertz, F. H., & Leirs, H. (2020) · Mammal Review · doi:10.1111/mam.12225 · Cited by 114
“taken place solely in its natural (horseshoe bat) reservoir or (partly) in another unidentified natural host [27].”
BackgroundInfluentialNeutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants
Ikegame, S., Siddiquey, M. N. A., Hung, C.-T., Haas, G. D., Brambilla, L., Oguntuyo, K. Y., Kowdle, S., Chiu, H.-P., Stevens, C. S., Vilardo, A. E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24909-9 · Cited by 141
Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreadersPreprint
Gómez‐Carballa, A., Bello, X., Pardo‐Seco, J., Martinón‐Torres, F., & Salas, A. (2020) · Genome Research · doi:10.1101/gr.266221.120 · Cited by 109
“that could have existed in a time frame between 1948 and 1982 (Boni et al. 2020).”
BackgroundSun, D., Sang, Z., Kim, Y. J., Xiang, Y., Cohen, T., Belford, A. K., Huet, A., Conway, J. F., Sun, J., Taylor, D. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24963-3 · Cited by 96
Towards integrated surveillance-response systems for the prevention of future pandemics
Zinsstag, J., Utzinger, J., Probst-Hensch, N. M., Lv, S., & Zhou, X. (2020) · Infectious Diseases of Poverty · doi:10.1186/s40249-020-00757-5 · Cited by 108
“COVID-19 is suspected to result from animal-to-human transmission of SARS coronavirus 2 (SARS-CoV-2) with most close relation to a bat coronavirus [10, 11].”
BackgroundCOVID-19—lessons for zoonotic disease
Holmes, E. C. (2022) · Science · doi:10.1126/science.abn2222 · Cited by 102
Amoutzias, G. D., Nikolaidis, M., Tryfonopoulou, E., Chlichlia, K., Markoulatos, P., & Oliver, S. G. (2022) · Viruses · doi:10.3390/v14010078 · Cited by 99
“The feasibility of this scenario is evidenced by recent analyses of the role of recombination in Sarbecovirus evolution [52,76,111].”
BackgroundInfluentialNo evidence for distinct types in the evolution of SARS-CoV-2
MacLean, O. A., Orton, R. J., Singer, J. B., & Robertson, D. L. (2020) · Virus Evolution · doi:10.1093/ve/veaa034 · Cited by 96
Self-citationThe Emergence and Evolution of SARS-CoV-2
Holmes, E. C. (2024) · Annual Review of Virology · doi:10.1146/annurev-virology-093022-013037 · Cited by 96
Host Diversity and Origin of Zoonoses: The Ancient and the New
Recht, J., Schuenemann, V. J., & Sánchez-Villagra, M. R. (2020) · Animals · doi:10.3390/ani10091672 · Cited by 105
“A very recent phylogenetic dating study based on bioinformatic approaches strongly suggests that SARS-CoV-2 emerged directly, without an intermediate host, from the same horseshoe bat subgenus of SARS-like coronaviruses, with both SARS-CoV and SARS-CoV-2 diverging at the same time (40–70 years ago) from currently know…”
BackgroundGenomic sequencing effort for SARS-CoV-2 by country during the pandemic
Furuse, Y. (2020) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2020.12.034 · Cited by 90
“Collecting viral sequence data is also important for conducting an evolutionary analysis to infer the origin of the virus (Boni et al., 2020), detect mutations that may affect the pathogenicity and infectivity of the virus (Korber et al.”
BackgroundDynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Nelson, C. W., Ardern, Z., Goldberg, T. L., Meng, C., Kuo, C.-H., Ludwig, C., Kolokotronis, S.-O., & Wei, X. (2020) · eLife · doi:10.7554/elife.59633 · Cited by 87
“Finally, given multiple recombination breakpoints in ORF3a (Boni et al., 2020) and the relative paucity of sequence data for viruses closely related to SARS-CoV-2, our analysis could not differentiate between convergence, recombination, or recurrent loss in the origin of ORF3d.”
BackgroundThe evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus
Wells, H., Letko, M. C., Lasso, G., Ssebide, B., Nziza, J., Byarugaba, D. K., Navarrete‐Macias, I., Liang, E., Cranfield, M. R., Han, B. A., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab007 · Cited by 97
Cross-species recognition of SARS-CoV-2 to bat ACE2
Liu, K., Tan, S., Niu, S., Wang, J., Wu, L., Sun, H., Zhang, Y., Pan, X., Qu, X., Du, P., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2020216118 · Cited by 89
“A growing body of research has identified that the binding capacity of ACE2 orthologs from different bat species to RBD of SARS-CoV or SARS-CoV-2 varied substantially, indicating the extensively diversified susceptibility of SARS-CoV and SARS-CoV-2 in different bat species (18, 25, 32, 33).”
Hosie, M. J., Epifano, I., Herder, V., Orton, R. J., Stevenson, A., Johnson, N., MacDonald, E., Dunbar, D., McDonald, M., Howie, F., et al. (2021) · Veterinary Record · doi:10.1002/vetr.247 · Cited by 91
Self-citationRandom-Forest-Bagging Broad Learning System With Applications for COVID-19 Pandemic
Zhan, C., Zheng, Y., Zhang, H., & Wen, Q. (2021) · IEEE Internet of Things Journal · doi:10.1109/jiot.2021.3066575 · Cited by 91
“The out-break of COVID-19 has progressed with a tremendous impact on the economic [3], social behavior [4], environment [5], climate [6], etc. Evolutionary virologist found bats may be the origins of SARS-CoV-2 [7], which has a long evolutionary history [8].”
BackgroundTian, J., Sun, J., Li, D., Wang, N., Wang, L., Zhang, C., Meng, X., Ji, X., Suchard, M. A., Zhang, X., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110969 · Cited by 98
“Divergence dates between SARS-CoV-2 and other bat sarbecoviruses were estimated to be between 1948 and 1982, indicating that this lineage for SARSCoV-2 had been circulating in bats for several decades (Boni et al., 2020).”
Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats
Moreno-Santillán, D. D., Lama, T. M., Gutiérrez‐Guerrero, Y. T., Brown, A. M., Donat, P., Zhao, H., Rossiter, S. J., Yohe, L. R., Potter, J. H. T., Teeling, E. C., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16027 · Cited by 87
“This probably includes the current SARS- CoV- 2 pandemic (Boni et al., 2020; Lau et al., 2020).”
BackgroundThe origins of COVID‐19 pandemic: A brief overview
Hao, Y., Wang, Y., Wang, M.-Y., Zhou, L., Shi, J., Cao, J., & Wang, D. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14732 · Cited by 139
COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans
Frutos, R., Cobo, J. S., Chen, T., & Devaux, C. A. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104493 · Cited by 94
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review