Microbiol. Boxes show 95% HPD credible intervals. 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. The web application was developed by the Centre for Genomic Pathogen Surveillance. Lond. Biol. PDF single centre retrospective study Bayesian evaluation of temporal signal in measurably evolving populations. Pink, green and orange bars show BFRs, with regionA (nt 13,29119,628) showing two trimmed segments yielding regionA (nt13,29114,932, 15,40517,162, 18,00919,628). The histogram allows for the identification of non-recombining regions (NRRs) by revealing regions with no breakpoints. Anderson, K. G. nCoV-2019 codon usage and reservoir (not snakes v2). Pango lineage designation and assignment using SARS-CoV-2 - PubMed 4), that region and shorter BFRs were not included in combined putative non-recombinant regions. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Time-measured phylogenetic reconstruction was performed using a Bayesian approach implemented in BEAST42 v.1.10.4. 62,63), the GTR+ model and 100bootstrap replicateswas inferred for each BFR >500nt. https://doi.org/10.1093/molbev/msaa163 (2020). The authors declare no competing interests. Because the SARS-CoV-2 S protein has been implicated in past recombination events or possibly convergent evolution12, we specifically investigated several subregions of the Sproteinthe N-terminal domain of S1, the C-terminal domain of S1, the variable-loop region of the C-terminal domain, and S2. Ge, X. et al. Sequence similarity. Katoh, K., Asimenos, G. & Toh, H. in Bioinformatics for DNA Sequence Analysis (ed. First, we took an approach that relies on identification of mosaic regions (via 3SEQ14 v.1.7) that are also supported by PI signals19. We find that the sarbecovirusesthe viral subgenus containing SARS-CoV and SARS-CoV-2undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. The plots are based on maximum likelihood tree reconstructions with a root position that maximises the residual mean squared for the regression of root-to-tip divergence and sampling time. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. Nature 558, 180182 (2018). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist For weather, science, and COVID-19 . . 4 TMRCAs for SARS-CoV and SARS-CoV-2. These authors contributed equally: Maciej F. Boni, Philippe Lemey. 1, vev003 (2015). Xiao, K. et al. Microbes Infect. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Phylogenetic Assignment of Named Global Outbreak LINeages, The pangolin web app is maintained by the Centre for Genomic Pathogen Surveillance. RegionC showed no PI signals within it. For the HCoV-OC43, MERS-CoV and SARS datasets we specified flexible skygrid coalescent tree priors. and T.A.C. B., Weaver, S. & Sergei, L. Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans. Divergence time estimates based on the three regions/alignments where the effects of recombination have been removed. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. 3). Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica). Ji, W., Wang, W., Zhao, X., Zai, J. MERS-CoV data were subsampled to match sample sizes with SARS-CoV and HCoV-OC43. Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M. & Kawaoka, Y. Evolution and ecology of influenza A viruses. Syst. Posada, D., Crandall, K. A. RegionsAC had similar phylogenetic relationships among the southern China bat viruses (Yunnan, Guangxi and Guizhou provinces), the Hong Kong viruses, northern Chinese viruses (Jilin, Shanxi, Hebei and Henan provinces, including Shaanxi), pangolin viruses and the SARS-CoV-2 lineage. Virological.org http://virological.org/t/ncovs-relationship-to-bat-coronaviruses-recombination-signals-no-snakes-no-evidence-the-2019-ncov-lineage-is-recombinant/331 (2020). But some theories suggest that pangolins may be the source of the novel coronavirus. We infer time-measured evolutionary histories using a Bayesian phylogenetic approach while incorporating rate priors based on mean MERS-CoV and HCoV-OC43 rates and with standard deviations that allow for more uncertainty than the empirical estimates for both viruses (see Methods). 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. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. Alternatively, combining 3SEQ-inferred breakpoints, GARD-inferred breakpoints and the necessity of PI signals for inferring recombination, we can use the 9.9-kb region spanning nucleotides 11,88521,753 (NRR2) as a putative non-recombining region; this approach is breakpoint-conservative because it is conservative in identifying breakpoints but not conservative in identifying non-recombining regions. Region A has been shortened to A (5,017nt) based on potential recombination signals within the region. The consistency of the posterior rates for the different prior means also implies that the data do contribute to the evolutionary rate estimate, despite the fact that a temporal signal was visually not apparent (Extended Data Fig. PI signals were identified (with bootstrap support >80%) for seven of these eight breakpoints: positions 1,684, 3,046, 9,237, 11,885, 21,753, 22,773 and 24,628. PANGOLIN lineage database (15, 16) was used to analyze the frequency of lineages among countries. Combining regions A, B and C and removing the five named sequences gives us putative NRR1, as an alignment of 63sequences. B.W.P. Maciej F. Boni, Philippe Lemey, Andrew Rambaut or David L. Robertson. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Eight other BFRs <500nt were identified, and the regions were named BFRAJ in order of length. Specifically, using a formal Bayesian approach42 (see Methods), we estimate a fast evolutionary rate (0.00169 substitutions per siteyr1, 95% highest posterior density (HPD) interval (0.00131,0.00205)) for SARS viruses sampled over a limited timescale (1year), a slower rate (0.00078 (0.00063,0.00092) substitutions per siteyr1) for MERS-CoV on a timescale of about 4years and the slowest rate (0.00024 (0.00019,0.00029) substitutions per siteyr1) for HCoV-OC43 over almost five decades. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins Using the most conservative approach to identification of a non-recombinant genomic region (NRR1), SARS-CoV-2 forms a sister lineage with RaTG13, with genetically related cousin lineages of coronavirus sampled in pangolins in Guangdong and Guangxi provinces (Fig. Based on the identified breakpoints in each genome, only the major non-recombinant region is kept in each genome while other regions are masked. PubMed Central This underscores the need for a global network of real-time human disease surveillance systems, such as that which identified the unusual cluster of pneumonia in Wuhan in December 2019, with the capacity to rapidly deploy genomic tools and functional studies for pathogen identification and characterization. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Of the nine breakpoints defining these ten BFRs, four showed phylogenetic incongruence (PI) signals with bootstrap support >80%, adopting previously published criteria on using a combination of mosaic and PI signals to show evidence of past recombination events19. collected SARS-CoV data and assisted in analyses of SARS-CoV and SARS-CoV-2 data. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the Spike protein. acknowledges support by the Research FoundationFlanders (Fonds voor Wetenschappelijk OnderzoekVlaanderen (nos. Trafficked pangolins can carry coronaviruses closely related to 88, 70707082 (2014). Zhou, P. et al. Correspondence to On first examination this would suggest that that SARS-CoV-2 is a recombinant of an ancestor of Pangolin-2019 and RaTG13, as proposed by others11,22. Add entries for pangolin-data/-assignment 1.18.1.1 (, Really add a document on testing strategy. If the latter still identified non-negligible recombination signal, we removed additional genomes that were identified as major contributors to the remaining signal. and D.L.R. Virus Evol. Our approach resulted in similar posterior rates using two different prior means, implying that the sarbecovirus data do inform the rate estimate even though a root-to-tip temporal signal was not apparent. Bioinformatics 30, 13121313 (2014). 21, 255265 (2004). Li, X. et al. In regionA, we removed subregion A1 (ntpositions 3,8724,716 within regionA) and subregion A4 (nt1,6422,113) because both showed PI signals with other subregions of regionA. Methods Ecol. Phylogenetic supertree reveals detailed evolution of SARS-CoV-2, Origin and cross-species transmission of bat coronaviruses in China, Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts, Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species, Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2, A Bayesian approach to infer recombination patterns in coronaviruses, Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe, A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic, Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape, https://github.com/plemey/SARSCoV2origins, https://doi.org/10.1101/2020.04.20.052019, https://doi.org/10.1101/2020.02.10.942748, https://doi.org/10.1101/2020.05.28.122366, http://virological.org/t/ncov-2019-codon-usage-and-reservoir-not-snakes-v2/339, http://virological.org/t/ncovs-relationship-to-bat-coronaviruses-recombination-signals-no-snakes-no-evidence-the-2019-ncov-lineage-is-recombinant/331. 31922087). Nature 583, 286289 (2020). While there is evidence of positive selection in the sarbecovirus lineage leading to RaTG13/SARS-CoV-2 (ref. Did Pangolin Trafficking Cause the Coronavirus Pandemic? with an alignment on which an initial recombination analysis was done. BEAST inferences made use of the BEAGLE v.3 library68 for efficient likelihood computations. Concurrent evidence also proposed pangolins as a potential intermediate species for SARS-CoV-2 emergence and suggested them as a potential reservoir species11,12,13. Wang, H., Pipes, L. & Nielsen, R. Synonymous mutations and the molecular evolution of SARS-Cov-2 origins. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. Evol. However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. 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. Lancet 395, 565574 (2020). Genetics 172, 26652681 (2006). Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins Furthermore, the other key feature thought to be instrumental in the ability of SARS-CoV-2 to infect humansa polybasic cleavage site insertion in the Sproteinhas not yet been seen in another close bat relative of the SARS-CoV-2 virus. PubMedGoogle Scholar. A hypothesis of snakes as intermediate hosts of SARS-CoV-2 was posited during the early epidemic phase54, but we found no evidence of this55,56; see Extended Data Fig. A new SARS-CoV-2 variant (B.1.1.523) capable of escaping immune protections The Artic Network receives funding from the Wellcome Trust through project no. Is the COVID-19 Outbreak the 'Revenge of the Pangolin'? | PETA We showed that severe acute respiratory syndrome coronavirus 2 is probably a novel recombinant virus. In early January, the aetiological agent of the pneumonia cases was found to be a coronavirus3, subsequently named SARS-CoV-2 by an International Committee on Taxonomy of Viruses (ICTV) Study Group4 and also named hCoV-19 by Wu et al.5. Press, 2009). In other words, a true breakpoint is less likely to be called as such (this is breakpoint-conservative), and thus the construction of a non-recombining region may contain true recombination breakpoints (with insufficient evidence to call them as such). At present, we analyzed the diversity of SARS-CoV-2 viral genomes in India to know the evolutionary patterns of viruses in the country through their pangolin lineage and GISAID-Clade. It compares the new genome against the large, diverse population of sequenced strains using a 3). obtained the genome sequences of 10 SARS-CoV-2 virus strains through nanopore sequencing of nasopharyngeal swabs in Malta and analyzed the assembled genome with pangolin software, and the results showed that these virus strains were assigned to B.1 lineage, indicating that SARS-CoV-2 was widely spread in Europe (Biazzo et al., 2021). Mol. Extended Data Fig. P.L. Biol. Extended Data Fig. Zhang, Y.-Z. Because the estimated rates and divergence dates were highly similar in the three datasets analysed, we conclude that our estimates are robust to the method of identifying a genomes NRRs. Two other bat viruses (CoVZXC21 and CoVZC45) from Zhejiang Province fall on this lineage as recombinants of the RaTG13/SARS-CoV-2 lineage and the clade of Hong Kong bat viruses sampled between 2005 and 2007 (Fig. S. China corresponds to Guangxi, Yunnan, Guizhou and Guangdong provinces. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. 2). We extracted a similar number (n=35) of genomes from a MERS-CoV dataset analysed by Dudas et al.59 using the phylogenetic diversity analyser tool60 (v.0.5). Google Scholar. Sliding window analysis of changes in the patterns of sequence similarity between human SARS-CoV-2, and pangolin and bat coronaviruses as described further in Fig. 92, 433440 (2020). In the absence of a strong temporal signal, we sought to identify a suitable prior rate distribution to calibrate the time-measured trees by examining several coronaviruses sampled over time, including HCoV-OC43, MERS-CoV, and SARS-CoV virus genomes. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. The new paper finds that the genetic sequences of several strains of coronavirus found in pangolins were between 88.5 percent and 92.4 percent similar to those of the novel coronavirus. The first available sequence data6 placed this novel human pathogen in the Sarbecovirus subgenus of Coronaviridae7, the same subgenus as the SARS virus that caused a global outbreak of >8,000 cases in 20022003. J. Virol. Phylogenetic trees and exact breakpoints for all ten BFRs are shown in Supplementary Figs. Conservatively, we combined the three BFRs >2kb identified above into non-recombining region1 (NRR1). performed Srecombination analysis. PubMed Central 4). Why Can't We Just Call BA.2 Omicron? - The Atlantic Wu, Y. et al. 36, 7597 (2002). Subsequently a bat sarbecovirusRaTG13, sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan Provincewas reported that clusters with SARS-CoV-2 in almost all genomic regions with approximately 96% genome sequence identity2. J. Virol. Coronavirus: Pangolins found to carry related strains - BBC News 2, vew007 (2016). Proc. We named the length-sorted BFRs as: BFRA (ntpositions 13,29119,628, length=6,338nt), BFRB (ntpositions 3,6259,150, length=5,526nt), BFRC (ntpositions 9,26111,795, length=2,535nt), BFRD (ntpositions 27,70228,843, length=1,142nt) and six further regions (EJ). This is evidence for numerous recombination events occurring in the evolutionary history of the sarbecoviruses22,33; specifying all past events in their correct temporal order34 is challenging and not shown here. In the meantime, to ensure continued support, we are displaying the site without styles Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China. Provided by the Springer Nature SharedIt content-sharing initiative, Molecular and Cellular Biochemistry (2023), Nature Microbiology (Nat Microbiol) PubMed performed recombination and phylogenetic analysis and annotated virus names with geographical and sampling dates. Wong, A. C. P., Li, X., Lau, S. K. P. & Woo, P. C. Y. 84, 31343146 (2010). Menachery, V. D. et al. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic, https://doi.org/10.1038/s41564-020-0771-4. The red and blue boxplots represent the divergence time estimates for SARS-CoV-2 (red) and the 2002-2003 SARS-CoV (blue) from their most closely related bat virus, with the light- and dark-colored versions based on the HCoV-OC43 and MERS-CoV centered priors, respectively. Preprint at https://doi.org/10.1101/2020.04.20.052019 (2020). Martin, D. P., Murrell, B., Golden, M., Khoosal, A. Evol. and JavaScript. This produced non-recombining alignment NRA3, which included 63 of the 68genomes. cov-lineages/pangolin - GitHub We use three bioinformatic approaches to remove the effects of recombination, and we combine these approaches to identify putative non-recombinant regions that can be used for reliable phylogenetic reconstruction and dating. Get the most important science stories of the day, free in your inbox. 2 Lack of root-to-tip temporal signal in SARS-CoV-2. Lancet 383, 541548 (2013). Published. Internet Explorer). PubMed Central It is available as a command line tool and a web application. When the genomic data included both coding and non-coding regions we used a single GTR+ substitution model; for concatenated coding genes we partitioned the alignment by codon position and specified an independent GTR+ model for each partition with a separate gamma model to accommodate inter-site rate variation. eLife 7, e31257 (2018). These residues are also in the Pangolin Guangdong 2019 sequence. Evol. Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2 Divergence time estimates based on the HCoV-OC43-centred rate prior for the separate BFRs (Supplementary Table 3) show consistency in TMRCA estimates across the genome. To begin characterizing any ancestral relationships for SARS-CoV-2, NRRs of the genome must be identified so that reliable phylogenetic reconstruction and dating can be performed. All three approaches to removal of recombinant genomic segments point to a single ancestral lineage for SARS-CoV-2 and RaTG13. Google Scholar. Genetic lineages of SARS-CoV-2 have been emerging and circulating around the world since the beginning of the COVID-19 pandemic. Transparent bands of interquartile range width and with the same colours are superimposed to highlight the overlap between estimates. Alexandre Hassanin, Vuong Tan Tu, Gabor Csorba, Nicola F. Mller, Kathryn E. Kistler & Trevor Bedford, Jack M. Crook, Ivana Murphy, Diana Bell, Simon Pollett, Matthew A. Conte, Irina Maljkovic Berry, Yatish Turakhia, Bryan Thornlow, Russell Corbett-Detig, Nature Microbiology We compare both MERS-CoV- and HCoV-OC43-centred prior distributions (Extended Data Fig. This statement informs us of the possibility that a virus has spilled over from a very rare and shy reptile-looking mammal . While it is possible that pangolins, or another hitherto undiscovered species, may have acted as an intermediate host facilitating transmission to humans, current evidence is consistent with the virus having evolved in bats resulting in bat sarbecoviruses that can replicate in the upper respiratory tract of both humans and pangolins25,32. This is notable because the variable-loop region contains the six key contact residues in the RBD that give SARS-CoV-2 its ACE2-binding specificity27,37. We used an uncorrelated relaxed clock model with log-normal distribution for all datasets, except for the low-diversity SARS data for which we specified a strict molecular clock model. Menachery, V. D. et al. USA 113, 30483053 (2016). However, formal testing using marginal likelihood estimation41 does provide some evidence of a temporal signal, albeit with limited log Bayes factor support of 3 (NRR1), 10 (NRR2) and 3 (NRA3); see Supplementary Table 1. Which animal did the novel coronavirus come from? | Live Science Phylogenetic Assignment of Named Global Outbreak Lineages Preprint at https://doi.org/10.1101/2020.05.28.122366 (2020). 4, vey016 (2018). The boxplots show divergence time estimates (posterior medians) for SARS-CoV-2 (red) and the 20022003 SARS-CoV virus (blue) from their most closely related bat virus. Open reading frames are shown above the breakpoint plot, with the variable-loop region indicated in the Sprotein. The idea is that pangolins carrying the virus, SARS-CoV-2, came into contact with humans. All sequence data analysed in this manuscript are available at https://github.com/plemey/SARSCoV2origins. Evol. Mol. Lie, P., Chen, W. & Chen, J.-P. Mol. 27) receptors and its RBD being genetically closer to a pangolin virus than to RaTG13 (refs. Nat Microbiol 5, 14081417 (2020). SARS-like WIV1-CoV poised for human emergence. To gauge the length of time this lineage has circulated in bats, we estimate the time to the most recent common ancestor (TMRCA) of SARS-CoV-2 and RaTG13. The existing diversity and dynamic process of recombination amongst lineages in the bat reservoir demonstrate how difficult it will be to identify viruses with potential to cause major human outbreaks before they emerge. P.L. & Bedford, T. MERS-CoV spillover at the camelhuman interface. For coronaviruses, however, recombination means that small genomic subregions can have independent origins, identifiable if sufficient sampling has been done in the animal reservoirs that support the endemic circulation, co-infection and recombination that appear to be common. Over relatively shallow timescales, such differences can primarily be explained by varying selective pressure, with mildly deleterious variants being eliminated more strongly by purifying selection over longer timescales44,45,46. Abstract. In light of these time-dependent evolutionary rate dynamics, a slower rate is appropriate for calibration of the sarbecovirus evolutionary history. 190, 20882095 (2004). PubMed Mol. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? Using these breakpoints, the longest putative non-recombining segment (nt1,88521,753) is 9.9kb long, and we call this region NRR2. and X.J. 6, e14 (2017). & Holmes, E. C. A genomic perspective on the origin and emergence of SARS-CoV-2. Calibration of priors can be performed using other coronaviruses (SARS-CoV, MERS-CoV and HCoV-OC43), but estimated rates vary with the timescale of sample collection. Indeed, the rates reported by these studies are in line with the short-term SARS rates that we estimate (Fig.

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