Green boxplots show the TMRCA estimate for the RaTG13/SARS-CoV-2 lineage and its most closely related pangolin lineage (Guangdong 2019), with the light and dark coloured version based on the HCoV-OC43 and MERS-CoV centred priors, respectively. Meet the people who warn the world about new covid variants with an alignment on which an initial recombination analysis was done. 23, 18911901 (2006). The presence in pangolins of an RBD very similar to that of SARS-CoV-2 means that we can infer this was also probably in the virus that jumped to humans. Frontiers | Novel Highly Divergent SARS-CoV-2 Lineage With the Spike In Extended Data Fig. Anderson, K. G. nCoV-2019 codon usage and reservoir (not snakes v2). Wong, A. C. P., Li, X., Lau, S. K. P. & Woo, P. C. Y. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. A new SARS-CoV-2 variant (B.1.1.523) capable of escaping immune protections 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. Figure 1 (top) shows the distribution of all identified breakpoints (using 3SEQs exhaustive triplet search) by the number of candidate recombinant sequences supporting them. As illustrated by the dashed arrows, these two posteriors motivate our specification of prior distributions with standard deviations inflated 10-fold (light color). A., Lytras, S., Singer, J. All four of these breakpoints were also identified with the tree-based recombination detection method GARD35. Python 379 102 pangoLEARN Public Store of the trained model for pangolin to access. Software package for assigning SARS-CoV-2 genome sequences to global lineages. P.L. ac, Root-to-tip (RtT) divergence as a function of sampling time for the three coronavirus evolutionary histories unfolding over different timescales (HCoV-OC43 (n=37; a) MERS (n=35; b) and SARS (n=69; c)). 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. 2). 1, vev003 (2015). Researchers have found that SARS-CoV-2 in humans shares about 90.3% of its genome sequence with a coronavirus found in pangolins (Cyranoski, 2020). 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. Wu, Y. et al. Nature 579, 265269 (2020). The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus . 35, 247251 (2018). More evidence Pangolin not intermediary in transmission of SARS-CoV-2 We thank T. Bedford for providing M.F.B. Annu Rev. 3). Coronavirus: Pangolins found to carry related strains. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. SARS-CoV-2 is an appropriate name for the new coronavirus. Martin, D. P., Murrell, B., Golden, M., Khoosal, A. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences. 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. Nature 583, 282285 (2020). Trafficked pangolins can carry coronaviruses closely related to CAS Phylogenetic trees and exact breakpoints for all ten BFRs are shown in Supplementary Figs. 5. Unfortunately, a response that would achieve containment was not possible. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. J. Med Virol. EPI_ISL_410538, EPI_ISL_410539, EPI_ISL_410540, EPI_ISL_410541 and EPI_ISL_410542) for the use of sequence data via the GISAID platform. Open reading frames are shown above the breakpoint plot, with the variable-loop region indicated in the Sprotein. M.F.B. SARS-CoV-2 Variant Classifications and Definitions 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. (Yes, Pango is a tongue-in-cheek reference to pangolins, which were briefly suspected to have had a role in the coronavirus's originseveral of the team's computational tools are named after. Emerg. Its origin and direct ancestral viruses have not been . 1c). Stegeman, A. et al. Transparent bands of interquartile range width and with the same colours are superimposed to highlight the overlap between estimates. In our analyses of the sarbecovirus datasets, we incorporated the uncertainty of the sampling dates when exact dates were not available. 13, e1006698 (2017). 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. Holmes, E. C. The Evolution and Emergence of RNA Viruses (Oxford Univ. 1, vev016 (2015). Bryant, D. & Moulton, V. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. While such models have recently been made available, we lack the information to calibrate the rate decline over time (for example, through internal node calibrations44). 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 Nature 538, 193200 (2016). The variable-loop region in SARS-CoV-2 shows closer identity to the 2019 pangolin coronavirus sequence than to the RaTG13 bat virus, supported by phylogenetic inference (Fig. These shy, quirky but cute mammals are one of the most heavily trafficked yet least understood animals in the world. 62,63), the GTR+ model and 100bootstrap replicateswas inferred for each BFR >500nt. Suchard, M. A. et al. This leaves the insertion of polybasic. 36, 17931803 (2019). While there is evidence of positive selection in the sarbecovirus lineage leading to RaTG13/SARS-CoV-2 (ref. We thank all authors who have kindly deposited and shared genome data on GISAID. Natl Acad. In December 2019, a cluster of pneumonia cases epidemiologically linked to an open-air live animal market in the city of Wuhan (Hubei Province), China1,2 led local health officials to issue an epidemiological alert to the Chinese Center for Disease Control and Prevention and the World Health Organizations (WHO) China Country Office. Get the most important science stories of the day, free in your inbox. Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China. Posada, D., Crandall, K. A. Given what was known about the origins of SARS, as well as identification of SARS-like viruses circulating in bats that had binding sites adapted to human receptors29,30,31, appropriate measures should have been in place for immediate control of outbreaks of novel coronaviruses. 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. Yu, H. et al. The authors declare no competing interests. Because these subclades had different phylogenetic relationships in regionD (Supplementary Fig. We say that this approach is conservative because sequences and subregions generating recombination signals have been removed, and BFRs were concatenated only when no PI signals could be detected between them. This statement informs us of the possibility that a virus has spilled over from a very rare and shy reptile-looking mammal . Allen O'Brien on LinkedIn: #r #rstudio #rstats #pangolin #covid19 # Curr. Provided by the Springer Nature SharedIt content-sharing initiative, Molecular and Cellular Biochemistry (2023), Nature Microbiology (Nat Microbiol) J. Virol. In case of DRAGEN COVID Lineage tool, the minimum accepted alignment score was set to 22 and results with scores <22 were discarded. Nature 503, 535538 (2013). & Andersen, K. G. Pandemics: spend on surveillance, not prediction. To estimate non-synonymous over synonymous rate ratios for the concatenated coding genes, we used the empirical Bayes Renaissance countingprocedure67. Syst. Proc. The proximal origin of SARS-CoV-2 | Nature Medicine Abstract. J. Med. When viewing the last 7kb of the genome, a clade of viruses from northern China appears to cluster with sequences from southern Chinese provinces but, when inspecting trees from different parts of ORF1ab, the N. China clade is phylogenetically separated from the S. China clade. PubMed Our most conservative approach attempted to ensure that putative NRRs had no mosaic or phylogenetic incongruence signals. Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. 2a. Specifically, we used a combination of six methods implemented in v.5.5 of RDP5 (ref. Overview of the SARS-CoV-2 genotypes circulating in Latin America Cov-Lineages PDF How COVID-19 Variants Get Their Name - doh.wa.gov B., Weaver, S. & Sergei, L. Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans. However, on closer inspection, the relative divergences in the phylogenetic tree (Fig. In the presence of time-dependent rate variation, a widely observed phenomenon for viruses43,44,52, slower prior rates appear more appropriate for sarbecoviruses that currently encompass a sampling time range of about 18years. The origins we present in Fig. 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. T.T.-Y.L. Maclean, O. Eden, J.-S., Tanaka, M. M., Boni, M. F., Rawlinson, W. D. & White, P. A. Recombination within the pandemic norovirus GII.4 lineage. and P.L.) The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. 4), that region and shorter BFRs were not included in combined putative non-recombinant regions. 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. Ge, X. et al. While there is involvement of other mammalian speciesspecifically pangolins for SARS-CoV-2as a plausible conduit for transmission to humans, there is no evidence that pangolins are facilitating adaptation to humans. Results and discussion Genomic surveillance has been a hallmark of the COVID-19 pandemic that, in contrast to other pandemics, achieves tracking of the virus evolution and spread worldwide almost in real-time ( 4 ). Lam, T. T. et al. Katoh, K., Asimenos, G. & Toh, H. in Bioinformatics for DNA Sequence Analysis (ed. CAS Centre for Genomic Pathogen Surveillance. Avian influenza a virus (H7N7) epidemic in The Netherlands in 2003: course of the epidemic and effectiveness of control measures. 68, 10521061 (2019). Wang, H., Pipes, L. & Nielsen, R. Synonymous mutations and the molecular evolution of SARS-Cov-2 origins. 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. The 2009 influenza pandemic and subsequent outbreaks of MERS-CoV (2012), H7N9 avian influenza (2013), Ebola virus (2014) and Zika virus (2015) were met with rapid sequencing and genomic characterization. 36) (RDP, GENECONV, MaxChi, Bootscan, SisScan and 3SEQ) and considered recombination signals detected by more than two methods for breakpoint identification. 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. The virus then. a, Breakpoints identified by 3SEQ illustrated by percentage of sequences (out of 68) that support a particular breakpoint position. Preprint at https://doi.org/10.1101/2020.05.28.122366 (2020). Posterior means with 95% HPDs are shown in Supplementary Information Table 2. Our third approach involved identifying breakpoints and masking minor recombinant regions (with gaps, which are treated as unobserved characters in probabilistic phylogenetic approaches). Viruses 11, 174 (2019). Its genome is closest to that of severe acute respiratory syndrome-related coronaviruses from horseshoe bats, and its receptor-binding domain is closest to that of pangolin viruses. In our second stage, we wanted to construct non-recombinant regions where our approach to breakpoint identification was as conservative as possible. Nature 583, 286289 (2020). Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Developed by the Centre for Genomic Pathogen Surveillance. 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. Impact of SARS-CoV-2 Gamma lineage introduction and COVID-19 - Nature Med. In the absence of any reasonable prior knowledge on the TMRCA of the sarbecovirus datasets (which is required for grid specification in a skygrid model), we specified a simpler constant size population prior. Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M. & Kawaoka, Y. Evolution and ecology of influenza A viruses. Zhou, H. et al. Gorbalenya, A. E. et al. 17, 15781579 (1999). Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. 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. The estimated divergence times for the pangolin virus most closely related to the SARS-CoV-2/RaTG13 lineage range from 1851 (17301958) to 1877 (17461986), indicating that these pangolin lineages were acquired from bat viruses divergent to those that gave rise to SARS-CoV-2. To examine temporal signal in the sequenced data, we plotted root-to-tip divergence against sampling time using TempEst39 v.1.5.3 based on a maximum likelihood tree. Early detection via genomics was not possible during Southeast Asias initial outbreaks of avian influenza H5N1 (1997 and 20032004) or the first SARS outbreak (20022003). Evol. We focused on these three non-recombining regions/alignments for divergence time estimation; this avoids inappropriate modelling of evolutionary processes with recombination on strictly bifurcating trees, which can result in different artefacts such as homoplasies that inflate branch lengths and lead to apparently longer evolutionary divergence times. We compiled a dataset including 27human coronavirus OC43 virus genomes and ten related animal virus genomes (six bovine, three white-tailed deer and one canine virus). PubMed Central Boni, M. F., Zhou, Y., Taubenberger, J. K. & Holmes, E. C. Homologous recombination is very rare or absent in human influenza A virus. eLife 7, e31257 (2018). 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. We thank originating laboratories at South China Agricultural University (Y. Shen, L. Xiao and W. Chen; no. July 26, 2021. Nat. Membrebe, J. V., Suchard, M. A., Rambaut, A., Baele, G. & Lemey, P. Bayesian inference of evolutionary histories under time-dependent substitution rates. 1 Phylogenetic relationships in the C-terminal domain (CTD). Using the most conservative approach (NRR1), the divergence time estimate for SARS-CoV-2 and RaTG13 is 1969 (95% HPD: 19302000), while that between SARS-CoV and its most closely related bat sequence is 1962 (95% HPD: 19321988); see Fig. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in PubMedGoogle Scholar. SARS-CoV-2 and RaTG13 are the most closely related (their most recent common ancestor nodes denoted by green circles), except in the 222-nt variable-loop region of the C-terminal domain (bar graphs at bottom). Dudas, G., Carvalho, L. M., Rambaut, A. The inset represents divergence time estimates based on NRR1, NRR2 and NRA3. Evol. Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2 1. Green boxplots show the TMRCA estimate for the RaTG13/SARS-CoV-2 lineage and its most closely related pangolin lineage (Guangdong 2019). Virology 507, 110 (2017). Rev. These differences reflect the fact that rate estimates can vary considerably with the timescale of measurement, a frequently observed phenomenon in viruses known as time-dependent evolutionary rates41,43,44. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Menachery, V. D. et al. cov-lineages/pangolin - GitHub A second breakpoint-conservative approach was conservative with respect to breakpoint identification, but this means that it is accepting of false-negative outcomes in breakpoint inference, resulting in less certainty that a putative NRR truly contains no breakpoints. Specifically, progenitors of the RaTG13/SARS-CoV-2 lineage appear to have recombined with the Hong Kong clade (with inferred breakpoints at 11.9 and 20.8kb) to form the CoVZXC21/CoVZC45-lineage. Boni, M. F., de Jong, M. D., van Doorn, H. R. & Holmes, E. C. Guidelines for identifying homologous recombination events in influenza A virus. Microbes Infect. Med. And this genotype pattern led to creating a new Pangolin lineage named B.1.640.2, a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Virus Evol. volume5,pages 14081417 (2020)Cite this article. Posterior means (horizontal bars) of patristic distances between SARS-CoV-2 and its closest bat and pangolin sequences, for the spike proteins variable loop region and CTD region excluding the variable loop. CAS from the European Research Council under the European Unions Horizon 2020 research and innovation programme (grant agreement no. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Across a large region of the virus genome, corresponding approximately to ORF1b, it did not cluster with any of the known bat coronaviruses indicating that recombination probably played a role in the evolutionary history of these viruses5,7. J. Virol. All three approaches to removal of recombinant genomic segments point to a single ancestral lineage for SARS-CoV-2 and RaTG13. Evol. Biol. and JavaScript. To evaluate the performance procedure, we confirmed that the recombination masking resulted in (1) a markedly different outcome of the PHI test64, (2) removal of well-supported (bootstrap value >95%) incompatible splits in Neighbor-Net65 and (3) a near-complete reduction of mosaic signal as identified by 3SEQ. Pangolins may have incubated the novel coronavirus, gene study shows If the latter still identified non-negligible recombination signal, we removed additional genomes that were identified as major contributors to the remaining signal. performed recombination analysis for non-recombining alignment3, calibration of rate of evolution and phylogenetic reconstruction and dating. For the current pandemic, the novel pathogen identification component of outbreak response delivered on its promise, with viral identification and rapid genomic analysis providing a genome sequence and confirmation, within weeks, that the December 2019 outbreak first detected in Wuhan, China was caused by a coronavirus3. D.L.R. 30, 21962203 (2020). Based on the identified breakpoints in each genome, only the major non-recombinant region is kept in each genome while other regions are masked. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. and T.A.C. Except for specifying that sequences are linear, all settings were kept to their defaults. Virus Evol. A new coronavirus associated with human respiratory disease in China. Lin, X. et al. The unsampled diversity descended from the SARS-CoV-2/RaTG13 common ancestor forms a clade of bat sarbecoviruses with generalist propertieswith respect to their ability to infect a range of mammalian cellsthat facilitated its jump to humans and may do so again. Graham, R. L. & Baric, R. S. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. 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). matics program called Pangolin was developed. 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. Grey tips correspond to bat viruses, green to pangolin, blue to SARS-CoV and red to SARS-CoV-2. 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. "This is an extremely interesting . Researchers in the UK had just set the scientific world . Our results indicate the presence of a single lineage circulating in bats with properties that allowed it to infect human cells, as previously described for bat sarbecoviruses related to the first SARS-CoV lineage29,30,31. 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. Preprint at https://doi.org/10.1101/2020.02.10.942748 (2020). Biol. Posterior distributions were approximated through Markov chain Monte Carlo sampling, which were run sufficiently long to ensure effective sampling sizes >100. As a proxy, it would be possible to model the long-term purifying selection dynamics as a major source of time-dependent rates43,44,52, but this is beyond the scope of the current study. With horseshoe bats currently the most plausible origin of SARS-CoV-2, it is important to consider that sarbecoviruses circulate in a variety of horseshoe bat species with widely overlapping species ranges57. & Li, X. Crossspecies transmission of the newly identified coronavirus 2019nCoV. Press, 2009). 1c). 5. Collectively our analyses point to bats being the primary reservoir for the SARS-CoV-2 lineage. Combining regions A, B and C and removing the five named sequences gives us putative NRR1, as an alignment of 63sequences. master 4 branches 94 tags Code AngieHinrichs Add entries for pangolin-data/-assignment 1.18.1.1 ( #512) ad16752 4 days ago 990 commits .github/ workflows Update pangolin.yml 7 months ago docs docs need guide tree now 3 years ago pangolin Lond. 21, 15081514 (2015). Indeed, the rates reported by these studies are in line with the short-term SARS rates that we estimate (Fig. Bayesian evaluation of temporal signal in measurably evolving populations. =0.00075 and one with a mean of 0.00024 and s.d. While pangolins could be acting as intermediate hosts for bat viruses to get into humansthey develop severe respiratory disease38 and commonly come into contact with people through traffickingthere is no evidence that pangolin infection is a requirement for bat viruses to cross into humans. Holmes, E. C., Rambaut, A. 2, vew007 (2016). Five example sequences with incongruent phylogenetic positions in the two trees are indicated by dashed lines. Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Holmes, E. C. Recombination in evolutionary genomics. Regions AC were further examined for mosaic signals by 3SEQ, and all showed signs of mosaicism. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Press, H.) 3964 (Springer, 2009). Visual exploration using TempEst39 indicates that there is no evidence for temporal signal in these datasets (Extended Data Fig. and X.J. Wan, Y., Shang, J., Graham, R., Baric, R. & Li, F. Receptor recognition by the novel Coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. The construction of NRR1 is the most conservative as it is least likely to contain any remaining recombination signals. & Muhire, B. RDP4: Detection and analysis of recombination patterns in virus genomes. When the first genome sequence of SARS-CoV-2, Wuhan-Hu-1, was released on 10January 2020 (GMT) on Virological.org by a consortium led by Zhang6, it enabled immediate analyses of its ancestry. 11,12,13,22,28)a signal that suggests recombinationthe divergence patterns in the Sprotein do not show evidence of recombination between the lineage leading to SARS-CoV-2 and known sarbecoviruses. Menachery, V. D. et al. . Region A has been shortened to A (5,017nt) based on potential recombination signals within the region. 91, 10581062 (2010). PLoS ONE 5, e10434 (2010). COVID-19 lineage names can be confusing to navigate; there are many aliases and if you want to catch them all to examine further in data analyses it helps to Allen O'Brien on LinkedIn: #r #rstudio #rstats #pangolin #covid19 #datascience #epidemiology Coronavirus Software Tools - Illumina, Inc. All authors contributed to analyses and interpretations. 5 Comparisons of GC content across taxa. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. CNN . CAS MC_UU_1201412). 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. 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. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. 6, eabb9153 (2020). Current Overview on Disease and Health Research Vol. 6 Yuan, J. et al. Nat. Su, S. et al. Extended Data Fig.
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