Emergence of SARS-CoV-2 through recombination and strong purifying selection.
Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 Individual sequences such as RpShaanxi2011, Guangxi GX2013 and two sequences from Zhejiang Province (CoVZXC21/CoVZC45), as previously shown22,25, have strong phylogenetic recombination signals because they fall on different evolutionary lineages (with bootstrap support >80%) depending on what region of the genome is being examined. As illustrated by the dashed arrows, these two posteriors motivate our specification of prior distributions with standard deviations inflated 10-fold (light color). Sequences are colour-coded by province according to the map. A., Filip, I., AlQuraishi, M. & Rabadan, R. Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2. D.L.R. For weather, science, and COVID-19 . J. Virol. pango-designation Public Repository for suggesting new lineages that should be added to the current scheme Python 968 73 pangolin Public Software package for assigning SARS-CoV-2 genome sequences to global lineages. 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. Despite the SARS-CoV-2 lineages acquisition of residues in its Spike (S) proteins receptor-binding domain (RBD) permitting the use of human ACE2 (ref. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. 36, 7597 (2002). Except for specifying that sequences are linear, all settings were kept to their defaults. 6, 8391 (2015). 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. 13, e1006698 (2017). Press, 2009). Given that these pangolin viruses are ancestral to the progenitor of the RaTG13/SARS-CoV-2 lineage, it is more likely that they are also acquiring viruses from bats. P.L. After removal of A1 and A4, we named the new region A. Ge, X. et al. Viruses 11, 979 (2019). 53), this is inferred to have occurred before the divergence of RaTG13 and SARS-CoV-2 and thus should not influence our inferences. Lu, R. et al. 3). Maciej F. Boni, Philippe Lemey, Andrew Rambaut or David L. Robertson. 25, 3548 (2017).
Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2 Emerg. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the current coronavirus disease (COVID-19) pandemic that has affected more than 35 million people and caused . Mol. Nevertheless, the viral population is largely spatially structured according to provinces in the south and southeast on one lineage, and provinces in the centre, east and northeast on another (Fig. A third approach attempted to minimize the number of regions removed while also minimizing signals of mosaicism and homoplasy. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV . Dis. B.W.P. J. Virol. Concatenated region ABC is NRR1. Evol. Nature 558, 180182 (2018). In light of these time-dependent evolutionary rate dynamics, a slower rate is appropriate for calibration of the sarbecovirus evolutionary history. Lie, P., Chen, W. & Chen, J.-P. All sequence data analysed in this manuscript are available at https://github.com/plemey/SARSCoV2origins.
Meet the people who warn the world about new covid variants Sci. 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. Scientists defined the pangolin lineage of this variant to be B.1.1.523 and it was originally recognized as a variant under monitoring on July 14, 2021. 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). Stegeman, A. et al. 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. M.F.B., P.L. Gray inset shows majority rule consensus trees with mean posterior branch lengths for the two regions, with posterior probabilities on the key nodes showing the relationships among SARS-CoV-2, RaTG13, and Pangolin 2019. We compiled a set of 69SARS-CoV genomes including 58 sampled from humans and 11 sampled from civets and raccoon dogs. Biol. 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. 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. Rev. Sequence similarity. Mol. b, Similarity plot between SARS-CoV-2 and several selected sequences including RaTG13 (black), SARS-CoV (pink) and two pangolin sequences (orange). The coverage threshold and consensus sequence generation threshold were set to 20 and 90 respectively. Although the human ACE2-compatible RBD was very likely to have been present in a bat sarbecovirus lineage that ultimately led to SARS-CoV-2, this RBD sequence has hitherto been found in only a few pangolin viruses. Further information on research design is available in the Nature Research Reporting Summary linked to this article. =0.00025. In March, when covid cases began spiking around India, Bani Jolly went hunting for answers in the virus's genetic code. Transparent bands of interquartile range width and with the same colours are superimposed to highlight the overlap between estimates.
Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand 2, bottom) show that SARS-CoV-2 is unlikely to have acquired the variable loop from an ancestor of Pangolin-2019 because these two sequences are approximately 1015% divergent throughout the entire Sprotein (excluding the N-terminal domain).
Coronavirus: Pangolins found to carry related strains - BBC News The SARS-CoV divergence times are somewhat earlier than dates previously estimated15 because previous estimates were obtained using a collection of SARS-CoV genomes from human and civet hosts (as well as a few closely related bat genomes), which implies that evolutionary rates were predominantly informed by the short-term SARS outbreak scale and probably biased upwards. Nat. 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. . GitHub - cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. Li, X. et al. B 281, 20140732 (2014). Genet. Despite the high frequency of recombination among bat viruses, the block-like nature of the recombination patterns across the genome permits retrieval of a clean subalignment for phylogenetic analysis.
COVID-19: Time to exonerate the pangolin from the transmission of SARS We compare both MERS-CoV- and HCoV-OC43-centred prior distributions (Extended Data Fig. 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.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist However, on closer inspection, the relative divergences in the phylogenetic tree (Fig. This statement informs us of the possibility that a virus has spilled over from a very rare and shy reptile-looking mammal . Mol. Sequencing from Malayan pangolins collected during anti-smuggling operations in southern China detected coronavirus lineages related to SARS-CoV-2. Posterior rate distributions for MERS-CoV (far left) and HCoV-OC43 (far right) using BEAST on n=27 sequences spread over 4 years (MERS-CoV) and n=27 sequences spread over 49 years (HCoV-OC43). and X.J. and P.L.) 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. Curr. Nature 579, 265269 (2020). 35, 247251 (2018). Sci. Smuggled pangolins were carrying viruses closely related to the one sweeping the world, say scientists. Scientists trying to trace the ancestry of SARS-CoV-2, the virus responsible for COVID-19, have found the pangolin is unlikely to be the source of the virus responsible for the current pandemic.
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage - Nature Anderson, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C. & Garry, R. F. The proximal origin of SARS-CoV-2. If stopping an outbreak in its early stages is not possibleas was the case for the COVID-19 epidemic in Hubeiidentification of origins and point sources is nevertheless important for containment purposes in other provinces and prevention of future outbreaks. Ji, W., Wang, W., Zhao, X., Zai, J. 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. PubMed The latter was reconstructed using IQTREE66 v.2.0 under a general time-reversible (GTR) model with a discrete gamma distribution to model inter-site rate variation. By 2009, however, rapid genomic analysis had become a routine component of outbreak response. 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. Cell 181, 223227 (2020).