Virology 507, 110 (2017). Region A has been shortened to A (5,017nt) based on potential recombination signals within the region. Nucleotide positions for phylogenetic inference are 147695, 9621,686 (first tree), 3,6259,150 (second tree, also BFR B), 9,26111,795 (third tree, also BFR C), 12,44319,638 (fourth tree) and 23,63124,633, 24,79525,847, 27,70228,843 and 29,57430,650 (fifth tree). A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Rambaut, A., Lam, T. T., Carvalho, L. M. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). All authors contributed to analyses and interpretations. 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. Its origin and direct ancestral viruses have not been . Nature 579, 265269 (2020). is funded by The National Natural Science Foundation of China Excellent Young Scientists Fund (Hong Kong and Macau; no. Preprint at https://doi.org/10.1101/2020.05.28.122366 (2020). Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. 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. 32, 268274 (2014). 1) and thus likely to be the product of recombination, acquiring a divergent variable loop from a hitherto unsampled bat sarbecovirus28. NTD, N-terminal domain; CTD, C-terminal domain. Google Scholar. Influenza viruses reassort17 but they do not undergo homologous recombination within RNA segments18,19, meaning that origins questions for influenza outbreaks can always be reduced to origins questions for each of influenzas eight RNA segments. Share .
Current Overview on Disease and Health Research Vol. 6 Lu, R. et al. For the HCoV-OC43, MERS-CoV and SARS datasets we specified flexible skygrid coalescent tree priors. Lancet 395, 565574 (2020). A.R. D.L.R. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. Wang, H., Pipes, L. & Nielsen, R. Synonymous mutations and the molecular evolution of SARS-Cov-2 origins. 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). Because 3SEQ identified ten BFRs >500nt, we used GARDs (v.2.5.0) inference on 10, 11 and 12 breakpoints. Yu, H. et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. These are in general agreement with estimates using NRR2 and NRA3, which result in divergence times of 1982 (19482009) and 1948 (18791999), respectively, for SARS-CoV-2, and estimates of 1952 (19061989) and 1970 (19321996), respectively, for the divergence time of SARS-CoV from its closest known bat relative. Coronavirus Disease 2019 (COVID-19) Situation Report 51 (World Health Organization, 2020). Posterior means with 95% HPDs are shown in Supplementary Information Table 2. Phylogenetic trees and exact breakpoints for all ten BFRs are shown in Supplementary Figs. 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. Bioinformatics 22, 26882690 (2006). Liu, P. et al.
Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolu : The In March, when covid cases began spiking around India, Bani Jolly went hunting for answers in the virus's genetic code. Sorting these breakpoint-free regions (BFRs) by length results in two segments >5kb: an ORF1a subregion spanning nucleotides (nt) 3,6259,150 and the first half of ORF1b spanning nt13,29119,628 (sequence numbering given in Source Data, https://github.com/plemey/SARSCoV2origins). PubMed Central 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. A single 3SEQ run on the genome alignment resulted in 67 out of 68sequences supporting some recombination in the past, with multiple candidate breakpoint ranges listed for each putative recombinant. 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. 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. Conservatively, we combined the three BFRs >2kb identified above into non-recombining region1 (NRR1). A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. 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. Boni, M. F., Posada, D. & Feldman, M. W. An exact nonparametric method for inferring mosaic structure in sequence triplets. USA 113, 30483053 (2016). Get the most important science stories of the day, free in your inbox.
cov-lineages/pangolin - GitHub 725422-ReservoirDOCS). Lancet 383, 541548 (2013). 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). Maclean, O.
Trafficked pangolins can carry coronaviruses closely related to 82, 18191826 (2008). 21, 15081514 (2015). Based on the identified breakpoints in each genome, only the major non-recombinant region is kept in each genome while other regions are masked. Xiao, K. et al. J. Virol. As informative rate priors for the analysis of the sarbecovirus datasets, we used two different normal prior distributions: one with a mean of 0.00078 and s.d. 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. PubMed Biol. Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China. Using both prior distributions, this results in six highly similar posterior rate estimates for NRR1, NRR2 and NRA3, centred around 0.00055 substitutions per siteyr1. An initial genomic sequence analysis found that the reemergence of COVID-19 in New Zealand was caused by a SARS-CoV-2 from the (now ancestral) lineage B.1.1.1 of the pangolin nomenclature ( 17 ). Divergence time estimates based on the three regions/alignments where the effects of recombination have been removed. From this perspective, it may be useful to perform surveillance for more closely related viruses to SARS-CoV-2 along the gradient from Yunnan to Hubei. 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. 2). 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. 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. 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.
Pangolins may have incubated the novel coronavirus, gene study shows In the variable-loop region, RaTG13 diverges considerably with the TMRCA, now outside that of SARS-CoV-2 and the Pangolin Guangdong 2019 ancestor, suggesting that RaTG13 has acquired this region from a more divergent and undetected bat lineage.
PDF single centre retrospective study 1c). & Boni, M. F. Improved algorithmic complexity for the 3SEQ recombination detection algorithm. Patino-Galindo, J.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to - PubMed We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new . 3). Download a free copy. The genetic distances between SARS-CoV-2 and RaTG13 (bottom) demonstrate that their relationship is consistent across all regions except for the variable loop. 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. M.F.B., P.L. But some theories suggest that pangolins may be the source of the novel coronavirus. These datasets were subjected to the same recombination masking approach as NRA3 and were characterized by a strong temporal signal (Fig. acknowledges support by the Research FoundationFlanders (Fonds voor Wetenschappelijk OnderzoekVlaanderen (nos. 26 March 2020. 1. the development of viral diversity. 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. . Uncertainty measures are shown in Extended Data Fig. 6, eabb9153 (2020). & Bedford, T. MERS-CoV spillover at the camelhuman interface. Zhou, P. et al. Extensive diversity of coronaviruses in bats from China. All custom code used in the manuscript is available at https://github.com/plemey/SARSCoV2origins. Ge, 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. 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. All four of these breakpoints were also identified with the tree-based recombination detection method GARD35. performed recombination analysis for non-recombining regions1 and 2, breakpoint analysis and phylogenetic inference on recombinant segments. The presence of SARS-CoV-2-related viruses in Malayan pangolins, in silico analysis of the ACE2 receptor polymorphism and sequence similarities between the Receptor Binding Domain (RBD) of the spike proteins of pangolin and human Sarbecoviruses led to the proposal of pangolin as intermediary. Combining regions A, B and C and removing the five named sequences gives us putative NRR1, as an alignment of 63sequences. 4). 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. Biol. Centre for Genomic Pathogen Surveillance. This leaves the insertion of polybasic. We thank A. Chan and A. Irving for helpful comments on the manuscript. Sequences were aligned by MAFTT58 v.7.310, with a final alignment length of 30,927, and used in the analyses below. Grey tips correspond to bat viruses, green to pangolin, blue to SARS-CoV and red to SARS-CoV-2. Nature 583, 286289 (2020). Genetics 176, 10351047 (2007). 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. BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. 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. Published. 5 Comparisons of GC content across taxa. B.W.P. The shaded region corresponds to the Sprotein. It is clear from our analysis that viruses closely related to SARS-CoV-2 have been circulating in horseshoe bats for many decades. 6, e14 (2017). Bryant, D. & Moulton, V. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Duchene, S., Holmes, E. C. & Ho, S. Y. W. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. 382, 11991207 (2020). 3 Priors and posteriors for evolutionary rate of SARS-CoV-2. Robertson, D. nCoVs relationship to bat coronaviruses & recombination signals (no snakes) no evidence the 2019-nCoV lineage is recombinant.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist 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). 17, 15781579 (1999). SARS-like WIV1-CoV poised for human emergence. Extended Data Fig. Split diversity in constrained conservation prioritization using integer linear programming. 21, 255265 (2004). 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. 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. Wong, A. C. P., Li, X., Lau, S. K. P. & Woo, P. C. Y. The difficulty in inferring reliable evolutionary histories for coronaviruses is that their high recombination rate48,49 violates the assumption of standard phylogenetic approaches because different parts of the genome have different histories. These authors contributed equally: Maciej F. Boni, Philippe Lemey. 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). In case of DRAGEN COVID Lineage tool, the minimum accepted alignment score was set to 22 and results with scores <22 were discarded. J. Virol. Because these subclades had different phylogenetic relationships in regionD (Supplementary Fig.