Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
By Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, T. T. Lam, B. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson. Nature Microbiology, 2020
865 citations recorded by the source corpus.
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. In this manuscript, the authors address evolutionary questions on the emergence of SARS-CoV-2. They find that SARS-CoV-2 is not a recombinant of any sarbecoviruses detected to date, and that the bat and pangolin sequences most closely related to SARS-CoV-2 probably diverged several decades ago or possibly earlier from human SARS-CoV-2 samples.
Subfields: Animal Science and Zoology, Infectious Diseases
View Paper: https://www.semanticscholar.org/paper/20afb2f840ddd9711ad0a04c381c27d56ddf6a53
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In Infectious Diseases
Citations in the corpus
- Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape (2021, background): “4 Main text: 37 SARS-CoV-2 emerged from a yet-to-be defined animal reservoir and initiated a pandemic in 2020 (1-5).”
- Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant (2020, neutral): “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).”
- Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (2020, neutral): “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).”
- On the origin and evolution of SARS-CoV-2 (2021, methodology): “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.”
- Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans (2020, background): “bat sequence is estimated somewhere between 1948-1982 (9).”
- Sarbecovirus ORF6 proteins hamper induction of interferon signaling (2021, neutral): “The inconsistent phylogenetic topologies of different viral genes of sarbecoviruses (Figure 1B) are in agreement with recent studies suggesting gene recombination events among sarbecoviruses (Boni et al., 2020; Li et al., 2020b).”