ArticlePLoS biology2021
Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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129 citing papers in PubMed, 221 citations in OpenAlex.
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- The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.Cell · 2025Article
- Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.Molecular biology and evolution · 2025Article
- Study of coronavirus diversity in wildlife in Northern Cambodia suggests continuous circulation of SARS-CoV-2-related viruses in bats.Scientific reports · 2025Article
- SARS-CoV-2: The Interplay Between Evolution and Host Immunity.Annual review of immunology · 2025Review
- Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein.Virus evolution · 2025Article
- Fomites Could Determine Severity of SARS-CoV-2 Outbreaks in Low-Density White-Tailed Deer (Transboundary and emerging diseases · 2025Article
- Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of theMicrobiology spectrum · 2024Article
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production.The EMBO journal · 2024Article
- Evolution at Spike protein position 519 in SARS-CoV-2 facilitated adaptation to humans.Npj viruses · 2024Article
- Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics.PLoS computational biology · 2024Article
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69 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered "facilitating" intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.
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