ArticleVirus evolution2026
Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.
Article in Virus evolution, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The emergence of variants has shaped the COVID-19 pandemic. The lack of directly observed precursors to these variants has led to proposals that variants emerge from either persistent infections, transmission in non-human animal populations after reverse-zoonosis, or cryptic transmission in the human population. We investigated the origin of variants by analysing the molecular clock and rate of nonsynonymous and synonymous substitutions in SARS-CoV-2 circulating in human population, persistently infected individuals, non-human animals, and along variant stems: the branches preceding emergence of SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Iota, B.1.637, Mu, and Omicron: BA.1, BA.2/BA.4/BA.5). Along the variant stems we find evidence for an acceleration in the non-synonymous substitution rate, as compared with the non-synonymous substitution rate along branches that represent the genetic diversity of circulating virus. We also find evidence for a slowdown in the synonymous substitution rate preceding the emergence of multiple named variants (e.g
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