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Synonymous substitution rate slowdown preceding the emergence of SARS-CoV-2 variants and during persistent infections

2026-01-28 epidemiology Title + abstract only
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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 analyzing the molecular clock and rate of nonsynonymous and synonymous substitutions in SARS-CoV-2 circulating in human population, persistently...

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