ArticleCurrent biology : CB2021
A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses.
Article in Current biology : CB, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 58 citations in OpenAlex.
- Article
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence.bioRxiv : the preprint server for biology · 2026Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- Review
- Review
- The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.Cell · 2025Article
- Population Genetic Structure and Human Adaptation of Kaposi Sarcoma-Associated Herpesvirus.Open forum infectious diseases · 2025Article
- Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Host-Calibrated Time Tree Caps the Age of Giant Viruses.Molecular biology and evolution · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals.The Journal of infectious diseases · 2024Article
- Sequencing RNA from old, dried specimens reveals past viromes and properties of long-surviving RNA.bioRxiv : the preprint server for biology · 2024Article
- Inference of Host-Pathogen Interaction Matrices from Genome-Wide Polymorphism Data.Molecular biology and evolution · 2024Article
- Article
- Substitution Models of Protein Evolution with Selection on Enzymatic Activity.Molecular biology and evolution · 2024Article
- Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses.PLoS pathogens · 2024Article
- Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.Proceedings. Biological sciences · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.