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Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range
Open accessAbstract
We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (Kt), synonymous substitutions (Ks), synonymous transitions (As), synonymous transversions (Bs), and nonsynonymous substitutions (Ka) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of 31 wild poliovirus type 1 isolates representing a well-defined phylogeny derived from a common imported ancestor. Similar rates were obtained by linear regression, the maximum likelihood/single-rate dated-tip method, and Bayesian inference. The very rapid Kt[(1.03 ± 0.10) × 10−2 substitutions/site/year] and Ks[(1.00 ± 0.08) × 10−2] clocks were driven primarily by the Asclock [(0.96 ± 0.09) × 10−2], the Bsclock was ∼10-fold slower [(0.10 ± 0.03) × 10−2], and the more stochastic Kaclock was ∼30-fold slower [(0.03 ± 0.01) × 10−2]. Nonsynonymous substitutions at all P1/capsid sites, including the neutralizing antigenic sites, appeared to be constrained by purifying selection. Simulation of the evolution of third-codon positions suggested that saturation of synonymous transitions would be evident at 10 years and complete at ∼65 years of independent transmission. Saturation of synonymous transversions was predicted to be minimal at 20 years and incomplete at 100 years. The rapid evolution of the Kt,Ks, and Asclocks can be used to estimate the dates of divergence of closely related viruses, whereas the slower Bsand Kaclocks may be used to explore deeper evolutionary relationships within and across poliovirus genotypes.
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“However, the capsid-encoding region, with a rate of fixation of total substitutions in the order of 10−2 substitutions/site/year, appears less genetically stable than the region encoding non-structural proteins [17,18].”
From Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence (2011) · cites this paper as [17]
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Metadata
- Authors
- Jorba, J., Campagnoli, R., De, L., & Kew, O.
- Affiliations
- Centers for Disease Control and Prevention (US)
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333
- Corresponding author
- Jorba, Jaume
- ORCID
- Jorba, Jaume
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 2008-05
- Volume
- 82
- Issue
- 9
- Pages
- 4429-4440
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- PMC
- PMC2293050
- OpenAlex
- W1981598477
- Cited by
- 177
- References
- 94
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 9 · 2023: 11 · 2022: 10 · 2021: 8 · 2020: 6 · 2019: 3 · 2018: 12 · 2017: 16 · 2016: 16 · 2015: 9 · 2014: 17 · 2013: 12 · 2012: 8
- FWCI
- 6.27
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Virology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Immunology Research
- Keywords
- poliovirus type 1, molecular clock calibration, synonymous substitution rate, nonsynonymous substitution rate, purifying selection, substitution saturation, divergence time estimation, viral evolution
- MeSH terms
- Calibration, Biological Evolution, Kinetics, Models, Genetic, Phylogeny, Point Mutation, Poliovirus, Capsid Proteins
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