Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

Jorba, Jaume; Campagnoli, Ray; De, Lina; Kew, Olen

doi:10.1128/jvi.02354-07

Cited by 177Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesViral Infections and Immunology Research

Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

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Jorba, Jaume, Campagnoli, Ray, De, Lina, Kew, Olen·2008·Journal of Virology

DOI 10.1128/jvi.02354-07PMC PMC2293050

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Abstract

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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The capsid-encoding region of poliovirus, 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.
“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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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
DOI: 10.1128/jvi.02354-07
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
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
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 › Cardiology and Cardiovascular Medicine › 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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Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

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