Cited by 204Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesAnimal Virus Infections Studies

Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded rna viruses

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Simmonds, Peter·2006·Journal of Virology

Abstract

Picornaviridae are a large virus family causing widespread, often pathogenic infections in humans and other mammals. Picornaviruses are genetically and antigenically highly diverse, with evidence for complex evolutionary histories in which recombination plays a major part. To investigate the nature of recombination and selection processes underlying the evolution of serotypes within different picornavirus genera, large-scale analysis of recombination frequencies and sites, segregation by serotype within each genus, and sequence selection and composition was performed, and results were compared with those for other nonenveloped positive-stranded viruses (astroviruses and human noroviruses) and with flavivirus and alphavirus control groups. Enteroviruses, aphthoviruses, and teschoviruses showed phylogenetic segregation by serotype only in the structural region; lack of segregation elsewhere was attributable to extensive interserotype recombination. Nonsegregating viruses also showed several characteristic sequence divergence and composition differences between genome regions that were absent from segregating virus control groups, such as much greater amino acid sequence divergence in the structural region, markedly elevated ratios of nonsynonymous-to-synonymous substitutions, and differences in codon usage. These properties were shared with other picornavirus genera, such as the parechoviruses and erboviruses. The nonenveloped astroviruses and noroviruses similarly showed high frequencies of recombination, evidence for positive selection, and differential codon use in the capsid region, implying similar underlying evolutionary mechanisms and pressures driving serotype differentiation. This process was distinct from more-recent sequence evolution generating diversity within picornavirus serotypes, in which neutral or purifying selection was prominent. Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity.

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  1. In C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger, and L. A. Ball (ed.), Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, London, United Kingdom.

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Authors
Simmonds, P.
Affiliations
Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
Venue
Journal of Virology
Published
2006-11
Volume
80
Issue
22
Pages
11124-11140
ISSN
  • 0022-538X (ISSN-L)
  • 1098-5514
OpenAlex
W2161400257
Cited by
204
References
71
Citations by year
2026: 6 · 2025: 9 · 2024: 6 · 2023: 6 · 2022: 3 · 2021: 4 · 2020: 12 · 2019: 11 · 2018: 10 · 2017: 11 · 2016: 5 · 2015: 14 · 2014: 15 · 2013: 5 · 2012: 9
FWCI
7.96
Type
journal article
Language
en
Open access
Locations
  • Journal of Virology (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
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
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords
recombination, positive selection, serotype differentiation, enterovirus, astrovirus, norovirus, codon usage, dN/dS ratio
MeSH terms
Mamastrovirus, Phylogeny, Picornaviridae, Recombination, Genetic, RNA, Viral, Selection, Genetic, Genome, Viral, Sequence Analysis, DNA, Evolution, Molecular, Norovirus

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