Статья

The evolution of Vp1 gene in enterovirus C species sub-group that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

T. Smura, S. Blomqvist, T. Vuorinen, O. Ivanova, E. Samoilovich, H. Al-Hello, C. Savolainen-Kopra, T. Hovi, M. Roivainen,
2021

Genus Enterovirus (Family Picornaviridae,) consists of twelve species divided into genetically diverse types by their capsid protein VP1 coding sequences. Each enterovirus type can further be divided into intra-typic sub-clusters (genotypes). The aim of this study was to elucidate what leads to the emergence of novel enterovirus clades (types and genotypes). An evolutionary analysis was conducted for a sub-group of Enterovirus C species that contains types Coxsackievirus A21 (CVA-21), CVA-24, Enterovirus C95 (EV-C95), EV-C96 and EV-C99. VP1 gene datasets were collected and analysed to infer the phylogeny, rate of evolution, nucleotide and amino acid substitution patterns and signs of selection. In VP1 coding gene, high intra-typic sequence diversities and robust grouping into distinct genotypes within each type were detected. Within each type the majority of nucleotide substitutions were synonymous and the non-synonymous substitutions tended to cluster in distinct highly polymorphic sites. Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. Despite robust clustering to intra-typic genotypes, only few genotype-specific 'signature' amino acids were detected. In contrast, when different enterovirus types were compared, there was a clear tendency towards fixation of type-specific 'signature' amino acids. The results suggest that permanent fixation of type-specific amino acids is a hallmark associated with evolution of different enterovirus types, whereas neutral evolution and/or (frequency-dependent) positive selection in few highly polymorphic amino acid sites are the dominant forms of evolution when strains within an enterovirus type are compared. © 2014 Smura et al.

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  • 1. Version of Record от 2021-04-27

Метаданные

Об авторах
  • T. Smura
    Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Helsinki, Finland
  • S. Blomqvist
    Haartman Institute, Faculty of Medicine, University of Helsinki, Helsinki, Finland
  • T. Vuorinen
    Department of Virology, University of Turku, Turku, Finland
  • O. Ivanova
    M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow, Russian Federation
  • E. Samoilovich
    Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
  • H. Al-Hello
  • C. Savolainen-Kopra
  • T. Hovi
  • M. Roivainen
Название журнала
  • PLoS ONE
Том
  • 9
Выпуск
  • 4
Страницы
  • -
Ключевые слова
  • amino acid; nucleotide; capsid protein; virus RNA; amino acid substitution; article; cladistics; Coxsackie virus A; coxsackie virus a24; Coxsackievirus A21; Enterovirus; Enterovirus C95; Enterovirus C96; Enterovirus C99; genetic code; genetic conservation; genetic variability; genotype; nonhuman; phylogeny; sequence analysis; species difference; DNA sequence; Enterovirus; genetics; genotype; human; molecular evolution; virus genome; Capsid Proteins; Enterovirus C, Human; Evolution, Molecular; Genome, Viral; Genotype; Humans; Phylogeny; RNA, Viral; Sequence Analysis, DNA
Издатель
  • Public Library of Science
Тип документа
  • journal article
Тип лицензии Creative Commons
  • CC
Правовой статус документа
  • Свободная лицензия
Источник
  • scopus