Abstract
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.
Highlights
Enteroviruses are small non-enveloped positive strand RNA viruses with icosahedral capsid symmetry
To gain insight into the evolution and epidemiology of enterovirus VP1 coding sequences, partial VP1 coding regions of six EV-C96 strains, 19 EV-C99 strains, nine CVA-21 strains, 36 CVA-24 strains and two CVA-24v strains that were isolated during poliovirus surveillance were sequenced and subjected to phylogenetic analysis together with overlapping sequences retrieved from the GenBank
With the previous studies [5,7,44,45], in the VP1 coding region, all of the EV-C types clustered into three subgroups, which were designated here as A (CVA-1, CVA-19, CVA22, EV-C104, EV-C105, EV-109, EV-C116, EV-C117 and EVC118), B (EV-C95, EV-C96, EV-C99, CVA-21 and CVA-24) and C (CVA-13, CVA-17, CVA-20, EV-C102, PV-1, PV-2 and PV-3) (Fig. 1), with the branching order of sub-group A diverging first from the common ancestor of sub-groups B and C
Summary
Enteroviruses (genus Enterovirus, family Picornaviridae) are small non-enveloped positive strand RNA viruses with icosahedral capsid symmetry. Enteroviruses are classified to twelve species, Enterovirus A to H, J and Rhinovirus A to C [1]. Enteroviruses are associated with a variety of clinical diseases, such as aseptic meningitis, encephalitis, paralytic disease, respiratory infections, and acute haemorrhagic conjunctivitis (AHC) most enterovirus infections are subclinical [2]. The genome consists of a single open reading frame (ORF) that is flanked by 59 end and 39 end untranslated regions (59UTR and 39UTR). The ORF is translated to a single polypeptide that is autocatalytically cleaved to P1, P2 and P3 polyproteins. The P1 polyprotein is further cleaved to capsid proteins VP4 to VP1, whereas P2 and P3 are cleaved to non-structural proteins 2A–2C and 3A–3D, respectively
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