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. 2013 Sep;94(Pt 9):1995-2004.
doi: 10.1099/vir.0.053462-0. Epub 2013 Jun 12.

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

Rafal Tokarz  1 , Saddef Haq  1 , Stephen Sameroff  1 , Stephen R C Howie  2 , W Ian Lipkin  1
Affiliations

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

Rafal Tokarz et al. J Gen Virol. 2013 Sep.

Abstract

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

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Figures

Fig. 1.
Fig. 1.
Maximum-likelihood phylogenetic tree constructed from all available complete P1 (a) P2 (b) and P3 (c) sequences of group II (non-respiratory tropic) and group III (respiratory tropic) viruses. For each virus, the accession number, serotype and strain name are provided. * indicates sequences identified for this study; # indicates the lone group III sequence obtained from a stool sample. Part (c) contains P3 sequences from recombinant EV-C96, which is not part of either group.
Fig. 1.
Fig. 1.
Maximum-likelihood phylogenetic tree constructed from all available complete P1 (a) P2 (b) and P3 (c) sequences of group II (non-respiratory tropic) and group III (respiratory tropic) viruses. For each virus, the accession number, serotype and strain name are provided. * indicates sequences identified for this study; # indicates the lone group III sequence obtained from a stool sample. Part (c) contains P3 sequences from recombinant EV-C96, which is not part of either group.
Fig. 1.
Fig. 1.
Maximum-likelihood phylogenetic tree constructed from all available complete P1 (a) P2 (b) and P3 (c) sequences of group II (non-respiratory tropic) and group III (respiratory tropic) viruses. For each virus, the accession number, serotype and strain name are provided. * indicates sequences identified for this study; # indicates the lone group III sequence obtained from a stool sample. Part (c) contains P3 sequences from recombinant EV-C96, which is not part of either group.
Fig. 2.
Fig. 2.
Analysis of EV-C104 from the Gambia. (a) Maximum-likelihood phylogenetic tree constructed on the complete VP1 sequence. (b) Maximum-likelihood phylogenetic tree constructed on a 398 bp fragment of all available sequences within the 3Dpol gene. For the 3Dpol tree, the year of collection is provided next to the accession numbers, serotype and strain designation.
Fig. 3.
Fig. 3.
Similarity plot (a) and bootscan plot (b) of EV-C104 GAM714 compared to other group III viruses.
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