Molecular phylogeny of Coxsackievirus A16 in Shenzhen, China, from 2005 to 2009

Abstract

Phylogenetic analysis of a Coxsackievirus A16 (CA16) sequence from Shenzhen, China, and other Chinese and international CA16 sequences revealed a pattern of endemic cocirculation of strains of clusters B2a and B2b within subtype B2 viruses. Amino acid evolution and nucleotide variation in the VP1 region were slight for 5 years.

Fig. 1.

Phylogenetic dendrogram constructed by using 891 nucleotides, the whole VP1 gene sequence of 25 Shenzhen CA16 strains, and sequences from 39 other Chinese and international CA16 strains. Details of each strain can be found in GenBank. The prototype HEV71 strain (BrCr) was used as an outgroup. Triangles and filled circles indicate CA16 strains derived from HFMD cases from 1999 to 2004 in a previous study and from 2005 to 2009 in this study in Shenzhen, China. Genotypes are shown at the right of the tree, and bootstrap values (percentage of 1,000 pseudoreplicates) are shown at the nodes of major clades. The scale at the bottom indicates a measurement of relative phylogenetic distance. SD, Shangdong Province, China; CHN, China; AUS, Australia; MAL, Malaysia.

Fig. 2.

Variations in amino acids in the VP1 region among different clusters of strains of genotype B. Filled triangles indicate amino acid residues. The asterisk indicates a change between amino acids in different subtypes. The abbreviations of amino acids in parentheses indicate the variations in amino acids among different strains in the same clusters.