Characterization of genome sequences and clinical features of coxsackievirus A6 strains collected in Hyogo, Japan in 1999‐2013

Coxsackievirus A6 (CV‐A6) is an enterovirus, which is known to cause herpangina. However, since 2009 it has frequently been isolated from children with hand, foot, and mouth disease (HFMD). In Japan, CV‐A6 has been linked to HFMD outbreaks in 2011 and 2013. In this study, the full‐length genome sequencing of CV‐A6 strains were analyzed to identify the association with clinical manifestations. Five thousand six hundred and twelve children with suspected enterovirus infection (0‐17 years old) between 1999 and 2013 in Hyogo Prefecture, Japan, were enrolled. Enterovirus infection was confirmed with reverse transcriptase‐PCR in 753 children (791 samples), 127 of whom (133 samples) were positive for CV‐A6 based on the direct sequencing of the VP4 region. The complete genomes of CV‐A6 from 22 positive patients with different clinical manifestations were investigated. A phylogenetic analysis divided these 22 strains into two clusters based on the VP1 region; cluster I contained strains collected in 1999‐2009 and mostly related to herpangina, and cluster II contained strains collected in 2011‐2013 and related to HFMD outbreak. Based on the full‐length polyprotein analysis, the amino acid differences between the strains in cluster I and II were 97.7 ± 0.28%. Amino acid differences were detected in 17 positions within the polyprotein. Strains collected in 1999‐2009 and those in 2011‐2013 were separately clustered by phylogenetic analysis based on 5′UTR and 3Dpol region, as well as VP1 region. In conclusion, HFMD outbreaks by CV‐A6 were recently frequent in Japan and the accumulation of genomic change might be associated with the clinical course.