Phylogenetic analysis of VP1 region of CA16 isolated from children with severe hand-foot-mouth disease

Background: CA16 and enterovirus 71 are two key etiological agents for children’s hand-foot-mouth disease (HFMD). Large-scale HFMD outbreaks have taken place every year in Liaocheng City, Shandong Province of China since 2008.

Objective: We investigated the genetic background and phyletic evolution of coxsackie virus A16 (CA16)-related severe HFMD in children from Liaocheng City.

Method: CA16 was screened from throat swab and anus specimens obtained from children with severe HFMD between 2008 and 2010. Specific primers were used to amplify the VP1 region of CA 16 for sequence analysis.

Result: A total of 461 specimens were detected to be enterovirus positive from 2008 to 2010 and 401 specimens were CA16 positive. The nucleotide and amino acid sequences of 16 isolates from children with severe HFMD were compared with the reference sequences, and the nucleotide homology was 91.43%-98.65%, and the amino acid homology was 97.98%-100%. Of the16 isolates, 9 isolates and BJ03-ZDP (AY821798), Shzh00-1 (AY790926), Shzh05-1 (EU262658), and GZ08 (FJ198212) strains isolated from Chinese mainland were located on the same branch; the remaining 7 isolates, the strains isolated from Malaysia, Thailand, Vietnam, Australia and other neighboring countries. AF177911 from Taiwan andshzh01-69 strain (AY895111) from Shenzhen were located on another branch.

Conclusion: CA16 is one of the major pathogens of HFMD and the homology of strains is high.