Genetic characteristics of Coxsackievirus A16 isolated from hand foot and mouth disease cases in Qingdao in winter of 2019

  Objective  To investigate the etiological and genetic characteristics of hand foot and mouth disease (HFMD) cases in Women and Children Hospital and Central Hospital of Qingdao in the winter of 2019, and analyze the genetic evolution of coxsackievirus A16 (Cox A16).

  Methods  After the collection of 104 throat swabs from hospitalized children with HFMD in Qingdao in the winter of 2019, enterovirus nucleic acid test was conducted by real-time fluorescent quantitative PCR (RT-qPCR), the positive samples were amplified with general typing primers of entrovirus. Blast alignment was conducted after sequence amplification. The full-length of Cox A16 VP1 gene was amplified by using semi-nested PCR with designed Cox A16 VP1 full length primers, and genetic analysis of nucleotides and amino acids was conducted by using DNAstar, and a phylogenetic tree was constructed by using MEGA software with reference sequences.

  Results  In the 104 throat swabs from the hospitalized children with HFMD, 60 were positive for enterovirus, and the overall positive rate was 57.7%. The positive rate of Cox A16 was 30.8% (32/104), and the positive rate of Coxsackievirus A6 (Cox A6) was 26.9% (28/104). After Cox A16 VP1 of 32 positive samples were amplified and sequenced, it was found that the nucleotide homology was 87.0%–100%, and the amino acid homology was 98.3%–100%. Phylogenetic analysis showed that 17 of the 32 Cox A16 strains belonged to Cox A16 B1a genotype, and the other 15 strains belonged to Cox A16 B1b genotype.

  Conclusion  The pathogens that caused HFMD hospitalizations in Qingdao in the winter of 2019 included Cox A16, and Cox A16 types B1a and B1b spread at the same time.