Pathogen spectrum of hand, foot, and mouth disease and genetic characteristics of the VP1 gene of coxsackievirus A6 in Putuo district of Shanghai, 2015-2018

Abstract

Objective To investigate the pathogenic spectrum of hand, foot, and mouth disease in Putuo district of Shanghai from 2015 to 2018, and to analyze the genetic characteristics of the VP1 gene of coxsackievirus A6 (CVA6), so as to understand the molecular epidemiological characteristics of CVA6 in this region. Methods Real-time RT-PCR methods were used to detect enteroviruses (EV) and virus genotypes in the collected samples. The VP1 genes of identified CVA6 were sequenced and analyzed. Results From 2015 to 2018, 942 specimens of hand, foot, and mouth disease were analyzed among which 522 (55.36%) were EV positive, 332 (63.60%) were coxsackievirus A6, 110 (21.07%) were coxsackievirus A16 (CVA16), 56 (10.73%) were enterovirus 71 (EV71), 11 (2.11%) were coxsackievirus A10 (CAV10) and 13 (2.49%) were other enteroviruses. The nucleotide and amino acid sequence similarities of VP1 gene in 20 CVA6 strains ranged from 92.9% to 100.0% and 98.4% to 100.0%, respectively. All strains belonged to genotype D cluster 3. Conclusions The pathogens causing hand, foot, and mouth disease in Putuo district of Shanghai from 2015 to 2018 were mainly CVA6, CVA16, EV71 and CVA10. CVA6 was the predominant pathogen of hand, foot, and mouth disease in Putuo district of Shanghai, especially D3 sub-genotype. Key words: Hand, foot, and mouth disease; Pathogen spectrum; CVA6; VP1 gene