Genomic phylogenetic analyses of four major hand, foot and mouth disease-related enteroviruses.

Enteroviruses had diverged into many types, some of which cause hand, foot and mouth disease (HFMD) in children. The predominant enterovirus types associated with HFMD are EVA71, CVA16, CVA6 and CVA10. Four enterovirus types were classified into subtypes based on VP1 sequences. However, the phylogenetics of these enteroviruses is rarely concerned at the genomic level. In this study, we performed the phylogenetic analyses of the EVA71, CVA16, CVA6 and CVA10 using available full-length genomic sequences. We found that the topologies of phylogenetic trees of full-length genomic sequences and VP1 sequences were almost consistent, except few subtypes of EVA71 and CVA10. The mean genetic divergence was 15.8-27% between subtypes and less than 12% within subtypes/sub-subtypes at genomic level. Comparison of phylogenetic topologies between genomic and VP1 sequences helped us to identify two new EVA71 inter-subtype recombinants RF01_CC4 and RF02_CC4. Furthermore, EVA71 subtypes C1 and C2 and CVA10 subtype D were found to originate through inter-subtype recombination. The genomic reference sequences of these enteroviruses are provided here for subtyping. The results provide important insights into the understanding of the evolution and epidemiology of the four enteroviruses. Keywords: enterovirus; hand; foot and mouth disease; classification; genetic distance; recombination.

National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016.

Hand, foot and mouth disease (HFMD) is a major public health concern in China. The most predominant enteroviruses that cause HFMD have traditionally been attributed to enterovirus A71 (EVA71) and coxsackievirus A16 (CVA16). Since its first large outbreak in 2008, the dominant HFMD pathogens are constantly changing. In 2013 and 2015, CVA6 exceeded both EVA71 and CVA16 to become the leading cause of HFMD in some provinces. However, there still lacks a comprehensive overview on the molecular epidemiology and evolution of HFMD-related enteroviruses at the national level. In this study, we performed systematic epidemiological analyses of HFMD-related enteroviruses using the data of 64 published papers that met the inclusion criteria, and conducted phylogenetic analyses based on 12,080 partial VP1 sequences identified in China before 31st June 2018. We found that EVA71 prevalence has decreased sharply but other enteroviruses have increased rapidly from 2008 to 2016 and that one subtype of each enterovirus is represented during the epidemic. In addition, four genotypes EVA71_C4, CVA16_B1, CVA6_D and CVA10_C are the most predominant enterovirus strains and collectively they cause over 90% of all HFMD cases in China according to the phylogenetic trees using representative partial VP1 sequences. These four major enterovirus genotypes have different geographical distributions, and they may co-circulate with other genotypes and serotypes. These results suggest that more molecular epidemiological studies should be performed on several enteroviruses simultaneously, and such information should have implications for virological surveillance, disease management, vaccine development and policy-making on the prevention and control of HFMD.

High proportion of coxsackievirus B3 genotype A in hand, foot and mouth disease in Zhenjiang, China, 2011-2016.

BACKGROUND: Hand, foot and mouth disease (HFMD) is usually caused by EVA71 and CVA16 except for a few cases that are caused by non-EVA71 non-CAV16 enteroviruses. Coxsackievirus B3 (CVB3) is mostly associated with myocarditis, occasionally with HFMD. METHODS: The partial VP1 gene of enteroviruses were amplified and sequenced from 610 throat swabs from clinically confirmed HFMD children. All available CVB3 near full-length genomic and VP1 sequences were downloaded from GenBank. Phylogenetic and distance analyses were performed using MEGA 7.0. RESULTS: A total of 238 partial VP1 sequences were obtained, including 93 EVA71 (39%), 79 CAV16 (33%), 29 CVB3 (12%), 24 CVA6 (10%), and 13 other enterovirus serotypes (5.5%). CVB3 is classified into seven genotypes A-G according to phylogenetic and distance analyses. All CVB3 strains from Zhenjiang belonged to genotype A. In contrast to other genotypes that are prevalent in Europe and other regions of China, and often associated with aseptic meningitis and myocarditis, CVB3 genotype A strains identified in Zhenjiang were only detected among HFMD patients. CONCLUSIONS: This high prevalence of CVB3 genotype A among HFMD children has never been reported. This phenomenon has revealed a new epidemic trend of CVB3 among HFMD in China, and it has epidemiological implications for monitoring the epidemic risk of CVB3.