Molecular characteristics of the VP1 region of enterovirus 71 strains in China

Abstract

Background: Enterovirus 71 (EV71) is the most commonly implicated causative agent of severe outbreaks of paediatric hand, foot, and mouth disease (HFMD).VP1 protein, a capsid protein of EV71, is responsible for the genotype of the virus and is essential for vaccine development and effectiveness. However, the genotypes of EV71 isolates in China are still not completely clear.

Methods: The VP1 gene sequences of 3712 EV71 virus strains from China, excluding repetitive sequences and 30 known EV71 genotypes as reference strains, between 1986 and 2019 were obtained from GenBank. Phylogenetic tree, amino acid homology, genetic variation and genotype analyses of the EV71VP1 protein were performed with MEGA 6.0 software.

Results: The amino acid identity was found to be 88.33%-100% among the 3712 EV71 strains, 93.47%-100% compared with vaccine strain H07, and 93.04%-100% compared with vaccine strains FY7VP5 or FY-23 K-B. Since 2000, the prevalent strains of EV71 were mainly of the C4 genotype. Among these, the C4a subgenotype was predominant, followed by the C4b subgenotype; other subgenotypes appeared sporadically between 2005 and 2018 in mainland China. The B4 genotype was the main genotype in Taiwan, and the epidemic strains were constantly changing. Some amino acid variations in VP1 of EV71 occurred with high frequencies, including A289T (20.99%), H22Q (16.49%), A293S (15.95%), S283T (15.11%), V249I (7.76%), N31D (7.25%), and E98K (6.65%).

Conclusion: The C4 genotype of EV71 in China matches the vaccine and should effectively control EV71. However, the efficacy of the vaccine is partially affected by the continuous change in epidemic strains in Taiwan. These results suggest that the genetic characteristics of the EV71-VP1 region should be continuously monitored, which is critical for epidemic control and vaccine design to prevent EV71 infection in children.

Keywords: Enterovirus 71; Genotype; Molecular characteristics; Mutation; VP1.

Fig. 1

The number of EV71 strains isolated in different years in China. The 3712 EV71 strains with complete VP1 gene sequences collected in China were obtained from the GenBank public database at the National Center for Biotechnology Information (NCBI) PubMed website (http://www.ncbi.nlm.nih.gov/genbank/) between 1986 and December 31, 2019. However, no EV71 strains were available for 2019

Fig. 2

The number of EV71 strains isolated in different provinces of China. A total of 3712 EV71 strains were collected in China, including different provinces of mainland China (3102), Hong Kong (24), Macao (0) and Taiwan (586), between 1986 and December 31, 2019

Fig. 3

Phylogenetic tree of the entire VP1 gene of EV71. The 30 reference strains are indicated in different coloured shapes, as shown below: :HQ328793(H07) :JX025561(FY7VP5) :EU812515(FY-23 K-B) :HQ828086(C4a) :EU753365(C4a) :KU936124(C4a) :KU936125(C4a) :KU936130(C4a) :JQ742002(C4b) :JQ742001(C4b) :AY207625(C3) :AF376081(C3) :AF304457(C2) :AF376110 (C2) :AY125969(C1) :AY125976 (C1) :JN874558 (C5) :KU888174(C5) :U22521(A) :GU434678(A) :AB059814(B1) :AF135886 (B1) :AF009534(B2) :AF009540(B2) :AF376119(B3) :AF376073(B3) :AF376084(B4) :AJ586873 (B4) :AB177815 (B5) :AB177816 (B5)

Fig. 4

Subgenotype percentages of EV71 for every year in China. In this study, 12 genotypes were detected among 3712 strains. The B4 genotype was the predominant strain between 1999 and 2003 and C3 genotypes from 2004 to 2005; the C4a subgenotype was the most common epidemic strain from 2006 to 2018

Fig. 5

The genotypic distribution of EV71 every year in mainland China. The C4a subgenotype was absolutely the predominant strain of EV71 from 2005 to 2018, followed by theC4b subgenotype; other subgenotypes appeared sporadically in mainland China

Fig. 6

The subgenotype percentages of EV71 for every year in Taiwan. Epidemic strains of EV71 in Taiwan in recent years are constantly changing. The B3 genotype first emerged in 1986. From 1999 to 2003, 2008 to 2009, and 2011 to 2012, the B4 genotype was the predominant strain. Between 2010 and 2011, C4a was the main genotype