Phylogenetic analysis of Enterovirus 71 circulating in Beijing, China from 2007 to 2009

Abstract

The major pathogens of hand, foot and mouth disease (HFMD) in Beijing, China from 2007 to 2009 were identified in this study. A total of 186 HFMD cases were included, and 136 cases (73%) were positive for enterovirus (EV). In 2007, 75% (27/36) were Coxsackievirus A16 (CA16) positive and 19% (7/36) were Enterovirus 71 (EV71) positive cases. However, EV71 was the predominant virus in 2008, when 56% (31/55) of the cases were positive for EV71 and 22% (12/55) were positive for CA16. In 2009, EV71 and CA16, with positive rates of 36% (16/45) and 29% (13/45), respectively, were still the major pathogens of HFMD. Phylogenetic analysis revealed that the dominant genotype of EV71 was C4, with co-circulation of genotype A in 2009. The prevalent cluster of the EV71 subgenotype C4 changed over time. A proposed new sublineage of EV71, C4a-2, was the predominant virus associated with the Beijing and nationwide HFMD outbreaks since 2008 and amino acid substitution, which possibly link to the central nervous system tropism of EV71, was found in genotype A viruses. Persistent surveillance of HFMD-associated pathogens is required for predicting potential emerging viruses and related disease outbreaks.

Figure 1. Phylogenetic relationship between 133 worldwide EV71 strains based on the complete VP1 gene.

Thirty six CMU BJ strains (), 20 other BJ strains (), 52 representative CHN strains and 25 international reference strains (including 14 EV71 C4 strains marked with , BrCr marked with and 10 representative strains of different subgenotypes) are included in this dendrogram. The 52 representative CHN strains were selected from more than 19 provinces and 20 cities in mainland China from 1987 to 2011 according to available locality, time distribution and grouping type. Details of all the EV71 strains included in the dendrogram are provided in Table S1. Country abbreviations: NL, Netherlands; AUS, Australia; KOR, Korea; AUT, Austria; GER, Germany; FRA, France; JPN, Japan; VNM, Vietnam; THA, Thailand; MAL, Malaysia; USA, United States of America; CHN, People's Republic of China. Region abbreviation: TW, Taiwan. Abbreviation of Chinese cities: BJ, Beijing; SH, Shanghai; CQ, Chongqing. Abbreviation of Chinese provinces: HLJ, Heilongjiang; SD, Shandong; GD, Guangdong; GX, Guang Xi; ZJ, Zhejiang; YN, Yunnan; AH, Anhui; HuB, Hubei; JS, Jiangsu; GS, Gansu; HeN, Henan; HeB, Hebei; SC, Si Chuan; SX, Shanxi (taiyuan); SHX, Shanxi (xi'an); NM, Neimeng; NX, Ning Xia; JL, Ji Lin; HuN, Hu Nan.