Enterovirus 71 (EV71) is a non-polio enterovirus (NPEV) and a known cause of severe poliomyelitis-like illness, often resulting in large outbreaks worldwide. EV serotypes have traditionally been grouped according to neutralization serotype, gradually replaced by genomic sequencing and thus, revised recently into four species. Phylogenetically, EV71 is closely related to Coxsackie virus A16 (CAV16).
EV71-associated severe neurological disease has been observed in many outbreaks throughout the world since first reported in California, USA in 1969. During the last 8–10 years, a shift in geographic location and frequency of reported EV71-associated brain stem encephalitis fatalities was observed, in particular during outbreaks in Malaysia in 1997 and Taiwan in 1998. Several smaller scale outbreaks have been recorded from Western Australia, Korea, Japan and Singapore. During 2006, large-scale HFMD outbreaks in India, Thailand, Hong Kong, Malaysia and Brunei were reported and in China during 2008. Since 1998, EV71 epidemics with more than 10 fatal cases occurred during 2000~2002, 2005 and 2008.
EV71 is in constant evolution with an estimated variation rate of 1.35 × 10-2 substitutions per nucleotide. For phylogenetic analysis, the capsid protein VP1 is considered most robust for evolutionary study and three distinct EV71 genotypes (A, B and C) were identified by Brown et al. The original prototype (BrCr strain) is the sole representative of genotype A, and genotypes B or C can be further sub-divided into genogroups B1–B4 and C1–C4. During the past decade, genotypes B3, B4, C1, and B5 were reported in Malaysia, B3, B4 and C1 in Singapore, B3, C2 and C1 in Australia and C4 in China. In Japan, genotypes B3~B5, C2 and C4 were identified. In Taiwan the longitudinal surveillance showed that genotype C2 was the major strain in 1998 epidemic, B4 dominated between 1999 and 2003, C4 during 2004 and 2005, C5 during 2006 and 2007, and B5 in 2008. No apparent outbreak was observed in 2009. The observations, when taken collectively, suggest that recombination and mutation may benefit the spread of EV71 in the human population.