Phylogenetic analysis of enterovirus 71 strains isolated during linked epidemics in Malaysia, Singapore, and Western Australia

Abstract

Enterovirus 71 (EV71) is a frequent cause of hand, foot, and mouth disease (HFMD) epidemics associated with severe neurological sequelae in a small proportion of cases. There has been a significant increase in EV71 epidemic activity throughout the Asia-Pacific region since 1997. Recent HFMD epidemics in this region have been associated with a severe form of brainstem encephalitis associated with pulmonary edema and high case fatality rates. In this study, we show that four genetic lineages of EV71 have been prevalent in the Asia-Pacific region since 1997, including two previously undescribed genogroups (B3 and B4). Furthermore, we show that viruses belonging to genogroups B3 and B4 have circulated endemically in Southeast Asia during this period and have been the primary cause of several large HFMD or encephalitis epidemics in Malaysia, Singapore, and Western Australia.

FIG. 1

Phylogenetic trees showing genetic relationships among 66 EV71 field isolates based on alignment of the complete VP1 gene sequence (nucleotide positions 2442 to 3332). Branch lengths are proportional to the number of nucleotide differences. Most strain names indicate a unique number/country or U.S. state of isolation/year of isolation. The trees were constructed by neighbor joining using the Kimura two-parameter distance method (17). The bootstrap values in 1,000 pseudoreplicates for major lineages within the tree are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. In panels B and C, the branches for genogroup A (BrCr-CA-70) and the outgroup (CA16-G10-51) have been removed from the dendrograms to save space. (A) Simplified dendrogram showing genogroups A, B, and C identified by Brown et al. (2). (B) Detailed dendrogram of strains belonging to genogroup B. (C) Detailed dendrogram of strains belonging to genogroup C.

FIG. 1

Phylogenetic trees showing genetic relationships among 66 EV71 field isolates based on alignment of the complete VP1 gene sequence (nucleotide positions 2442 to 3332). Branch lengths are proportional to the number of nucleotide differences. Most strain names indicate a unique number/country or U.S. state of isolation/year of isolation. The trees were constructed by neighbor joining using the Kimura two-parameter distance method (17). The bootstrap values in 1,000 pseudoreplicates for major lineages within the tree are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. In panels B and C, the branches for genogroup A (BrCr-CA-70) and the outgroup (CA16-G10-51) have been removed from the dendrograms to save space. (A) Simplified dendrogram showing genogroups A, B, and C identified by Brown et al. (2). (B) Detailed dendrogram of strains belonging to genogroup B. (C) Detailed dendrogram of strains belonging to genogroup C.

FIG. 1

Phylogenetic trees showing genetic relationships among 66 EV71 field isolates based on alignment of the complete VP1 gene sequence (nucleotide positions 2442 to 3332). Branch lengths are proportional to the number of nucleotide differences. Most strain names indicate a unique number/country or U.S. state of isolation/year of isolation. The trees were constructed by neighbor joining using the Kimura two-parameter distance method (17). The bootstrap values in 1,000 pseudoreplicates for major lineages within the tree are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. In panels B and C, the branches for genogroup A (BrCr-CA-70) and the outgroup (CA16-G10-51) have been removed from the dendrograms to save space. (A) Simplified dendrogram showing genogroups A, B, and C identified by Brown et al. (2). (B) Detailed dendrogram of strains belonging to genogroup B. (C) Detailed dendrogram of strains belonging to genogroup C.

FIG. 2

Partial alignment of deduced VP1 amino acid sequences (residues 150 to 200) of the EV71 isolates from WA belonging to genogroup C2. The deduced amino acid sequence in the same region of VP1 is also shown for CA16-G10-51 (25), the EV71 consensus sequence (2), genogroup A (BrCr-CA-70), consensus sequences for genogroups B and C (2), and the 1998 Taiwanese isolate NCKU9822 (30). Amino acid residues that are identical to those in the EV71 consensus sequence are denoted with hyphens.