Molecular epidemiology of human enterovirus 71 strains and recent outbreaks in the Asia-Pacific region: comparative analysis of the VP1 and VP4 genes

Abstract

This study provides a comprehensive overview of the molecular epidemiology of human enterovirus 71 (HEV71) in the Asia-Pacific region from 1997 through 2002. Phylogenetic analysis of the VP4 and VP1 genes of recent HEV71 strains indicates that several genogroups of the virus have been circulating in the Asia-Pacific region since 1997. The first of these recent outbreaks, described in Sarawak (Malaysian Borneo) in 1997, was caused by genogroup B3. This outbreak was followed by large outbreaks in Taiwan in 1998, caused by genogroup C2, and in Perth (Western Australia) in 1999, where viruses belonging to genogroups B3 and C2 cocirculated. Singapore, Taiwan, and Sarawak had HEV71 epidemics in 2000, caused predominantly by viruses belonging to genogroup B4; however, large numbers of fatalities were observed only in Taiwan. HEV71 was identified during an epidemic of hand, foot and mouth disease in Korea; that epidemic was found to be due to viruses constituting a new genogroup, C3.

Figure 1

An overview of the genetic relationships of human enterovirus 71 (HEV71) strains isolated from 1970 through 2002. Dendrogram showing the genetic relationships among 53 HEV71 strains based on the alignment of the complete VP4 gene sequence (nucleotide positions 744–950). Details of the HEV71 strains included in the dendrogram are provided in Appendix Tables 1 and 2. Branch lengths are proportional to the number of nucleotide differences. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. The VP4 nucleotide sequence of coxsackie virus A16 (CA16) (29) was used as an outgroup in the analysis. *Denotes HEV71 isolates from fatal cases; †denotes HEV71 strains falling outside existing genogroup boundaries.

Figure 2

An overview of the genetic relationships of human enterovirus 71 (HEV71) strains isolated from 1970 through 2002. Unrooted cladogram shows the genogroup relationships of HEV71 based on an alignment of the partial VP4 gene (nucleotide positions 744–950) consensus sequences for genogroups B1, B2, B3, B4, C1, C2, and C3. The complete VP4 gene sequence of the prototype strain BrCr-CA-70 (30) was used as an outgroup in the analysis. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance.

Figure 3

Phylogenetic relationships of human enterovirus 71 (HEV71) strains belonging to genogroup B (21). Dendrogram shows the genetic relationships among 56 HEV71 strains belonging to genogroup B, based on the alignment of the complete VP4 gene sequence (nucleotide positions 744-950). Details of the HEV71 strains included in the dendrogram are provided in Appendix Tables 1 and 2. Branch lengths are proportional to the number of nucleotide differences. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. The VP4 nucleotide sequence of coxsackie virus A16 (CA16) (29) was used as an outgroup in the analysis. *Denotes HEV71 isolates from fatal cases; †Denotes HEV71 strains falling outside existing genogroup boundaries.

Figure 4

Phylogenetic relations of human enterovirus 71 (HEV71) strains belonging to genogroup B (21). Dendrogram shows the genetic relationships among 24 HEV71 strains belonging to genogroup B, based on the alignment of a partial VP1 (nucleotide positions 2442–3281) or complete VP1 (nucleotide positions 2442–3332) gene sequences. Details of the HEV71 strains included in the dendrogram are provided in Appendix Tables 1 and 2. Branch lengths are proportional to the number of nucleotide differences. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. The VP1 nucleotide sequence of the prototype BrCr-CA-70 (30) was used as an outgroup in the analysis.

Figure 5

Phylogenetic relationships of human enterovirus 71 (HEV71) strains belonging to genogroup C (21). Dendrogram shows the genetic relationships among 74 HEV71 strains belonging to genogroup C, based on the alignment of the complete VP4 gene sequence (nucleotide positions 744–950). Details of the HEV71 strains included in the dendrogram are provided in Tables 2 and 3. Branch lengths are proportional to the number of nucleotide differences. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. The VP4 nucleotide sequence of coxsackie virus A16 (29) was used as an outgroup in the analysis. *Denotes HEV71 isolates from fatal cases; †Denotes HEV71 strains falling outside existing genogroup boundaries.

Figure 6

Phylogenetic relationships of human enterovirus 71 (HEV71) strains belonging to genogroup C (21). Dendrogram shows the genetic relationships among 30 HEV71 strains belonging to genogroup C, based on the alignment of a partial VP1 (nucleotide positions 2442–3281) or complete VP1 (nucleotide positions 2442–3332) gene sequences. Details of the HEV71 strains included in the dendrogram are provided in Tables 2 and 3. Branch lengths are proportional to the number of nucleotide differences. The bootstrap values in 1,000 pseudoreplicates for major lineages within the dendrogram are shown as percentages. The marker denotes a measurement of relative phylogenetic distance. The VP1 nucleotide sequence of the prototype BrCr-CA-70 (30) was used as an outgroup in the analysis.