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. 2010 Sep;155(9):1413-24.
doi: 10.1007/s00705-010-0722-0. Epub 2010 Jun 13.

Emergence of enterovirus 71 "double-recombinant" strains belonging to a novel genotype D originating from southern China: first evidence for combination of intratypic and intertypic recombination events in EV71

Cyril C Y Yip  1 , Susanna K P Lau, Boping Zhou, Ming-Xia Zhang, Hoi-Wah Tsoi, Kwok-Hung Chan, Xin-Chun Chen, Patrick C Y Woo, Kwok-Yung Yuen
Affiliations

Emergence of enterovirus 71 "double-recombinant" strains belonging to a novel genotype D originating from southern China: first evidence for combination of intratypic and intertypic recombination events in EV71

Cyril C Y Yip et al. Arch Virol. 2010 Sep.

Abstract

Hand-foot-mouth disease due to enterovirus 71 (EV71) and coxsackievirus A16 (CA16) has recently caused large outbreaks in mainland China in 2008. We performed complete genome sequencing on two EV71 (SZ/HK08-5 and SZ/HK08-6) and two CA16 (SZ/HK08-3 and SZ/HK08-7) strains from patients in Shenzhen, China. Phylogenetic, similarity plot and bootscan analyses revealed recombination between EV71 genotypes B and C at the 2A-2B junction, and between EV71 genotype B and CA16 strain G-10 in the 3C region for EV71 strains. A similar phenomenon was also found upon further gene sequencing with other EV71 strains. Recombination between CA16 strain G-10 and EV71 genotype A at the 2A-2B junction was also observed for CA16 strains. The present "double-recombinant" EV71 strains circulating in China and other EV71 subgenotype "C4" strains represent an additional genotype, D. CA16 strains should also be classified into two genotypes. This represents the first evidence for a combination of intratypic and intertypic recombination in EV71 strains.

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Figures

Fig. 1
Fig. 1
Schematic representation of the human enterovirus A genome. VP4, partial 2B and partial 3D regions used for phylogenetic analysis are indicated by black bars
Fig. 2
Fig. 2
Phylogenetic analysis of a complete VP4, b partial 2B and c partial 3D regions of EV71 and CA16. Bootstrap values expressed as percentage are shown at the nodes, and the scale reflects the number of nucleotide substitutions per site along the branches
Fig. 3
Fig. 3
Phylogenetic analysis of a 5′ NCR, b P1, c P2 and d P3 regions of the two EV71 and two CA16 strains with complete genome sequences. Bootstrap values expressed as percentage are shown at the nodes, and the scale reflects the number of nucleotide substitutions per site along the branches
Fig. 4
Fig. 4
Recombination analysis of the two EV71 and two CA16 complete genomes. Bootscanning (upper panel) and similarity plot analysis (lower panel) were conducted with SimPlot version 3.5.1 (Kimura distance model; window size, 1,000 bp; step, 20 bp) on a gapless nucleotide alignment, generated with ClustalX, with the genome sequences of the a two EV71 strains (SZ/HK08-5 and SZ/HK08-6) and b two CA16 strains (SZ/HK08-3 and SZ/HK08-7) as the query sequences
Fig. 4
Fig. 4
Recombination analysis of the two EV71 and two CA16 complete genomes. Bootscanning (upper panel) and similarity plot analysis (lower panel) were conducted with SimPlot version 3.5.1 (Kimura distance model; window size, 1,000 bp; step, 20 bp) on a gapless nucleotide alignment, generated with ClustalX, with the genome sequences of the a two EV71 strains (SZ/HK08-5 and SZ/HK08-6) and b two CA16 strains (SZ/HK08-3 and SZ/HK08-7) as the query sequences
Fig. 5
Fig. 5
Phylogenetic analysis of sequences before and after recombination breakpoints revealed by SimPlot analysis. Three phylogenetic trees were constructed using a the region upstream of nucleotide position 3600, b the region between nucleotide positions 3600 and 5430, and c the region downstream of nucleotide position 5430. EV71 strains with evidence of recombination are shaded. Bootstrap values expressed as percentage are shown at the nodes, and the scale reflects the number of nucleotide substitutions per site along the branches
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