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Epidemics and Frequent Recombination within Species in Outbreaks of Human Enterovirus B-Associated Hand, Foot and Mouth Disease in Shandong China in 2010 and 2011.

Zhang T, Du J, Xue Y, Su H, Yang F, Jin Q - PLoS ONE (2013)

Bottom Line: Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points.In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup.Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy Medical Sciences & Peking Union Medical College, Beijing, China.

ABSTRACT
The epidemiology and molecular characteristics of human enterovirus B (HEV-B) associated with hand, foot and mouth disease (HFMD) outbreaks in China are not well known. In the present study, we tested 201 HEV isolates from 233 clinical specimens from patients with severe HFMD during 2010-2011 in Linyi, Shandong, China. Of the 201 isolates, 189 were fully typed and 18 corresponded to HEV-B species (six serotypes CVA9, CVB1, CVB4, Echo 6, Echo 25 and Echo 30) using sensitive semi-nested polymerase chain reaction analysis of VP1 gene sequences. Phylogenetic analysis based on the VP1 region showed that eight E30SD belonged to a novel sub-genogroup D2; E25SD belonged to a novel sub-genogroup D6; E6SD belonged to sub-lineage C6 and five CVB1SD belonged to subgroup 4C; and B4SD belonged sub-lineage D2. The full viral genomes of the CVB1SD, E6SD, E25SD and E30SD isolates were sequenced. Analysis of phylogenetic and similarity plots indicated that E25SD recombined with E25-HN-2, E30FDJS03 and E4AUS250 at noncontiguous P2A-P3D regions, while E30SD, E30FDJ03, E25-HN-2 and E9 DM had shared sequences in discrete regions of P2 and P3. Both E6SD and B1SD shared sequences with E1-HN, B4/GX/10, B5-HN, and A9-Alberta in contiguous regions of most of P2 and P3. Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points. In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup. Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.

No MeSH data available.


Related in: MedlinePlus

Phylogeny of E30 based on 875 nt of the VP1 gene generated by the neighbor-joining algorithm implemented in MEGA (version 5.0) using the Kimura two-parameter substitution model and 1000 bootstrap pseudo-replicates.•Strains isolated in this investigation. ♦Strains isolated from Shandong. ○Strains isolated from other provinces of China.
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pone-0067157-g003: Phylogeny of E30 based on 875 nt of the VP1 gene generated by the neighbor-joining algorithm implemented in MEGA (version 5.0) using the Kimura two-parameter substitution model and 1000 bootstrap pseudo-replicates.•Strains isolated in this investigation. ♦Strains isolated from Shandong. ○Strains isolated from other provinces of China.

Mentions: According to the molecular epidemiological study, genotypes were defined as clusters of related strains with >85% nt sequence identity in the VP1 region [20]. Individual phylogenetic dendrograms for E6, CVB1, CVB4, E25SD and E30SD were drawn based on VP1 sequences from all representative strains responsible for international or domestic epidemics during the past decade. There were four E25 genetic groups, designated A–D (subgroups D1–D6) [11].The E25SD10 sequence detected in the present study belonged to the novel subgenogroup D6 (Figure 2). Four genetic groups were classified for the E30 strains, designated A–D (subgroups D1–D2) [7], [21]. The Ukraine and E30 JS2003 strains belonged to subgroup D1, while the E30SD strains isolated in this study and E30Linyi (the latest strains available in GenBank) were categorized as novel subgenogroup D2 with nt sequence identities ranging from 95.6–98.9%, and amino acid identities ranging from 98.9–100% (Figure 3), which have not been reported previously. The E30 TW, Zhejiang, and GX strains belonged to group C. There were three Echo6 genetic groups designated A–C (subgroups C1–6), and four CVB1 genetic groups designated A–D (subgenogroups D1–6), which had been previously identified [4], [9]. Based on this classification, the E6SD sequence detected in the present study belonged to subgroup C6 (Figure 4) and five B1SD sequences belonged to the sublineage D6 (Figure 5). Finally, CVB4 was classified into three genetic groups A–C (subgroup C1–2), and two CVB4 sequences formed a cluster in the C2 sublineage (Figure 6). In addition, phylogenetic dendrograms of the EV71 and CA16 strains indicated that E71 and CA16 formed new subgenogroups C4a and C3c, respectively, as shown in Figures S1 and S2.


Epidemics and Frequent Recombination within Species in Outbreaks of Human Enterovirus B-Associated Hand, Foot and Mouth Disease in Shandong China in 2010 and 2011.

Zhang T, Du J, Xue Y, Su H, Yang F, Jin Q - PLoS ONE (2013)

Phylogeny of E30 based on 875 nt of the VP1 gene generated by the neighbor-joining algorithm implemented in MEGA (version 5.0) using the Kimura two-parameter substitution model and 1000 bootstrap pseudo-replicates.•Strains isolated in this investigation. ♦Strains isolated from Shandong. ○Strains isolated from other provinces of China.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3686723&req=5

pone-0067157-g003: Phylogeny of E30 based on 875 nt of the VP1 gene generated by the neighbor-joining algorithm implemented in MEGA (version 5.0) using the Kimura two-parameter substitution model and 1000 bootstrap pseudo-replicates.•Strains isolated in this investigation. ♦Strains isolated from Shandong. ○Strains isolated from other provinces of China.
Mentions: According to the molecular epidemiological study, genotypes were defined as clusters of related strains with >85% nt sequence identity in the VP1 region [20]. Individual phylogenetic dendrograms for E6, CVB1, CVB4, E25SD and E30SD were drawn based on VP1 sequences from all representative strains responsible for international or domestic epidemics during the past decade. There were four E25 genetic groups, designated A–D (subgroups D1–D6) [11].The E25SD10 sequence detected in the present study belonged to the novel subgenogroup D6 (Figure 2). Four genetic groups were classified for the E30 strains, designated A–D (subgroups D1–D2) [7], [21]. The Ukraine and E30 JS2003 strains belonged to subgroup D1, while the E30SD strains isolated in this study and E30Linyi (the latest strains available in GenBank) were categorized as novel subgenogroup D2 with nt sequence identities ranging from 95.6–98.9%, and amino acid identities ranging from 98.9–100% (Figure 3), which have not been reported previously. The E30 TW, Zhejiang, and GX strains belonged to group C. There were three Echo6 genetic groups designated A–C (subgroups C1–6), and four CVB1 genetic groups designated A–D (subgenogroups D1–6), which had been previously identified [4], [9]. Based on this classification, the E6SD sequence detected in the present study belonged to subgroup C6 (Figure 4) and five B1SD sequences belonged to the sublineage D6 (Figure 5). Finally, CVB4 was classified into three genetic groups A–C (subgroup C1–2), and two CVB4 sequences formed a cluster in the C2 sublineage (Figure 6). In addition, phylogenetic dendrograms of the EV71 and CA16 strains indicated that E71 and CA16 formed new subgenogroups C4a and C3c, respectively, as shown in Figures S1 and S2.

Bottom Line: Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points.In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup.Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy Medical Sciences & Peking Union Medical College, Beijing, China.

ABSTRACT
The epidemiology and molecular characteristics of human enterovirus B (HEV-B) associated with hand, foot and mouth disease (HFMD) outbreaks in China are not well known. In the present study, we tested 201 HEV isolates from 233 clinical specimens from patients with severe HFMD during 2010-2011 in Linyi, Shandong, China. Of the 201 isolates, 189 were fully typed and 18 corresponded to HEV-B species (six serotypes CVA9, CVB1, CVB4, Echo 6, Echo 25 and Echo 30) using sensitive semi-nested polymerase chain reaction analysis of VP1 gene sequences. Phylogenetic analysis based on the VP1 region showed that eight E30SD belonged to a novel sub-genogroup D2; E25SD belonged to a novel sub-genogroup D6; E6SD belonged to sub-lineage C6 and five CVB1SD belonged to subgroup 4C; and B4SD belonged sub-lineage D2. The full viral genomes of the CVB1SD, E6SD, E25SD and E30SD isolates were sequenced. Analysis of phylogenetic and similarity plots indicated that E25SD recombined with E25-HN-2, E30FDJS03 and E4AUS250 at noncontiguous P2A-P3D regions, while E30SD, E30FDJ03, E25-HN-2 and E9 DM had shared sequences in discrete regions of P2 and P3. Both E6SD and B1SD shared sequences with E1-HN, B4/GX/10, B5-HN, and A9-Alberta in contiguous regions of most of P2 and P3. Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points. In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup. Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.

No MeSH data available.


Related in: MedlinePlus