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Inferring nonneutral evolution from contrasting patterns of polymorphisms and divergences in different protein coding regions of enterovirus 71 circulating in Taiwan during 1998-2003.

Wang HY, Tsao KC, Hsieh CH, Huang LM, Lin TY, Chen GW, Shih SR, Chang LY - BMC Evol. Biol. (2010)

Bottom Line: Contrasting patterns of polymorphisms and divergences were found between structural (VP1) and non-structural segments (2A and 3C), i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two.Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution.Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan.

ABSTRACT

Background: Enterovirus (EV) 71 is one of the common causative agents for hand, foot, and, mouth disease (HFMD). In recent years, the virus caused several outbreaks with high numbers of deaths and severe neurological complications. Despite the importance of these epidemics, several aspects of the evolutionary and epidemiological dynamics, including viral nucleotide variations within and between different outbreaks, rates of change in immune-related structural regions vs. non-structural regions, and forces driving the evolution of EV71, are still not clear.

Results: We sequenced four genomic segments, i.e., the 5' untranslated region (UTR), VP1, 2A, and 3C, of 395 EV71 viral strains collected from 1998 to 2003 in Taiwan. The phylogenies derived from different genomic segments revealed different relationships, indicating frequent sequence recombinations as previously noted. In addition to simple recombinations, exchanges of the P1 domain between different species/genotypes of human enterovirus species (HEV)-A were repeatedly observed. Contrasting patterns of polymorphisms and divergences were found between structural (VP1) and non-structural segments (2A and 3C), i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two. Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution. Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity. Viruses sampled in successive epidemic seasons were not sister to each other, indicating that the annual outbreaks of EV71 were due to genetically distinct lineages.

Conclusions: Based on observations of accelerated amino acid changes and frequent exchanges of the P1 domain, we propose that positive selection and subsequent frequent domain shuffling are two important mechanisms for generating new genotypes of HEV-A. Our viral dynamics analysis suggested that the importation of EV71 from surrounding areas likely contributes to local EV71 outbreaks.

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Observed (filled box) and simulated (open box) Ka and Ka/Ks values for VP1 (A), 2A (B), and 3C (C), respectively, between enterovirus (EV) 71-B4 and human enterovirus(HEV)-A. Simulated Ks values were set equal to the observations. The proportions of nonsynonymous (N) and synonymous (S) mutations were determined according to the observed N/S ratios in polymorphisms which were 0.10 for VP1, 0.24 and 0.12 for 2A, and 0.21 for 3C (see Table 2 and text for details). The error bar represents 1 standard deviation. p values were determined by 10,000 simulations. * p < 0.05; *** p < 0.001; NS, not significant (p > 0.05).
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Figure 4: Observed (filled box) and simulated (open box) Ka and Ka/Ks values for VP1 (A), 2A (B), and 3C (C), respectively, between enterovirus (EV) 71-B4 and human enterovirus(HEV)-A. Simulated Ks values were set equal to the observations. The proportions of nonsynonymous (N) and synonymous (S) mutations were determined according to the observed N/S ratios in polymorphisms which were 0.10 for VP1, 0.24 and 0.12 for 2A, and 0.21 for 3C (see Table 2 and text for details). The error bar represents 1 standard deviation. p values were determined by 10,000 simulations. * p < 0.05; *** p < 0.001; NS, not significant (p > 0.05).

Mentions: Simulations were done for both EV71-C2 and B4, and the results were essentially the same. For illustrative purposes, we only present the results of genotype B4 (Figure 4). For VP1, the observed Ka and Ka/Ks values were significantly higher than the simulated results (p < 10-3; Figure 4a), indicating accelerated fixation of amino acid replacement substitutions. Such a pattern was reversed for 2A and 3C (Figure 4b, c). In the 3C region, the observed Ka and Ka/Ks values were lower than the predictions, but the difference was insignificant. Significantly lower Ka and Ka/Ks values in the simulations than in observations for 2A suggest the effect of negative selection preventing deleterious mutations from becoming fixed. Deleterious mutations are usually at a low frequency and inflate the N/S ratio of polymorphisms. This problem can be partially overcome by removing rare mutations from the sample [26]. The N/S ratio of 2A was largely reduced, from 0.24 to 0.12 (Table 2), after singletons were removed. We then reset the N/S ratio from 0.24 to 0.12 for 2A in the simulation, and differences in Ka and Ka/Ks between observations and predictions became non-significant (Figure 4b). In short, when singletons were not counted, 2A and 3C showed good agreement with the neutral mutation hypothesis.


Inferring nonneutral evolution from contrasting patterns of polymorphisms and divergences in different protein coding regions of enterovirus 71 circulating in Taiwan during 1998-2003.

Wang HY, Tsao KC, Hsieh CH, Huang LM, Lin TY, Chen GW, Shih SR, Chang LY - BMC Evol. Biol. (2010)

Observed (filled box) and simulated (open box) Ka and Ka/Ks values for VP1 (A), 2A (B), and 3C (C), respectively, between enterovirus (EV) 71-B4 and human enterovirus(HEV)-A. Simulated Ks values were set equal to the observations. The proportions of nonsynonymous (N) and synonymous (S) mutations were determined according to the observed N/S ratios in polymorphisms which were 0.10 for VP1, 0.24 and 0.12 for 2A, and 0.21 for 3C (see Table 2 and text for details). The error bar represents 1 standard deviation. p values were determined by 10,000 simulations. * p < 0.05; *** p < 0.001; NS, not significant (p > 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2958165&req=5

Figure 4: Observed (filled box) and simulated (open box) Ka and Ka/Ks values for VP1 (A), 2A (B), and 3C (C), respectively, between enterovirus (EV) 71-B4 and human enterovirus(HEV)-A. Simulated Ks values were set equal to the observations. The proportions of nonsynonymous (N) and synonymous (S) mutations were determined according to the observed N/S ratios in polymorphisms which were 0.10 for VP1, 0.24 and 0.12 for 2A, and 0.21 for 3C (see Table 2 and text for details). The error bar represents 1 standard deviation. p values were determined by 10,000 simulations. * p < 0.05; *** p < 0.001; NS, not significant (p > 0.05).
Mentions: Simulations were done for both EV71-C2 and B4, and the results were essentially the same. For illustrative purposes, we only present the results of genotype B4 (Figure 4). For VP1, the observed Ka and Ka/Ks values were significantly higher than the simulated results (p < 10-3; Figure 4a), indicating accelerated fixation of amino acid replacement substitutions. Such a pattern was reversed for 2A and 3C (Figure 4b, c). In the 3C region, the observed Ka and Ka/Ks values were lower than the predictions, but the difference was insignificant. Significantly lower Ka and Ka/Ks values in the simulations than in observations for 2A suggest the effect of negative selection preventing deleterious mutations from becoming fixed. Deleterious mutations are usually at a low frequency and inflate the N/S ratio of polymorphisms. This problem can be partially overcome by removing rare mutations from the sample [26]. The N/S ratio of 2A was largely reduced, from 0.24 to 0.12 (Table 2), after singletons were removed. We then reset the N/S ratio from 0.24 to 0.12 for 2A in the simulation, and differences in Ka and Ka/Ks between observations and predictions became non-significant (Figure 4b). In short, when singletons were not counted, 2A and 3C showed good agreement with the neutral mutation hypothesis.

Bottom Line: Contrasting patterns of polymorphisms and divergences were found between structural (VP1) and non-structural segments (2A and 3C), i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two.Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution.Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan.

ABSTRACT

Background: Enterovirus (EV) 71 is one of the common causative agents for hand, foot, and, mouth disease (HFMD). In recent years, the virus caused several outbreaks with high numbers of deaths and severe neurological complications. Despite the importance of these epidemics, several aspects of the evolutionary and epidemiological dynamics, including viral nucleotide variations within and between different outbreaks, rates of change in immune-related structural regions vs. non-structural regions, and forces driving the evolution of EV71, are still not clear.

Results: We sequenced four genomic segments, i.e., the 5' untranslated region (UTR), VP1, 2A, and 3C, of 395 EV71 viral strains collected from 1998 to 2003 in Taiwan. The phylogenies derived from different genomic segments revealed different relationships, indicating frequent sequence recombinations as previously noted. In addition to simple recombinations, exchanges of the P1 domain between different species/genotypes of human enterovirus species (HEV)-A were repeatedly observed. Contrasting patterns of polymorphisms and divergences were found between structural (VP1) and non-structural segments (2A and 3C), i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two. Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution. Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity. Viruses sampled in successive epidemic seasons were not sister to each other, indicating that the annual outbreaks of EV71 were due to genetically distinct lineages.

Conclusions: Based on observations of accelerated amino acid changes and frequent exchanges of the P1 domain, we propose that positive selection and subsequent frequent domain shuffling are two important mechanisms for generating new genotypes of HEV-A. Our viral dynamics analysis suggested that the importation of EV71 from surrounding areas likely contributes to local EV71 outbreaks.

Show MeSH
Related in: MedlinePlus