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Evolutionary analysis of structural protein gene VP1 of foot-and-mouth disease virus serotype Asia 1.

Zhang Q, Liu X, Fang Y, Pan L, Lv J, Zhang Z, Zhou P, Ding Y, Chen H, Shao J, Zhao F, Lin T, Chang H, Zhang J, Wang Y, Zhang Y - ScientificWorldJournal (2015)

Bottom Line: Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare.In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains.On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Disease Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.

ABSTRACT
Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I-VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10(-3) substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown.

No MeSH data available.


Related in: MedlinePlus

Chronogram and maximum clade credibility (MCC) tree of 3199 complete VP1 gene sequences of FMDV serotype Asia 1 generated using BEAST. The major eight groups (I–VIII) of viruses have circulated in Asia. The analysis demonstrates that mean divergence time estimates with 95% highest posterior density (HPD) credible intervals are shown in italics.
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fig2: Chronogram and maximum clade credibility (MCC) tree of 3199 complete VP1 gene sequences of FMDV serotype Asia 1 generated using BEAST. The major eight groups (I–VIII) of viruses have circulated in Asia. The analysis demonstrates that mean divergence time estimates with 95% highest posterior density (HPD) credible intervals are shown in italics.

Mentions: Rates of nucleotide substitution for VP1 gene sequences were using Bayesian MCMC approach implemented in the BEAST program. To calculate the rate of evolution in Asia 1 virus, isolates spanning a period of 59 years (1954 to 2012) were selected. Though lineages A, B, C, and D formed individual monophyletic clusters, they were excluded in the calculation as including the vaccine strains and some strains epidemiologically related to the vaccine virus which might lead to erroneous results. The mean rate of mutation in VP1 region was estimated at 5.745 × 10−3 nt substitutions per site, per year (95% HPD 4.923 × 10−3–6.639 × 10−3). On the basis of divergence time analyses, we infer that the TMRCA of 319 Asia 1 virus is 86.29 (95% HPD 66.17–113.59) (Figure 2). The estimated mean divergence time of groups IV and V was 72.11 (95% HPD 62.07–82.01) and 41.27 (95% HPD 36.43–50.74), respectively. Our analyses demonstrate that a FMDV gave rise to two primary diversification events that diverged approximately 52.75 years ago; the first diversification event generated groups II, III, VI, and VIII, whereas the second gave rise to groups I and VII (14.23 years ago). The common ancestor of groups III, VI, II, and VIII existed around 28.20 (95% HPD 21.95 and 36.14), 15.79 (95% HPD 14.70 and 17.95), 11.37 (95% HPD 10.60 and 12.27), and 11.75 (95% HPD 10.34 and 13.75) years ago, respectively.


Evolutionary analysis of structural protein gene VP1 of foot-and-mouth disease virus serotype Asia 1.

Zhang Q, Liu X, Fang Y, Pan L, Lv J, Zhang Z, Zhou P, Ding Y, Chen H, Shao J, Zhao F, Lin T, Chang H, Zhang J, Wang Y, Zhang Y - ScientificWorldJournal (2015)

Chronogram and maximum clade credibility (MCC) tree of 3199 complete VP1 gene sequences of FMDV serotype Asia 1 generated using BEAST. The major eight groups (I–VIII) of viruses have circulated in Asia. The analysis demonstrates that mean divergence time estimates with 95% highest posterior density (HPD) credible intervals are shown in italics.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4352495&req=5

fig2: Chronogram and maximum clade credibility (MCC) tree of 3199 complete VP1 gene sequences of FMDV serotype Asia 1 generated using BEAST. The major eight groups (I–VIII) of viruses have circulated in Asia. The analysis demonstrates that mean divergence time estimates with 95% highest posterior density (HPD) credible intervals are shown in italics.
Mentions: Rates of nucleotide substitution for VP1 gene sequences were using Bayesian MCMC approach implemented in the BEAST program. To calculate the rate of evolution in Asia 1 virus, isolates spanning a period of 59 years (1954 to 2012) were selected. Though lineages A, B, C, and D formed individual monophyletic clusters, they were excluded in the calculation as including the vaccine strains and some strains epidemiologically related to the vaccine virus which might lead to erroneous results. The mean rate of mutation in VP1 region was estimated at 5.745 × 10−3 nt substitutions per site, per year (95% HPD 4.923 × 10−3–6.639 × 10−3). On the basis of divergence time analyses, we infer that the TMRCA of 319 Asia 1 virus is 86.29 (95% HPD 66.17–113.59) (Figure 2). The estimated mean divergence time of groups IV and V was 72.11 (95% HPD 62.07–82.01) and 41.27 (95% HPD 36.43–50.74), respectively. Our analyses demonstrate that a FMDV gave rise to two primary diversification events that diverged approximately 52.75 years ago; the first diversification event generated groups II, III, VI, and VIII, whereas the second gave rise to groups I and VII (14.23 years ago). The common ancestor of groups III, VI, II, and VIII existed around 28.20 (95% HPD 21.95 and 36.14), 15.79 (95% HPD 14.70 and 17.95), 11.37 (95% HPD 10.60 and 12.27), and 11.75 (95% HPD 10.34 and 13.75) years ago, respectively.

Bottom Line: Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare.In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains.On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Disease Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.

ABSTRACT
Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I-VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10(-3) substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown.

No MeSH data available.


Related in: MedlinePlus