Das Biswajit, Mohapatra Jajati K, Pande Veena, Subramaniam Saravanan, Sanyal Aniket
ICAR-Project Directorate on Foot-and-Mouth Disease, Mukteswar-Kumaon, Nainital 263138, India.
ICAR-Project Directorate on Foot-and-Mouth Disease, Mukteswar-Kumaon, Nainital 263138, India.
Infect Genet Evol. 2016 Jul;41:36-46. doi: 10.1016/j.meegid.2016.03.024. Epub 2016 Mar 25.
Three decades-long (1977-2013) evolutionary trend of the capsid coding (P1) region of foot-and-mouth disease virus (FMDV) serotype A isolated in India was analysed. The exclusive presence of genotype 18 since 2001 and the dominance of the VP3(59)-deletion group of genotype 18 was evident in the recent years. Clade 18c was found to be currently the only active one among the three clades (18a, 18b and 18c) identified in the deletion group. The rate of evolution of the Indian isolates at the capsid region was found to be 4.96×10(-3)substitutions/site/year. The timescale analysis predicted the most recent common ancestor to have existed during 1962 for Indian FMDV serotype A and around 1998 for the deletion group. The evolutionary pattern of serotype A in India appears to be homogeneous as no spatial or temporal structure was observed. Bayesian skyline plots indicate a sharp decline in the effective number of infections after 2008, which might be a result of mass vaccination or inherent loss of virus fitness. Analyses of variability at 38 known antigenically critical positions in a countrywide longitudinal data set suggested that the substitutions neither followed any specific trend nor remained fixed for a long period since frequent reversions and convergence was noticed. A maximum of 6 different amino acid residues was seen in the gene pool at any antigenically critical site over the decades, suggesting a limited combination of residues being responsible for the observed antigenic variation. Evidence of positive selection at some of the antigenically critical residues and the structurally proximal positions suggest a possible role of pre-existing immunity in the host population in driving evolution. The VP1 C-terminus neither revealed variability nor positive selection, suggesting the possibility that this stretch does not contribute to the antigenic variation and adaptation under immune selection.
分析了1977年至2013年三十年间在印度分离的口蹄疫病毒A型衣壳编码（P1）区的进化趋势。自2001年以来，18型的独特存在以及近年来18型VP3(59)缺失组的优势明显。在缺失组中鉴定出的三个进化枝（18a、18b和18c）中，18c进化枝目前是唯一活跃的。发现印度分离株在衣壳区域的进化速率为4.96×10(-3)替换/位点/年。时间尺度分析预测，印度口蹄疫病毒A型的最近共同祖先存在于1962年左右，而缺失组的最近共同祖先存在于1998年左右。印度A型血清型的进化模式似乎是均匀的，因为未观察到空间或时间结构。贝叶斯天际线图表明，2008年后感染有效数量急剧下降，这可能是大规模疫苗接种或病毒适应性固有丧失的结果。对全国纵向数据集中38个已知抗原关键位置的变异性分析表明，由于频繁出现回复和趋同现象，这些替换既没有遵循任何特定趋势，也没有长期固定不变。几十年来，在任何抗原关键位点的基因库中最多观察到6种不同的氨基酸残基，这表明有限的残基组合是观察到的抗原变异的原因。在一些抗原关键残基和结构近端位置存在正选择的证据表明，宿主群体中预先存在的免疫可能在推动进化中发挥作用。VP1 C末端既没有显示出变异性也没有显示出正选择，这表明这段序列可能在免疫选择下对抗原变异和适应性没有贡献。
