Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography
Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography
复制标题
DOI：
10.1007/s00705-017-3288-2
复制
发表时间：
2017-06-01
影响因子：
2.7
通讯作者：
Gandham, Ravi Kumar
中科院分区：
文献类型：
--
作者：
Sahu, Amit Ranjan;Wani, Sajad Ahmad;Gandham, Ravi Kumar
小反刍兽疫是影响小反刍动物的一种重要跨界疾病。基因组或基因序列分析丰富了我们对这种疾病的病原体，小反刍兽疫病毒（PPRV）的进化和跨界性质的认识。虽然使用病原体的全基因组序列的分析导致更精确的系统发育关系，当与单个基因或部分序列相比时，仍然需要鉴定可以提供与用全长基因组序列预测的那些一致的进化评估的特定基因/基因组区域。在此，将毒性Izatnagar/94 PPRV分离株组装并与所有可用的完整基因组序列（目前在NCBI数据库中）进行比较，以估计核苷酸多样性并推断基因/基因组区域与全长基因组之间的进化关系。我们的目的是确定首选的候选基因作为系统发育标记，以及预测分歧的时间和探索PPRV的地理。在所有的PPRV基因中，H基因被鉴定为是最多样的，与全基因组序列的进化关系最高。因此，它被认为是最优选的候选基因的系统发育研究与93%的同一性设置为核苷酸截断。全基因组核苷酸序列的临界值为94%，允许特异性区分PPRV谱系。研究中检测的所有分离物都发现最近的共同祖先在19世纪末或世纪初，后验概率值很高。贝叶斯天际线图显示，自疫苗接种计划开始以来，谱系IV分离株的遗传多样性减少，网络分析将PPRV的祖先定位于非洲。
Peste des petits ruminants is an important transboundary disease infecting small ruminants. Genome or gene sequence analysis enriches our knowledge about the evolution and transboundary nature of the causative agent of this disease, peste des petits ruminants virus (PPRV). Although analysis using whole genome sequences of pathogens leads to more precise phylogenetic relationships, when compared to individual genes or partial sequences, there is still a need to identify specific genes/genomic regions that can provide evolutionary assessments consistent with those predicted with full-length genome sequences. Here the virulent Izatnagar/94 PPRV isolate was assembled and compared to all available complete genome sequences (currently in the NCBI database) to estimate nucleotide diversity and to deduce evolutionary relationships between genes/genomic regions and the full length genomes. Our aim was to identify the preferred candidate gene for use as a phylogenetic marker, as well as to predict divergence time and explore PPRV phylogeography. Among all the PPRV genes, the H gene was identified to be the most diverse with the highest evolutionary relationship with the full genome sequences. Hence it is considered as the most preferred candidate gene for phylogenetic study with 93% identity set as a nucleotide cutoff. A whole genome nucleotide sequence cutoff value of 94% permitted specific differentiation of PPRV lineages. All the isolates examined in the study were found to have a most recent common ancestor in the late 19th or in the early 20th century with high posterior probability values. The Bayesian skyline plot revealed a decrease in genetic diversity among lineage IV isolates since the start of the vaccination program and the network analysis localized the ancestry of PPRV to Africa.