ICMR-National Institute of Virology, 20-A Dr. Ambedkar Road, Pune 411001, India.
Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, India; HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, C-DAC Innovation Park, Panchavati, Pashan, Pune 411008, India.
J Infect. 2020 Mar;80(3):301-309. doi: 10.1016/j.jinf.2019.11.025. Epub 2020 Jan 17.
To map genomic diversity of Measles virus (MeV) isolates collected during 2009-2017 from ten states of India.
Genome sequencing of Indian isolates and comparative genomics with global MeV using phylogeny, population stratification and selection pressure approaches were performed.
The first report of complete genome sequences of forty-three Indian MeV isolates belonging to genotypes D4 (eight) and D8 (thirty-five). Three Indian isolates mapped to named strains D4-Enfield, D8-Villupuram and D8-Victoria. Indian D4 isolates deviate from standard genome length due to indels in M-F intergenic region. Estimated nucleotide substitution rates of Indian MeV derived using genome and individual genes are lower than that of global isolates. Phylogeny revealed genotype-based temporal clustering, suggesting existence of two lineages of D4 and three lineages of D8 in India. Absence of spatial clustering suggests role of cross-border travel in MeV transmission.
Evolutionary analyses suggest the need for surveillance of MeV in India, particularly in view of diversified trajectories of D4 and D8 isolates. This study contributes to global measles epidemiology and indicates no major impact on antigenicity in Indian isolates, thereby substantiating the use of current vaccines to meet measles elimination target of 2023 set by World Health Organization for South-East Asia Region.
绘制 2009 年至 2017 年间从印度十个邦收集的麻疹病毒（MeV）分离株的基因组多样性图谱。
对印度分离株进行基因组测序，并利用系统发育、群体分层和选择压力方法，对全球 MeV 进行比较基因组学分析。
首次报告了属于基因型 D4（8 个）和 D8（35 个）的 43 个印度 MeV 分离株的完整基因组序列。三个印度分离株与命名株 D4-Enfield、D8-Villupuram 和 D8-Victoria 相对应。印度 D4 分离株由于 M-F 基因间区的插入缺失而偏离标准基因组长度。使用基因组和单个基因估计的印度 MeV 核苷酸取代率低于全球分离株。系统发育显示基于基因型的时间聚类，表明印度存在 D4 的两个谱系和 D8 的三个谱系。没有空间聚类表明跨境旅行在 MeV 传播中的作用。
进化分析表明需要在印度监测 MeV，特别是考虑到 D4 和 D8 分离株的多样化轨迹。本研究为全球麻疹流行病学做出了贡献，表明印度分离株的抗原性没有重大影响，从而证实了使用当前疫苗来实现世界卫生组织为东南亚地区设定的 2023 年消除麻疹目标。
