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Characterization of diversity of measles viruses in India: Genomic sequencing and comparative genomics studies

Published:January 17, 2020DOI:https://doi.org/10.1016/j.jinf.2019.11.025

      Highlights

      • Genome sequencing of 43 measles virus isolates from 10 Indian states sampled during 2009–2017.
      • MeV named strains for one D4 and two D8 isolates were identified based on N-450.
      • D4 isolates have non-standard genome length due to indels in M-F intergenic region.
      • Genotype-based temporal clustering devoid of geography-based monophyly was observed.
      • Observed variations may not impact antigenicity and support use of current vaccines.

      Summary

      Objective

      To map genomic diversity of Measles virus (MeV) isolates collected during 2009–2017 from ten states of India.

      Methods

      Genome sequencing of Indian isolates and comparative genomics with global MeV using phylogeny, population stratification and selection pressure approaches were performed.

      Results

      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.

      Conclusions

      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.

      Keywords

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