Sunil R Vaidya1, Sunitha M Kasibhatla2, Divya R Bhattad1, Mukund R Ramtirthkar3, Mohan M Kale3, Chandrashekhar G Raut4, Urmila Kulkarni-Kale5. 1. ICMR-National Institute of Virology, 20-A Dr. Ambedkar Road, Pune 411001, India. 2. 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. 3. Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, India. 4. ICMR-National Institute for Research in Tribal Health, Nagpur Road, Jabalpur 482003, India. 5. Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, India. Electronic address: urmila.kulkarni.kale@gmail.com.
Abstract
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.
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.