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Molecular characterization of chikungunya virus isolates from two localized outbreaks during 2014-2019 in Kerala, India

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Abstract

After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission routes can be traced by complete genome sequencing studies. We investigated two outbreaks in 2014 and 2019 in Kerala, India. Chikungunya virus (CHIKV) was isolated from the samples, and whole genomes were sequenced for a 2014 isolate and a 2019 isolate. Phylogenetic analysis revealed that the isolates formed a separate group with a 2019 isolate from Pune, Maharashtra, and belonged to the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of the E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have been caused by a virus that had been circulating in India since 2014. A detailed study is needed to investigate the evolution of CHIKV in India.

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Acknowledgements

The authors acknowledge the Department of Health Research for financially supporting the study through extramural funding. We thank the Director of the National Institute of Virology and the NIV Kerala team, especially Mrs. Sreelekha, Kunjila K, and Miss Aiswarya Babu for all the support during the study. We also thank the institute manuscript review committee members, Drs. Bondre, Vaidya, Gurav, Alagarasu, and Sarah Cherian, for critical comments and suggestions. Our special gratitude goes to Thermo Fisher Scientific India Ltd. and the team for their sequencing work.

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Authors and Affiliations

  1. ICMR-National Institute of Virology, Kerala Unit, Govt. T. D. Medical College Hospital, Vandanam, Alappuzha, Kerala, India

    B. Anukumar, T. Asia Devi, Jijo Koshy, N. T. Nikhil & A. P. Sugunan

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  1. B. Anukumar
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  2. T. Asia Devi
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  3. Jijo Koshy
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  4. N. T. Nikhil
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  5. A. P. Sugunan
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Correspondence to B. Anukumar.

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Anukumar, B., Asia Devi, T., Koshy, J. et al. Molecular characterization of chikungunya virus isolates from two localized outbreaks during 2014-2019 in Kerala, India. Arch Virol 166, 2895–2899 (2021). https://doi.org/10.1007/s00705-021-05186-9

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  • DOI: https://doi.org/10.1007/s00705-021-05186-9

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