Chikungunya Virus Molecular Evolution in India Since its Re-emergence in 2005

Abstract

Abstract Chikungunya virus (CHIKV), an alphavirus of the Togaviridae family, is amongst the most medically significant mosquito-borne viruses, capable of causing major epidemics of febrile disease and severe, chronic arthritis. Identifying viral mutations is crucial for understanding virus evolution and evaluating those genetic determinants that directly impact pathogenesis and transmissibility. The present study was undertaken to expand on past CHIKV evolutionary studies through robust genome-scale phylogenetic analysis to better understand CHIKV genetic diversity and evolutionary dynamics since its reintroduction into India in 2005. We sequenced the complete genomes of 50 clinical isolates collected between 2010 and 2016 from two geographic locations, Delhi and Mumbai. We then analyzed them along with 753 genomes available on the VIPR database sampled over 15 years (2005–2020) from a range of locations across the globe, and identified novel genetic variants present in samples from this study. Our analyses show evidence of frequent reintroduction of the virus into India, and that the most recent CHIKV outbreak shares a common ancestor as recently as 2006.