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.
Highlights
Chikungunya virus (CHIKV) is an enveloped, single-stranded positive sense RNA virus that belongs to the Togaviridae family alphavirus genus
We investigated two outbreaks in the year 2014 and 2019 in Kerala, India
The phylogenetic tree revealed that the isolates formed a separate group with 2019 isolate from Pune, Maharashtra and belonged to the East/ Central/ South African (ECSA) genotype, Indian subcontinent sub lineage of Indian Ocean Lineage (IOL)
Summary
Chikungunya virus (CHIKV) is an enveloped, single-stranded positive sense RNA virus that belongs to the Togaviridae family alphavirus genus. CHIKV has three distinct genotypes; West African (WA), East/Central/South African (ECSA), and Asian [2]. These genotypes represent the independent evolution of the virus in different geographical regions. The Indian Ocean lineage (IOL) within the ECSA genotype was responsible for the Reunion Island outbreak in 2005 [3]. Afterwards the virus spread across several islands in Indian Ocean and India. The circulation of CHIKV has been recorded during 2011 and 2012 in many countries of central Africa, Western Africa, Oceania, Southern and Southeastern Asia (SEA), Europe and Western Indian Ocean islands. The Indian subcontinent sub lineage within the IOL of the ECSA genotype continues to circulate in India and surrounding countries [8]. Some of the mutations were known to improve the virus fitness [9]
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