Chikungunya virus (CHIKV) is an enveloped, single-stranded positive sense RNA virus that belongs to the Togaviridae family alphavirus genus. The virus genome size is around 12 kb, and has two open reading frames (ORF) ORF 1, and ORF 2. ORF 1 codes for the non-structural proteins (nsP); nsP1, nsP2, nsP3 and nsP4 while ORF 2 codes for five structural proteins E1, E2, E3, C (capsid), and 6K . The genotype of CHIKV is determined based on sequencing of the gene E1. CHIKV has three distinct genotypes; West African (WA), East/Central/South African (ECSA), and Asian . These genotypes represent the independent evolution of the virus in different geographical regions. Evolutionary studies have revealed that WA genotype originated in Africa and subsequently moved into Asia where it evolved into Asian genotype. The Indian Ocean lineage (IOL) within the ECSA genotype was responsible for the Reunion Island outbreak in 2005 . In Asia, the CHIKV was first isolated in Bangkok, Thailand in 1958. In India the first outbreak was recorded in Kolkata during 1963. It spread to the states of Tamil Nadu, Andra Pradesh, and Maharashtra during 1964 to 1965 and disappeared in 1973. Earlier outbreaks in India were caused by Asian genotype . In 2004, there was a major outbreak in Kenya and in 2005 it spread to La Reunion via neighboring islands. Afterwards the virus spread across several islands in Indian Ocean and India. In India, the virus re-emerged in 2006 after a gap of 32 years and caused an explosive outbreak that affected 13 states. Andhra Pradesh, Karnataka, Maharashtra, Madhya Pradesh, Tamil Nadu, Gujarat, and Kerala were the mainly affected states. The isolates of virus belonged to the ECSA genotype . In 2007 it spread from India to Sri Lanka, Thailand, Malaysia, and Italy. In La Reunion islands, the second outbreak occurred in the year 2009 and contributed to the 2010 outbreak in Europe. 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 Asian genotype continues to circulate in the regions of SEA and the Western Pacific . Pyke et al. (2018) reported a case of Asian genotype CHIKV imported from the Philippines into Australia in 2016 . The Indian subcontinent sub lineage within the IOL of the ECSA genotype continues to circulate in India and surrounding countries .
Following 2006–2009 CHIKV epidemic, India recorded several outbreaks every year (IDSP: www.idsp.nic.in). Two CHIKV outbreaks occurred in two separate locations in the state of Kerala between 2014 and 2019. The outbreaks were attended to obtain epidemiological details, as well as acute samples for virus isolation. The present study was carried out to perform molecular characterization of CHIKV responsible for the outbreaks in Kerala between 2014 and 2019. Molecular characterization of virus genome is important for studying the molecular epidemiology of the virus. Virus evolved with occurrence of many synonymous and non-synonymous mutations in the structural and non structural genes during subsequent outbreaks. Some of the mutations were known to improve the virus fitness .