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Updated: Oct 25, 2025
Multiplexed Isothermal Amplification Based Diagnostic Platform to Detect Zika, Chikungunya, and Dengue 1
Published on: March 13, 2018
Molecular characterization of chikungunya virus isolates from two localized outbreaks during 2014-2019 in Kerala,
B Anukumar1, T Asia Devi2, Jijo Koshy2
1ICMR-National Institute of Virology, Kerala Unit, Govt. T. D. Medical College Hospital, Vandanam, Alappuzha, Kerala, India. anukumar74@gmail.com.
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.
Insights
Chikungunya virus (CHIKV) outbreaks in India may stem from a single strain circulating since 2014. Genome sequencing revealed a novel mutation, suggesting ongoing viral evolution and the need for further research.
Area of Science:
- Virology
- Epidemiology
- Genomics
Background:
- Chikungunya virus (CHIKV) has caused intermittent outbreaks in India since the 2005-2009 epidemic.
- Outbreaks are attributed to local strains or imported viruses, necessitating tracking transmission routes.
Purpose of the Study:
- To investigate the genetic origins and evolutionary dynamics of CHIKV in two outbreaks in Kerala, India, during 2014 and 2019.
Main Methods:
- Isolation of CHIKV from patient samples.
- Whole genome sequencing of 2014 and 2019 isolates.
- Phylogenetic analysis to determine viral lineage and relationships.
Main Results:
- Phylogenetic analysis placed the Kerala isolates within the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL).
- A novel mutation at amino acid position 76 in the E2 gene was identified in the studied isolates.
- The findings suggest a potential continuous circulation of CHIKV in India since 2014.
Conclusions:
- The 2014 and 2019 Kerala outbreaks may be linked to a CHIKV strain circulating within India.
- The identification of a novel mutation warrants further investigation into CHIKV evolution in the region.
- Comprehensive studies are crucial to understand the long-term evolution and epidemiology of CHIKV in India.
