Sri Lanka is currently grappling with a significant outbreak of the Chikungunya virus—the largest since 2008—according to renowned Sri Lankan scientist, Professor Neelika Malavige.
In a post shared on ‘X’ (formerly Twitter), Professor Malavige stated that whole-genomic sequencing of the virus was conducted using the Oxford Nanopore analysis system. The analysis revealed that the circulating virus strain belongs to the Indian Ocean Lineage (IOL) and carries several previously unreported mutations.
She explained that while the E1:226V mutation—known to enhance transmission by Aedes albopictus mosquitoes—was absent in the 2025 viral sequences, the virus carried the E1:K211E and E2:V264A mutations. These are believed to boost viral fitness in Aedes aegypti, the primary mosquito vector responsible for transmission in urban areas.
Additional mutations were identified in non-structural proteins, including nsP1:I167V, nsP2:I171V, nsP2:T224I, and nsP3:A382I. Notably, unique mutations such as nsP3:T224I and nsP4:S90A were found in the 2025 Sri Lankan strains.
“These novel mutations have not been previously characterized,” Professor Malavige noted, emphasizing the urgent need for further research to understand their impact on mosquito transmission efficiency, viral replication, and immune evasion.
The outbreak, which began in late 2024, marks Sri Lanka’s most serious resurgence of the disease in nearly two decades and poses a growing public health challenge.
