The Re-emergence of Chikungunya in Sri Lanka: A Genomic investigation
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Sri Lanka is currently experiencing a large Chikungunya outbreak, since the end of 2024, after 16 years. We carried out whole genomic sequencing of the currently circulating Chikungunya virus (CHIKV) strain and found that it was of the Indian ocean lineage (IOL), similar to the currently circulating CHIKV strains in South Asia. While the E:226V mutation, which has been associated with Aedes albopictus transmission efficiency, was absent in all 2025 CHIKV viral sequences, they carried the E1:K211E and E2: V264A mutations, which result in enhanced viral fitness within the Aedes aegpti mosquito. The mutations nsP1:I167V, nsP2:I171V, nsP2:T224I, nsP3:A382I and nsp4: were detected in the non-structural protein, with the Sri Lankan 2025 CHIKV strains showing unique mutations within nsP3:T224I and nsP4: S90A. As some of these novel mutations have not been characterized previously, it is important to find out how they affect fitness within mosquitoes, viral replication and immune evasion.
One-sentence summary line
The currently ongoing large outbreak in Sri Lanka, is due to the Indian-ocean lineage and E1:K211E/E2:V264A sub lineage of the Chikungunya virus, which has acquired certain previously uncharacterized unique mutations.
