Genomic surveillance reveals fast evolving Chikungunya virus during an outbreak in 2023 in eastern Senegal, West Africa.

The Chikungunya virus, a mosquito-borne alphavirus, continues to pose a significant public health challenge with its capacity to cause widespread outbreaks. In 2023, Senegal experienced a major outbreak, initially emerging in the Kedougou region and subsequently spreading to Tambacounda. This study aimed to monitor the molecular evolution of Chikungunya virus using real-time genomic surveillance during the epidemic progression. A total of fourteen human samples blood collected from Chikungunya suspected cases in Tambacounda were analyzed. Whole genome sequencing revealed that the outbreak strain belonged to the West African genotype, closely related to strains from the Kedougou 2023 outbreak. Phylogenetic analysis highlighted three distinct genetic groups within the 2023 strains, with notable genetic variations between the Kedougou and Tambacounda clusters. Specifically, two amino acid mutations, A13T in the non-structural protein 1 (nsP1) and K270R in the structural E2 glycoprotein, were identified in the Tambacounda strains, suggesting potential adaptive changes. Our findings demonstrate the rapid evolution of Chikungunya virus in eastern Senegal, emphasizing the necessity for continuous genomic surveillance to detect emerging variants and understand their implications for virus transmissibility and virulence. This study underscores the critical role of genomic analysis in managing viral outbreaks and informing public health strategies.