Genomic Epidemiology of Coxsackievirus A24 Variant During the 2024 Acute Hemorrhagic Conjunctivitis Outbreak in Coastal Kenya
Morobe, J. M.; Moraa, E. O.; Lambisia, A. W.; Odoyo, S. O.; Mutunga, M.; Katama, E. N.; Cheruiyot, R.; Nyiro, J. U.; Kamau, E.; Houldcroft, C. J.; Keeling, M. J.; Gallagher, K.; Holmes, E. C.; Agoti, C. N.
Show abstract
Several African countries experienced a surge in acute hemorrhagic conjunctivitis (AHC) cases in 2024. Investigations in Kenya, Mayotte and Tanzania identified coxsackievirus A24 variant (CV-A24v) as the causative agent. To date, limited genomic data exist to elucidate the sources, epidemiology, and evolution of CV-A24v in Africa. We generated 245 CV-A24v genomes from samples collected between January and September 2024 in coastal Kenya. Phylogenetic analysis showed that these viruses belonged to genotype IV, with two major clusters identified that differed by 52 nucleotides and five amino acids, with recombination detected in the 3Dpol gene. The sequences clustered closely with contemporaneous Mayotte and Malawi sequences but were distinct from Asian sequences from 2023. Molecular clock dating revealed that the Kenyan sequences had a Most Recent Common Ancestor (MRCA) between June and October 2023. Our study provides the first detailed genomic analysis of CV-A24v from Africa to inform its future control strategies.
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