Morobe JM, Odoyo S, Lambisia AW, Moraa E, Houldcroft CJ, Holmes EC, Githinji G, Agoti CN
Wellcome Open Res. 2025;10
In January 2024, the Kenya Ministry of Health issued an outbreak alert following a surge in acute hemorrhagic conjunctivitis (AHC) cases along the Kenyan coast. Our investigations identified coxsackievirus A24 variant (CV-A24v) as the causative agent. In this study, we developed a novel whole genome sequencing assay for CV-A24v, and used it to recover three near complete genomes from the 2024 AHC outbreak in Kenya. This method will support future studies on CV-A24v genomic epidemiology and evolution across Kenya and beyond. In January 2024, an outbreak of acute hemorrhagic conjunctivitis (AHC) along the Kenyan coast prompted an alert from the Ministry of Health. AHC is characterized by the sudden onset of painful, swollen, and red eyes, often with subconjunctival haemorrhage and a foreign body sensation. Our investigations identified coxsackievirus A24 variant (CA24v) as the causative agent. To characterize the diversity of the circulating strains, we developed a whole-genome sequencing protocol. This approach leverages tiled amplicon sequencing, wherein the viral genome is amplified in overlapping amplicons and subsequently reassembled to generate consensus sequences. We successfully recovered near-complete genomes from three clinical samples collected during the outbreak. This protocol enables rapid and cost-effective genomic characterization of CA24v, particularly in resource-limited settings. Our protocol lays the groundwork for improved surveillance of CA24v in Kenya and beyond. eng
