Coxsackievirus A24 variant whole genome sequencing from clinical samples using a three overlapping amplicons strategy.
Morobe JM., Odoyo S., Lambisia AW., Moraa E., Houldcroft CJ., Holmes EC., Githinji G., Agoti CN.
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.