We developed a whole genome sequencing assay for coxsackievirus A24 variant (CA24v), a major cause of acute hemorrhagic conjunctivitis, and used it to recover three near complete genomes from the 2024 CA24v outbreak in Kenya. This assay will support studies on CA24v genomic epidemiology and evolution across Africa.

The authors have declared no competing interest.

Funding for this work is from a Wellcome (grant no. 226002/A/22/Z), The Rockefeller Foundation (Grant OXF-FDG01), and National Institute of Health and Care Research (grant. NIHR156467).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

This study/analysis was reviewed and approved by KEMRI Scientific Ethics Review Unit (SERU) Committee based in Nairobi, Kenya (Protocol #: KEMRI/SERU/CGMR-C/304/4894).

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

The genome sequences reported in this work are available in GenBank under accessions PQ683184 - PQ683186. The raw sequencing reads are available in NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1193512.