# Coxsackievirus A24 variant whole genome sequencing from clinical samples using a three overlapping amplicons strategy

## TL;DR

Researchers developed a sequencing method to study the coxsackievirus A24 variant causing an eye disease outbreak in Kenya.

## Contribution

A novel whole-genome sequencing protocol for CA24v using overlapping amplicons was developed and applied to clinical samples.

## Key findings

- Three near-complete CA24v genomes were recovered from clinical samples during the 2024 outbreak.
- The amplicon-based sequencing approach is rapid, cost-effective, and suitable for resource-limited settings.
- The protocol supports genomic surveillance and evolutionary studies of CA24v in Kenya and beyond.

## Abstract

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 (CA24v) as the causative agent. In this study, we developed a whole genome sequencing assay for CA24v, and used it to recover three near complete genomes from the 2024 AHC outbreak in Kenya. This assay will support studies on CA24v 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.