# Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024

## TL;DR

A 2024 outbreak of red eye disease in Kenya was likely caused by coxsackievirus A24 variant, identified using metagenomic sequencing.

## Contribution

The study identifies coxsackievirus A24 variant as the likely cause of an AHC outbreak in Kenya using metagenomic sequencing.

## Key findings

- Coxsackievirus A24 variant (CA24v) was detected in three out of 13 patient samples.
- Phylogenetic analysis showed CA24v strains were closely related to genotype IV.
- Metagenomic sequencing proved effective in identifying the causative agent of the outbreak.

## Abstract

In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as “red eye” disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.

Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.

Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CA24v detections were confirmed by both CA24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CA24v genotype IV.

The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.

In early 2024, there was a significant increase in cases of acute hemorrhagic conjunctivitis (AHC), commonly known as "red eye" or “pink eye’ disease, in coastal Kenya, which led to the Ministry of Health issuing an outbreak alert. To understand the cause of this outbreak, we collected eye swabs from 13 patients at an eye clinic in Mombasa City, coastal Kenya. Initial testing of these samples was performed by checking for growth of pathogenic bacteria, and presence of a commonly known viral agent of AHC, adenovirus, using a polymerase chain reaction. The results showed no presence of harmful bacteria in the samples, and all tested negative for adenovirus. However, on further analysis of these samples by characterizing all non-human genetic material in the samples using an approach known as metagenomic sequencing, we detected the presence coxsackievirus A24 variant (CA24v) genetic material, a well-recognized cause of AHC, in three patients. The presence of this virus in the samples was confirmed through its specific in-house molecular test and a second genetic analysis approach. The CA24v strains detected in the samples were determined to be closely related to a known CA24v genotype assigned IV. Our findings suggest that the AHC disease outbreak observed in coastal Kenya in early 2024 was likely caused by CA24v. We highlight the usefulness of metagenomic sequencing as a tool for identifying the causes of new disease outbreaks, crucial for public health responses.