Detection of Coxsackievirus A24v during an acute haemorrhagic conjunctivitis outbreak in Dar es Salaam, Tanzania, January-February 2024

Abstract

Background In January 2024, an outbreak of acute viral conjunctivitis was declared in Dar es Salaam, Tanzania, following initial case clusters reported in December 2023 and continuing through February. Patients presented with red, itchy, and burning eyes, eyelid swelling, photophobia, and eye discharges. As the responsible pathogen had not been laboratory-identified, this study aimed to detect and characterize potential viral agents of the outbreak through an urgent outbreak response investigation. Methods Conjunctival swabs were collected from 25 suspected cases using a convenience sampling approach. Bacterial culture was performed on MacConkey and blood agar. Viral detection used a multiplex real-time RT-PCR targeting adenovirus, metapneumovirus, enterovirus (EV), and parainfluenza virus. All enterovirus-positive samples with a Ct value <30 (four samples) were selected for genomic sequencing on an Illumina MiSeq platform. Maximum-likelihood phylogenetic analysis was conducted with IQ-TREE. Results Nine of 25 samples (36%) were positive for enterovirus (EV) by real-time reverse transcription PCR. Genomic sequencing of the four eligible samples (Ct < 30) detected Coxsackievirus A24 variant (CVA24v) in two of four sequenced samples. Phylogenetic analysis showed that the Tanzanian outbreak sequences formed a clade with CVA24v strains from a concurrent 2024 outbreak in France/Mayotte and were closely related to recent sequences from East Africa and South America. Bacterial culture yielded no significant pathogens. Conclusion We detected enterovirus (EV) during an outbreak of acute hemorrhagic conjunctivitis in Tanzania. Of nine EV-positive samples, CVA24v genomes were reconstructed from genomic sequencing in two samples, with phylogenetic analysis placing Tanzania sequencences within a clade with sequences from France (Mayotte), Mexico, Brazil, and Uganda strains consistent with regional circulation. Given that sequencing was performed on only two samples, a causal role for CVA24v in this outbreak cannot be definitively established; however, these findings provide the first genomic evidence of CVA24v circulation in Tanzania and demonstrate the value of rapid genomic epidemiology for outbreak pathogen detection in resource-limited settings.