Genomic epidemiology of coxsackievirus A24 variant during the 2024 acute hemorrhagic conjunctivitis outbreak in Coastal Kenya
8 affiliations
- 1Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- 2The Open University, Milton Keynes, United Kingdom
- 3University of California, San Francisco, United States of America
- 4Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- 5The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology, Research (SBIDER), University of Warwick, Coventry, United Kingdom
- 6Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- 7School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- 8School of Public Health, Pwani University, Kilifi, Kenya
Abstract
Several African countries experienced a surge in acute hemorrhagic conjunctivitis (AHC) cases in 2024. Investigations in Kenya, Mayotte (an Indian Ocean island) and Tanzania identified coxsackievirus A24 variant (CVA24v) as the causative agent. To date, however, limited genomic data exist to elucidate the sources, epidemiology, and evolution of CVA24v in Africa. We generated 245 CVA24v genomes from samples collected between January and September 2024 in coastal Kenya, representing the largest outbreak CVA24v genomic data set available globally. Phylogenetic analysis showed that these viruses belonged to genotype IV, falling into two major clusters that differed by 52 nucleotide and five amino acid changes, and with an intra-species recombination event involving another enterovirus in the 3Dpol gene. Notably, the Kenyan sequences clustered closely with contemporaneous Africa (2024) sequences, specifically Mayotte and Malawi, reflecting a regionally connected CVA24v outbreak, but were distinct from those sampled previously in Asia in 2023, with phylodynamic analysis revealing that the Most Recent Common Ancestor of Kenyan sequences existed between June and October 2023. In summary, this study provides the first detailed genomic analysis of CVA24v from Africa to inform future surveillance and control strategies. Author summary: Acute hemorrhagic conjunctivitis (AHC) is a highly contagious eye disease that can cause explosive outbreaks and widespread morbidity, yet its viral drivers remain poorly understood in many regions, especially Africa. In 2024, coastal Kenya experienced a major AHC outbreak caused by coxsackievirus A24 variant (CVA24v). Using samples collected through routine disease surveillance and outbreak response activities, we generated the largest collection of CVA24v genomes from a single African setting. Our analyses show that the 2024 Kenyan outbreak was driven by two closely related viral lineages within genotype IV that have a history of recent intra-species recombination and were linked to viruses circulating in Eastern and Southern Africa and nearby Indian Ocean islands. These viruses were genetically different from those causing outbreaks in Asia in the preceding months, despite both regions experiencing near concurrent outbreaks, suggesting that other factors such as waning population immunity and favorable environmental conditions may play a role in driving new epidemics. Phylogenetic and phylodynamic analyses revealed an epidemiological pattern of short, intense epidemic waves separated by extended periods of low-level undetected transmission. Together, these findings highlight the importance of sustained genomic surveillance to understand CVA24v transmission, evolution, and outbreak emergence.
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BibTeX
@article{morobe2026genomic,
title = {{Genomic epidemiology of coxsackievirus A24 variant during the 2024 acute hemorrhagic conjunctivitis outbreak in Coastal Kenya}},
author = {John Mwita Morobe and Edidah M. Ong’era and Arnold W. Lambisia and Samuel O. Odoyo and Martin Mutunga and Esther N. Katama and Robinson Cheruiyot and Joyce U. Nyiro and Everlyn Kamau and Charlotte J. Houldcroft and Matt Keeling and Katherine Gallagher and Edward C. Holmes and Charles N. Agoti},
journal = {PLOS Pathogens},
year = {2026},
month = sep,
doi = {10.1371/journal.ppat.1014589},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014589},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genomic epidemiology of coxsackievirus A24 variant during the 2024 acute hemorrhagic conjunctivitis outbreak in Coastal Kenya
AU - John Mwita Morobe
AU - Edidah M. Ong’era
AU - Arnold W. Lambisia
AU - Samuel O. Odoyo
AU - Martin Mutunga
AU - Esther N. Katama
AU - Robinson Cheruiyot
AU - Joyce U. Nyiro
AU - Everlyn Kamau
AU - Charlotte J. Houldcroft
AU - Matt Keeling
AU - Katherine Gallagher
AU - Edward C. Holmes
AU - Charles N. Agoti
PY - 2026
DA - 2026/09/15
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014589
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014589
AB - Several African countries experienced a surge in acute hemorrhagic conjunctivitis (AHC) cases in 2024. Investigations in Kenya, Mayotte (an Indian Ocean island) and Tanzania identified coxsackievirus A24 variant (CVA24v) as the causative agent. To date, however, limited genomic data exist to elucidate the sources, epidemiology, and evolution of CVA24v in Africa. We generated 245 CVA24v genomes from samples collected between January and September 2024 in coastal Kenya, representing the largest outbreak CVA24v genomic data set available globally. Phylogenetic analysis showed that these viruses belonged to genotype IV, falling into two major clusters that differed by 52 nucleotide and five amino acid changes, and with an intra-species recombination event involving another enterovirus in the 3Dpol gene. Notably, the Kenyan sequences clustered closely with contemporaneous Africa (2024) sequences, specifically Mayotte and Malawi, reflecting a regionally connected CVA24v outbreak, but were distinct from those sampled previously in Asia in 2023, with phylodynamic analysis revealing that the Most Recent Common Ancestor of Kenyan sequences existed between June and October 2023. In summary, this study provides the first detailed genomic analysis of CVA24v from Africa to inform future surveillance and control strategies. Author summary: Acute hemorrhagic conjunctivitis (AHC) is a highly contagious eye disease that can cause explosive outbreaks and widespread morbidity, yet its viral drivers remain poorly understood in many regions, especially Africa. In 2024, coastal Kenya experienced a major AHC outbreak caused by coxsackievirus A24 variant (CVA24v). Using samples collected through routine disease surveillance and outbreak response activities, we generated the largest collection of CVA24v genomes from a single African setting. Our analyses show that the 2024 Kenyan outbreak was driven by two closely related viral lineages within genotype IV that have a history of recent intra-species recombination and were linked to viruses circulating in Eastern and Southern Africa and nearby Indian Ocean islands. These viruses were genetically different from those causing outbreaks in Asia in the preceding months, despite both regions experiencing near concurrent outbreaks, suggesting that other factors such as waning population immunity and favorable environmental conditions may play a role in driving new epidemics. Phylogenetic and phylodynamic analyses revealed an epidemiological pattern of short, intense epidemic waves separated by extended periods of low-level undetected transmission. Together, these findings highlight the importance of sustained genomic surveillance to understand CVA24v transmission, evolution, and outbreak emergence.
SN - 1553-7374
ER -