{ "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.", "abstract_shown": true, "affiliations": [ "Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya", "The Open University, Milton Keynes, United Kingdom", "University of California, San Francisco, United States of America", "Department of Genetics, University of Cambridge, Cambridge, United Kingdom", "The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology, Research (SBIDER), University of Warwick, Coventry, United Kingdom", "Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom", "School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia", "School of Public Health, Pwani University, Kilifi, Kenya" ], "article_type": "Research Article", "arxiv": null, "author_total": 14, "authors": [ { "affs": [ 0 ], "name": "John Mwita Morobe" }, { "affs": [ 1 ], "name": "Edidah M. Ong’era" }, { "affs": [ 2 ], "name": "Arnold W. Lambisia" }, { "affs": [ 3 ], "name": "Samuel O. Odoyo" }, { "affs": [ 4 ], "name": "Martin Mutunga" }, { "affs": [ 5 ], "name": "Esther N. Katama" }, { "affs": [ 6 ], "name": "Robinson Cheruiyot" }, { "affs": [ 7 ], "name": "Joyce U. Nyiro" }, { "name": "Everlyn Kamau" }, { "name": "Charlotte J. Houldcroft" }, { "name": "Matt Keeling" }, { "name": "Katherine Gallagher" }, { "name": "Edward C. Holmes" }, { "name": "Charles N. Agoti" } ], "bibtex": "https://research.draconitic.com/paper/4agq075t47vfs.bib", "cited_by": 0, "doi": "10.1371/journal.ppat.1014589", "fulltext_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014589", "id": "4agq075t47vfs", "issns": [ "1553-7374" ], "landing_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014589", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "2731|Ocular Infections and Treatments" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Sequencing techniques/Nucleotide sequencing" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Medicine and health sciences/Epidemiology" ], [ "plos", "/Medicine and health sciences/Epidemiology/Disease surveillance/Infectious disease surveillance" ], [ "plos", "/Medicine and health sciences/Medical conditions/Infectious diseases/Infectious disease control/Infectious disease surveillance" ], [ "plos", "/People and places/Geographical locations/Africa" ], [ "plos", "/People and places/Geographical locations/Africa/Kenya" ], [ "plos", "/People and places/Geographical locations/Asia" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/Nucleotide sequencing" ] ], "openalex": "W7213259025", "pdf_url": "https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1014589&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-15", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/4agq075t47vfs.ris", "sources": [ { "first_seen": "2026-10-30T12:17:49Z", "native_id": "10.1371/journal.ppat.1014589", "source": "plos", "url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014589" } ], "subjects": [ { "field": "biology", "origin": "plos:evolutionary biology", "subfield": "evolutionary-biology" }, { "field": "biology", "origin": "plos:genomics", "subfield": "genetics-genomics" }, { "field": "medicine", "origin": "plos:epidemiology", "subfield": "epidemiology-public-health" } ], "title": "Genomic epidemiology of coxsackievirus A24 variant during the 2024 acute hemorrhagic conjunctivitis outbreak in Coastal Kenya", "title_text": "Genomic epidemiology of coxsackievirus A24 variant during the 2024 acute hemorrhagic conjunctivitis outbreak in Coastal Kenya", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:49Z", "url": "https://research.draconitic.com/paper/4agq075t47vfs", "venue": "PLOS Pathogens", "versions": [] }