{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T07:13:35Z","timestamp":1782458015771,"version":"3.54.5"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.23522.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000}}],"reference-count":57,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["226002"],"award-info":[{"award-number":["226002"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["OXF-FDG01"],"award-info":[{"award-number":["OXF-FDG01"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Health and Care Research","award":["NIHR156467"],"award-info":[{"award-number":["NIHR156467"]}]},{"name":"Cambridge-Africa ALBORADA Research Fund"}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>Background In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as \u201cred eye\u201d disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak. Methods 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. Results 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. CV-A24v detections were confirmed by both CV-A24v 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 CV-A24v genotype IV. Conclusion 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.<\/ns3:p>","DOI":"10.12688\/wellcomeopenres.23522.2","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T05:05:31Z","timestamp":1743397531000},"page":"28","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024"],"prefix":"10.12688","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5312-0960","authenticated-orcid":false,"given":"Arnold W.","family":"Lambisia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2398-6717","authenticated-orcid":false,"given":"John","family":"Mwita Morobe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edidah","family":"Moraa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salim","family":"Mwarumba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredrick","family":"K.N. Korir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raila","family":"Seif Athman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Kiptui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7655-3416","authenticated-orcid":false,"given":"Micheal","family":"Mbee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelly","family":"Mugo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Amoth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Penny","family":"Muange","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"J. Houldcroft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edwine","family":"Barasa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Mwangangi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9640-7371","authenticated-orcid":false,"given":"George","family":"Githinji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":false,"given":"Edward","family":"C. Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynette","family":"Isabella Ochola-Oyier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2160-567X","authenticated-orcid":false,"given":"Charles","family":"N. Agoti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"628-30","DOI":"10.1136\/bjo.54.9.628","article-title":"Unusual type of epidemic conjunctivitis in Ghana.","volume":"54","author":"S Chatterjee","year":"1970","journal-title":"Br J Ophthalmol."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"692-3","DOI":"10.1136\/bjo.57.9.692","article-title":"Epidemic haemorrhagic conjunctivitis in Ghana. Further observations.","volume":"57","author":"C Quarcoopome","year":"1973","journal-title":"Br J Ophthalmol."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"533-44","DOI":"10.1093\/oxfordjournals.aje.a112191","article-title":"Serosurvey for \"Acute Hemorrhagic Conjunctivitis\" virus (Enterovirus 70) antibodies in the Southeastern United States, with review of the literature and some epidemiologic implications.","volume":"102","author":"J Hierholzer","year":"1975","journal-title":"Am J Epidemiol."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"368-378","DOI":"10.1017\/S0950268816002338","article-title":"Dynamic modelling of strategies for the control of Acute Haemorrhagic Conjunctivitis outbreaks in schools in Changsha, China (2004-2015).","volume":"145","author":"S Chen","year":"2017","journal-title":"Epidemiol Infect."},{"key":"ref-5","first-page":"173-8","article-title":"Acute Hemorrhagic Conjunctivitis.","volume":"45","author":"P Wright","year":"1992","journal-title":"Am Fam Physician."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"168-170","DOI":"10.3201\/eid2401.170916","article-title":"Costs of conjunctivitis outbreak, Reunion Island, France.","volume":"24","author":"L Filleul","year":"2018","journal-title":"Emerg Infect Dis."},{"key":"ref-7","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph191811723","article-title":"Appropriateness of antibiotic prescribing for acute conjunctivitis: a cross-sectional study at a specialist eye hospital in Ghana, 2021.","volume":"19","author":"P Hope","year":"2022","journal-title":"Int J Environ Res Public Health."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"1953-61","DOI":"10.1185\/03007990903038269","article-title":"Acute conjunctivitis: truth and misconceptions.","volume":"25","author":"T O'Brien","year":"2009","journal-title":"Curr Med Res Opin."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"869-73","DOI":"10.1136\/bjo.70.11.869","article-title":"A recent epidemic of Coxsackie virus type A24 Acute Haemorrhagic Conjunctivitis in Singapore.","volume":"70","author":"M Yin-Murphy","year":"1986","journal-title":"Br J Ophthalmol."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"242-5","DOI":"10.4314\/eajph.v7i3.64735","article-title":"Understanding of Acute Hemorrhagic Conjunctivitis (AHC) epidemics and outbreaks of Paederus spp keratoconjunctivitis, periorbital oedema (\"Nairobi red eyes\") and dermatitis.","volume":"7","author":"L Mbonile","year":"2010","journal-title":"East Afr J Public Health."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"1721-9","DOI":"10.1001\/jama.2013.280318","article-title":"Conjunctivitis: a systematic review of diagnosis and treatment.","volume":"310","author":"A Azari","year":"2013","journal-title":"JAMA."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"1140-1144","DOI":"10.1001\/jamaophthalmol.2023.4785","article-title":"Pathogen surveillance for acute infectious conjunctivitis.","volume":"141","author":"E Tsui","year":"2023","journal-title":"JAMA Ophthalmol."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"595-598","DOI":"10.4269\/ajtmh.22-0600","article-title":"Viruses associated with acute conjunctivitis in Vanuatu.","volume":"108","author":"K Johnson","year":"2023","journal-title":"Am J Trop Med Hyg."},{"key":"ref-14","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2022.105318","article-title":"Deep sequencing analysis of clinical samples from patients with acute infectious conjunctivitis during the COVID-19 delta surge in Madurai, India.","volume":"157","author":"P Lalitha","year":"2022","journal-title":"J Clin Virol."},{"key":"ref-15","first-page":"632-4","article-title":"Acute Hemorrhagic Conjunctivitis outbreak caused by Coxsackievirus A24--Puerto Rico, 2003.","volume":"53","year":"2004","journal-title":"MMWR Morb Mortal Wkly Rep."},{"key":"ref-16","first-page":"245-6","article-title":"Acute Hemorrhagic Conjunctivitis caused by coxsackievirus A24--Caribbean.","volume":"36","year":"1987","journal-title":"MMWR Morb Mortal Wkly Rep."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"1283-9","DOI":"10.1001\/jama.249.10.1283","article-title":"Acute Hemorrhagic Conjunctivitis investigation of a large-scale community outbreak in Dade County, Florida.","volume":"249","author":"P Patriarca","year":"1983","journal-title":"JAMA."},{"key":"ref-18","doi-asserted-by":"publisher","DOI":"10.1097\/coa.0000000000000009","article-title":"Apollo rising: acute conjunctivitis outbreak in India, 2022.","volume":"2","author":"N Prajna","year":"2023","journal-title":"Cornea Open."},{"key":"ref-19","doi-asserted-by":"publisher","first-page":"676","DOI":"10.3390\/v15030676","article-title":"Viral conjunctivitis.","volume":"15","author":"T Muto","year":"2023","journal-title":"Viruses."},{"key":"ref-20","article-title":"Viral conjunctivitis.","author":"D Solano","year":"2024"},{"key":"ref-21","doi-asserted-by":"publisher","first-page":"24-26","DOI":"10.31729\/jnma.8391","article-title":"Acute conjunctivitis among patients visiting the outpatient department of ophthalmology in a tertiary care centre.","volume":"62","author":"R Shrestha","year":"2024","journal-title":"JNMA J Nepal Med Assoc."},{"key":"ref-22","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2024.107133","article-title":"Coxsackievirus A24 causing acute conjunctivitis in a 2023 outbreak in Vietnam.","volume":"146","author":"H Tran","year":"2024","journal-title":"Int J Infect Dis."},{"key":"ref-23","doi-asserted-by":"publisher","DOI":"10.1101\/2023.10.11.23296878","article-title":"Genomic insights into the 2023 outbreak of Acute Hemorrhagic Conjunctivitis in Pakistan: identification of Coxsackievirus A24 variant through next generation sequencing.","author":"S Haider","year":"2023","journal-title":"medRxiv."},{"key":"ref-24","doi-asserted-by":"publisher","DOI":"10.1101\/2024.04.16.24305920","article-title":"Investigation of the causative pathogen in the 2023 conjunctivitis outbreak of Nepal using unbiased metagenomic next generation sequencing.","author":"E Shrestha","year":"2024","journal-title":"medRxiv."},{"key":"ref-25","doi-asserted-by":"publisher","first-page":"228-39","DOI":"10.1002\/jmv.10382","article-title":"Rapid and quantitative detection of human adenovirus DNA by real-time PCR.","volume":"70","author":"A Heim","year":"2003","journal-title":"J Med Virol."},{"key":"ref-26","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-016-0580-9","article-title":"Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens.","volume":"13","author":"A Nguyen","year":"2016","journal-title":"Virol J."},{"key":"ref-27","doi-asserted-by":"publisher","first-page":"227-239","DOI":"10.1016\/j.ijid.2022.10.007","article-title":"Evolutionary phylogeography reveals novel genotypes of Coxsackievirus A24 variant and updates the spatiotemporal dynamics in the population with Acute Hemorrhagic Conjunctivitis.","volume":"124","author":"P Chen","year":"2022","journal-title":"Int J Infect Dis."},{"key":"ref-28","doi-asserted-by":"publisher","first-page":"89-94","DOI":"10.1016\/j.jviromet.2007.01.009","article-title":"Rapid diagnosis of Acute Hemorrhagic Conjunctivitis due to Coxsackievirus A24 variant by real-time one-step RT-PCR.","volume":"142","author":"N L\u00e9v\u00eaque","year":"2007","journal-title":"J Virol Methods."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"128","DOI":"10.12688\/wellcomeopenres.14836.1","article-title":"Human Rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015\u20132016, observed through outpatient surveillance [version 1; peer review: 2 approved].","volume":"3","author":"J Morobe","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref-30","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.29.579666","article-title":"CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis.","author":"S Simmonds","year":"2024","journal-title":"bioRxiv."},{"key":"ref-31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.","volume":"20","author":"N Grubaugh","year":"2019","journal-title":"Genome Biol."},{"key":"ref-32","doi-asserted-by":"publisher","first-page":"660","DOI":"10.3390\/pathogens9080660","article-title":"Epidemiological trends of five common diarrhea-associated enteric viruses pre- and post-rotavirus vaccine introduction in Coastal Kenya.","volume":"9","author":"A Lambisia","year":"2020","journal-title":"Pathogens."},{"key":"ref-33","article-title":"Coast on alert: 'Red eye' disease spreads, prompting caution and care.","author":"P Okumu","year":"2024"},{"key":"ref-34","doi-asserted-by":"publisher","first-page":"119-27","DOI":"10.1159\/000149850","article-title":"Enterovirus etiology of the 1970 Singapore epidemic of acute conjunctivitis.","volume":"4","author":"R Mirkovic","year":"1974","journal-title":"Intervirology."},{"key":"ref-35","doi-asserted-by":"publisher","first-page":"1187-1198","DOI":"10.1093\/oxfordjournals.aje.a115447","article-title":"An epidemic of Acute Hemorrhagic Conjunctivitis in American Samoa caused by Coxsackievirus A24 variant.","volume":"130","author":"L Sawyer","year":"1989","journal-title":"Am J Epidemiol."},{"key":"ref-36","doi-asserted-by":"publisher","first-page":"323-7","DOI":"10.1016\/j.jcv.2008.07.017","article-title":"Molecular characterization of a Coxsackievirus A24 variant that caused an outbreak of Acute Haemorrhagic Conjunctivitis in Spain, 2004.","volume":"43","author":"M Cabrerizo","year":"2008","journal-title":"J Clin Virol."},{"key":"ref-37","first-page":"878-86","article-title":"Epidemic Acute Haemorrhagic Conjunctivitis due to Coxsackie virus A24 variant in Ghana.","volume":"67","author":"J Brandful","year":"1990","journal-title":"East Afr Med J."},{"key":"ref-38","doi-asserted-by":"publisher","DOI":"10.2807\/ese.17.22.20185-en","article-title":"2012 outbreak of Acute Haemorrhagic Conjunctivitis in Indian Ocean Islands: identification of Coxsackievirus A24 in a returned traveller.","volume":"17","author":"C Aubry","year":"2012","journal-title":"Euro Surveill."},{"key":"ref-39","doi-asserted-by":"publisher","first-page":"1085-92","DOI":"10.2147\/OPTH.S81386","article-title":"Virological and epidemiological analysis of Coxsackievirus A24 variant epidemic of Acute Hemorrhagic Conjunctivitis in Okinawa, Japan, in 2011.","volume":"9","author":"K Harada","year":"2015","journal-title":"Clin Ophthalmol."},{"key":"ref-40","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2016.21.26.30271","article-title":"A major outbreak of conjunctivitis caused by Coxsackievirus A24, R\u00e9union, January to April 2015.","volume":"21","author":"N Marguerite","year":"2016","journal-title":"Euro Surveill."},{"key":"ref-41","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-017-3007-9","article-title":"An outbreak of Acute Haemorrhagic Conjunctivitis associated with Coxsackievirus A24 variant in The Gambia, West Africa.","volume":"10","author":"S Burr","year":"2017","journal-title":"BMC Res Notes."},{"key":"ref-42","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-03987-1","article-title":"Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.","volume":"12","author":"M Phan","year":"2022","journal-title":"Sci Rep."},{"key":"ref-43","first-page":"1024","article-title":"Notes from the field: Acute Hemorrhagic Conjunctivitis outbreaks caused by Coxsackievirus A24v --- Uganda and southern Sudan, 2010.","volume":"59","year":"2010","journal-title":"MMWR Morb Mortal Wkly Rep."},{"key":"ref-44","article-title":"Acute Hemorrhagic Conjunctivitis outbreaks caused by Coxsakievirus A24 in three prisons, Gulu District, Uganda 2017","author":"L Nakiire","year":"2021"},{"key":"ref-45","article-title":"Red eyes outbreak in Tanzania, health ministry advises caution.","year":"2024"},{"key":"ref-46","article-title":"Red eye cases rise to 7,500 in 3 weeks.","author":"T Abet","year":"2024"},{"key":"ref-47","article-title":"Conjunctivitis: a contagious worrying epidemic in Bujumbura.","author":"C Ndayizeye","year":"2024"},{"key":"ref-48","article-title":"Malawi's viral conjunctivitis outbreak surges to 13,400 cases","year":"2024"},{"key":"ref-49","article-title":"On the Conjunctivitis Red Eye Outbreak in Zambia","year":"2024"},{"key":"ref-50","article-title":"South Sudan declares massive Red Eye outbreak on Uganda border","year":"2024"},{"key":"ref-51","article-title":"Confirmed cases of pink eye in eThekwini: good personal hygiene is key; do is seeking medical treatment, says KZN Health MEC, Ms Nomagugu Simelane","year":"2024"},{"key":"ref-52","article-title":"GenBank. Coxsackievirus A24 isolate KEN\/MSA\/15\/2024 partial polyprotein gene","author":"J Morobe","year":"2024"},{"key":"ref-53","article-title":"GenBank. polyprotein, partial [Coxsackievirus A24]","author":"J Morobe","year":"2024"},{"key":"ref-54","article-title":"GenBank. Coxsackievirus A24 isolate KEN\/MSA\/2\/2024 partial polyprotein gene, partial cds","author":"J Morobe","year":"2024"},{"key":"ref-55","article-title":"GenBank. polyprotein, partial [Coxsackievirus A24]","author":"J Morobe","year":"2024"},{"key":"ref-56","article-title":"GenBank. Genomic data for Coxsackievirus A24 isolate KEN\/MSA\/4\/2024 partial polyprotein gene, partial cds","author":"J Morobe","year":"2024"},{"key":"ref-57","article-title":"GenBank. polyprotein, partial [Coxsackievirus A24]","author":"J Morobe","year":"2024"}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,11]],"date-time":"2025-04-11T03:05:09Z","timestamp":1744340709000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,31]]},"references-count":57,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.23522.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/wellcomeopenres.23522.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.26498.r121520","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26498.r121519","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26498.r121522","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26498.r121520","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,31]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.26498.r121520, Anchal Thakur, Post Graduate Institute of Medical Education and Research, Chandigarh, 11 Apr 2025, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2#referee-response-121520","order":0,"name":"referee-response-121520","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.25943.r118292, Milton Mogotsi, Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, 24 Feb 2025, version 1, 4 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v1#referee-response-118292","order":1,"name":"referee-response-118292","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Arnold Wasike Lambisia<\/b>; \n<i>Posted: 21 Mar 2025<\/i>; \n<b>Comments:<\/b>  The study addresses a significant public health concern by identifying the potential causative agent of a recent AHC outbreak in Kenya, providing critical information for public health responses. Metagenomic sequencing allowed for the detection of CA24v, a pathogen not typically identified through conventional diagnostic methods. On the other hand, phylogenetic analysis offered valuable insights into the genetic relationship of the Kenyan strains with global CA24v variants, contributing to the understanding of the virus's epidemiology. \n<b>However, the study's conclusions are based on a small number of samples from a single geographic region, which may not fully represent the broader epidemiological landscape of AHC in Kenya<\/b>. Additionally, the \n<b>absence of detailed patient demographics and clinical data limits<\/b> the ability to assess the full impact of the outbreak and the virus's behaviour in different populations. Furthermore, the study relies on samples from symptomatic cases, which may not capture the full spectrum of infection, including asymptomatic or mild cases. &nbsp; Our response: Thanks for these comments. We agree that our study is indeed limited by the small number samples analysed coupled to lack of detailed clinical data. This to some extent limits our conclusions. However de do still think this analysus gives us some important first insight on the likely cause of the AHC outbreak we recorded. Follow up bigger and carefully designed epidemiological study analysing samples collected over a broader geographical area and from individiduals with and without these symptoms or of different clinical severity will be an important follow up to our findings here. Indeed we are already currently leveraging a study that was going on in the community at this time of the outbreak that collected serial samples and detailed clinical data from the same individual and ongoing analysis will identify the role of the virus in symptomatic and asymptomatic individuals and other potential pathogens involved in AHC.  Moreover, I have a concern regarding the absence of a positive control especially in the real-time PCR assay for adenovirus detection. We cannot conclude with certainty that the samples were negative for adenovirus when there was no positive control included. The negative results could be a results of PCR conditions, or issues with the primers, for instance. Also, the authors performed DNase treatment to digest all DNA in the samples prior cDNA and metagenomic sequencing. However, I am of the opinion that the authors should have processed the samples in parallel (DNase-treated and DNase-non treated) to confirm if indeed the samples were adenovirus negative considering that it is a DNA virus and it might have been removed by nuclease digestion. &nbsp; Our response: The adenovirus real-time PCR had a negative and positive control and these performed well. A statement has been added for the same. The metagenomics protocol may have missed any additional DNA virus but if it was actively replicating there is a good chance of detecting it. Actually our previous metagenomic work despite DNAase digestion we detected a number of DNA viruses e.g. bocavirus, herpesvirus 1 and 5, see in https:\/\/www.nature.com\/articles\/s41598-021-03987-1. Our assay has still a good chance of detecting DNA virus, probably because of their transcriptomes. None-the less this is still a nice suggestion for taking DNase-treated and DNase-non treated approach for future work although the latter has challange of alot of host DNA contamination.  My recommendations regarding this paper are that future studies should include a larger and more diverse sample set from multiple regions to provide a more comprehensive understanding of the outbreak's scope and the virus's epidemiology. Authors need to also incorporate detailed patient demographics, and clinical presentations which will be useful in assessing the impact of the outbreak and inform targeted public health interventions. &nbsp; Our response: We agree. Indeed we how have a study underway looking at a well followed cohort over time is currently evaluating the extent of CA24v locally during the same period and this will provide a much clearer picture on the impact of the outbreak in the community  I concur with the authors that long-term surveillance and studies are necessary to monitor the persistence and evolution of CA24v in the region, as well as to evaluate the effectiveness of public health measures implemented in response to the outbreak. While the findings are significant, providing valuable insights into the aetiology of the AHC outbreak in Kenya, I strongly recommend that the authors consider publishing these results as a brief report instead of a full research article due to the above-mentioned limitations such as small sample size and lack of demographic\/clinical data. &nbsp; Our response: Many thanks for the suggestion. We did consider this but the challange is that such a report ends up even trimming further the details we have provided which are already considered as limited and more information has been requested. Here we have really attempted providing all details that were within our disposal to enhance readers understanding.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2#referee-comment-6085","order":2,"name":"referee-comment-6085","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.25943.r118289, Sanjay Tikute, ICMR- National Institute of Virology, Pune, 24 Feb 2025, version 1, 4 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v1#referee-response-118289","order":3,"name":"referee-response-118289","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Arnold Wasike Lambisia<\/b>; \n<i>Posted: 21 Mar 2025<\/i>; 1. In abstract (result section) coxsackievirus A24 is written in short form as \u2018CV24v\u2019. Please change it and rewrite as \u201cCV-A24v\u201d. Also correct it in entire article. Our response: Thanks \u2013 This is now corrected  2. The outbreak was in the coastal area of Kenya. Therefore more population should be considered for the study. Thirteen patients is a very low number of study subjects. Our response: The samples were obtianed as part of an outbreak response initiative by the ministry of health. This was not a research study. In such scenarios a few purposively selected samples can be adequate to tease out the cause of the outbreak disease. This convience sampling appraoch is a limitation of the analysis we present. Indeed we have currently a larger molecular epidemiological study underway that will reinforce out findings here.  3. Clinical details or symptomatic conditions of all the patients should be included. Our response: Unfortunately more detailed symptom data of the cases we analysed are not available to us. As previously indicated , the samples were collected for outbreak response to determine the aetiology of AHC epidemic.The only symptom recorded from the patients was having a&nbsp; &quot;red eye&quot;\/ AHC.  4. In background after the word blurred vision the sign \u2018=\u2019 is added, please remove it. Our response: This has been removed  5. In study population paragraph, it is mentioned that after sample collection it was transported to KWTRP at ambient temperature which is not advisable. Our response: We agreed that this is not advisable. This may have affected the intergrity of the samples and moving forward we stress cold chain transport.  6.&nbsp; Metagenomic screening paragraph, the word \u2018incubating\u2019 is written as \u2018Incubating\u2019 remove capital and small one. Our response: This has been corrected  7. In abstract, in the result section, it is mentioned that VP4\/2 junction, please explain. Our response: The polyprotein has multiple gens which include the VP4 and VP2 so the primers target the VP4\/VP2 junction.  8. In metagenomics sequencing paragraph, it is mentioned that 3 samples mapped to RVA. After reanalyzing with specific primers all the samples were RVA negative. Add about the primers used and explain about negative results. &nbsp; Our response: The primers have been added to the methods section. Since the rotavirus reads in the metagenomic sequence output were very few and this was nt confirmed on PCR processing. We assume this may have been contaminants in the samples perharps in the sample processing steps.  9. The Ct values of the 3 samples ranged between 32.29 to 37.65, what was the positive control and its value. Our response: We did not have a positive control for CV-A24v at the time of running the assay. This was not a commercial kit.  10. In table number 1, it is shown that only 2 samples that is , sample 3 and sample 4 after blast hits to rotavirus. What about the third sample previously mentioned. Needs to specify. &nbsp; Our response: That was sample 13 shown in table 1","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2#referee-comment-6086","order":4,"name":"referee-comment-6086","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.25943.r118288, Savitri Sharma, Jhaveri Microbiology Center, Brien Holden Eye Research Centre (BHERC), L V Prasad Eye Institute (LVPEI), Hyderabad, Telangana, 26 Feb 2025, version 1, 4 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v1#referee-response-118288","order":5,"name":"referee-response-118288","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Arnold Wasike Lambisia<\/b>; \n<i>Posted: 21 Mar 2025<\/i>; 1.&nbsp;Please clarify whether different swabs were collected for different tests. It would be good to describe the sample collection method for each of the tests. &nbsp;  Our response: Thank you for the comment. We clarify that only ocular swabs were collected and these were used for all the laboratory analysis described; for cultures and nucleic acid analysis approaches that were used for the different molecular tests in the article.  2.&nbsp;\n<b>Methods-Bacterial culture:<\/b>&nbsp;The method adopted is inadequate in terms of incubation time which should be at least 48 hours. The method of identification of the bacteria has not been given. This lacunae may be noted as a limitation. &nbsp;  Our response: An incubation time of 18-24 hours was sufficient to identify the suspected pathogens and other bacteria known to cause \u201cred eye\u201d e.g., Staphylococcus and Streptococcus. The method of identification the bacteria is added in the methods.  3. Clinical data is completely missing. The number being small it should have been possible to describe the clinical features along with representative figures. Stage of the disease might have been variable in the patients that may explain why all cases were not positive for the virus.&nbsp; &nbsp; Our response: These were outbreak samples collected at one timepoint i.e when the individuals visited the clinic with \u201cred eye\u201d as the symptom no further clinicla data was provided to describe what stage of the infection the patients were in. We appreciate that this wa one of the limitations of the article and we follow up work with larger sample size underway.  The manuscript is well written.&nbsp; Our response: Thank you for a positive view of our work.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-28\/v2#referee-comment-6087","order":6,"name":"referee-comment-6087","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [226002]; The Rockefeller Foundation [OXF-FDG01]; Cambridge-Africa ALBORADA Research Fund, and National Institute of Health and Care Research [NIHR156467]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":7,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}