{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:11:27Z","timestamp":1772169087320,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.24183.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000}}],"reference-count":22,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"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":["GrantOXF-FDG01"],"award-info":[{"award-number":["GrantOXF-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"]}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>In January 2024, the Kenya Ministry of Health issued an outbreak alert following a surge in acute hemorrhagic conjunctivitis (AHC) cases along the Kenyan coast. Our investigations identified coxsackievirus A24 variant (CV-A24v) as the causative agent. In this study, we developed a novel whole genome sequencing assay for CV-A24v, and used it to recover three near complete genomes from the 2024 AHC outbreak in Kenya. This method will support future studies on CV-A24v genomic epidemiology and evolution across Kenya and beyond.<\/ns3:p>","DOI":"10.12688\/wellcomeopenres.24183.2","type":"journal-article","created":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T09:40:08Z","timestamp":1759743608000},"page":"316","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Coxsackievirus A24 variant whole genome sequencing from clinical samples using a three overlapping amplicons strategy"],"prefix":"10.12688","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2398-6717","authenticated-orcid":false,"given":"John 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Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T11:34:12Z","timestamp":1768390452000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,6]]},"references-count":22,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.24183.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/wellcomeopenres.24183.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r136393","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r135507","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r135120","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r136393","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r135120","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.27491.r135507","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,6]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.26675.r125724, Peter van Heusden, South African National Bioinformatics Institute, University of the Western Cape Faculty of Natural Science (Ringgold ID: 274799), Bellville, Western Cape, 14 Aug 2025, version 1, 2 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v1#referee-response-125724","order":0,"name":"referee-response-125724","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>John Morobe<\/b>; \n<i>Posted: 10 Sep 2025<\/i>;  &nbsp;The &quot;laboratory optimization&quot; involved in selecting the final 6 primers was not explained. The sequence numbers used in the multiple sequence alignment used for primer design were also not specified.  \n<b>Our response:<\/b> &nbsp;Primer design was performed using Primal Scheme inputting all 119 complete CV-A24v genome sequences available on GenBank database as of March 2024. This was following a multiple sequence alignment (MSA). Laboratory optimization involved iterative testing of various primer pairs to determine their target region amplification success across a panel of CV-A24v-positive samples with varied viral loads. The final three primers pairs selected were those showing:  Consistent amplification across CV-A24v isolates.  Expected amplicon size following gel electrophoresis. Primer-pair positioning to maximize genome coverage.  These details have now been added in the methods section of the manuscript. &nbsp;  Details of base calling were omitted.  \n<b>Our response:<\/b> Thanks for pointing this out. In this protocol, basecalling &nbsp;was automatically performed on the Oxford Nanopore GridION platform following sequencing using Guppy v6.5.7 under high-accuracy mode. These details have now been included in the Methods section of the updated manuscript. &nbsp;  The link https:\/\/github.com\/kwtrp-peo\/viralphyl leads to a 404 indicating either a missing or private Github repository.  Our response: We apologize for the problem in accessing the link. The repository has now been made publicly accessible and the link is provided in the revised manuscript should work fine. &nbsp;  Versions of Guppyplex and MiniMap2 are omitted and Guppyplex is not cited.  Our response: &nbsp;The version of the tools have now been added to the Methods section. ARTIC&nbsp; guppyplex v1.6.2 and Minimap2-v2.30 Additionally, full details of the tools used in the assembly and their respective versions are available on the ViralPhyl GitHub repository. &nbsp;  Most importantly, however, a BED file of the primers is not provided. PHA4GE provides draft guidance on what is expected in a primer scheme specification and at least the reference.fasta and primer.bed as per that guidance should be included: https:\/\/github.com\/pha4ge\/primer-schemes?tab=readme-ov-file#scheme-specification  Our response: The BED file of the primers and reference used in assembly is provided on the viralphyl GitHub repository https:\/\/github.com\/kwtrp-peo\/viralphyl\/tree\/main\/primerschemes\/cva-24\/V1.2.0","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2#referee-comment-6233","order":1,"name":"referee-comment-6233","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.27491.r135120, Sanjay Tikute, ICMR- National Institute of Virology, Pune, 25 Oct 2025, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2#referee-response-135120","order":2,"name":"referee-response-135120","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.27491.r135507, Charles Patrick Mcclure, University of Nottingham, Nottingham, England, 28 Oct 2025, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2#referee-response-135507","order":3,"name":"referee-response-135507","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.27491.r136393, Jake D'Addiego, UK Health Security Agency, Salisbury, 06 Nov 2025, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-316\/v2#referee-response-136393","order":4,"name":"referee-response-136393","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [226002]; The Rockefeller Foundation [OXF-FDG01]; 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":5,"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"}]}}