{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T04:28:36Z","timestamp":1789014516362,"version":"build-2803163510"},"reference-count":43,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T00:00:00Z","timestamp":1747353600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["SCHISTO_PERSIST_680088"],"award-info":[{"award-number":["SCHISTO_PERSIST_680088"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218492\/Z\/19\/Z"],"award-info":[{"award-number":["218492\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    Background Whole-genome sequencing (WGS) is now widely used in\n                    <ns3:italic>Schistosoma<\/ns3:italic>\n                    genomics. Whilst adult worms typically provide sufficient DNA for molecular analyses, their inaccessibility in live definitive hosts presents a challenge for population studies. Larval stages, such as miracidia can be collected non-invasively and preserved on Whatman FTA cards, however these samples typically yield low quantities of DNA and have high levels of contamination, particularly when obtained from stool samples. To counteract contamination, multiple washing steps prior to placement onto Whatman FTA cards can be performed, but this is labour-intensive and can limit the number of larvae collected. Methods Nanopore sequencing technologies includes an \u201cadaptive sampling\u201d feature, which enables selective enrichment or depletion of target DNA sequences during sequencing. In this study, we evaluated the potential of adaptive sampling to selectively enrich\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    DNA from both washed and unwashed larval stage miracidia. We used Kraken2 to characterise sample contamination and assessed sequencing breadth and depth of genome coverage to determine whether adaptive sampling could provide sufficient\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    DNA for WGS. Results and conclusion Our results demonstrate that washed samples contained a higher proportion of\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    DNA, validating the effectiveness of washing for contamination removal. However, adaptive sampling failed to generate sufficient\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    reads for effective WGS. These findings suggest that, at present, washing remains critical for maximising\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    DNA purity as adaptive sampling alone is insufficient for enrichment. Alternative enrichment strategies will be necessary to improve sequencing efficiency and data quality for\n                    <ns3:italic>S. mansoni<\/ns3:italic>\n                    WGS.\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.24094.1","type":"journal-article","created":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T10:25:12Z","timestamp":1747391112000},"page":"239","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["How useful is Nanopore adaptive sampling for sequencing Schistosoma mansoni miracidia?"],"prefix":"10.12688","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5247-7028","authenticated-orcid":false,"given":"Rivka M.","family":"Lim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas 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B.","family":"Pedersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8616-4919","authenticated-orcid":false,"given":"Joanne P.","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Poppy H.L.","family":"Lamberton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2025,5,16]]},"reference":[{"key":"ref-1","article-title":"Schistosomiasis factsheet"},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"2253-2264","DOI":"10.1016\/S0140-6736(13)61949-2","article-title":"Human schistosomiasis.","volume":"383","author":"D Colley","year":"2014","journal-title":"Lancet."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"646-652","DOI":"10.1016\/B978-0-12-809633-8.01187-0","article-title":"Propagule behavior and parasite 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Sequencing summary, taxonomic classification, and coverage metrics for Schistosoma mansoni miracidia samples using Nanopore adaptive sampling.","author":"R Lim","year":"2025","journal-title":"Zenodo."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T11:00:07Z","timestamp":1758020407000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,16]]},"references-count":43,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.24094.1","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123825","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123821","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123823","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123825","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123823","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26581.r123821","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,16]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.26581.r123825, Lucas Huggins, The University of Melbourne, Parville, 02 Jun 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-response-123825","order":0,"name":"referee-response-123825","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rivka Lim<\/b>; \n<i>Posted: 25 Jul 2025<\/i>; Thank you very much&nbsp;for your thorough and extremely helpful comments on the manuscript. I am working my way through the suggestions and will implement all that I can. Some of the suggestions will not be possible for me to carry out now as the lab work has completed but if this is the case I will add them as areas&nbsp;of further exploration\/ limitations in the discussion.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-comment-6182","order":1,"name":"referee-comment-6182","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.26581.r123823, Hanwen Yang, Biology, Saint Louis University College of Arts and Sciences, St. Louis, Missouri, 09 Jun 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-response-123823","order":2,"name":"referee-response-123823","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rivka Lim<\/b>; \n<i>Posted: 25 Jul 2025<\/i>; Thank you very much for taking the time to review this manuscript. The idea of pooling to samples is an excellent one and I will carry this new analysis and report the findings. Thank you again.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-comment-6183","order":3,"name":"referee-comment-6183","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.26581.r123821, Kaylee S. Herzog, University of Nebraska Medical Center, Omaha, Nebraska, 16 Jun 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-response-123821","order":4,"name":"referee-response-123821","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Rivka Lim<\/b>; \n<i>Posted: 25 Jul 2025<\/i>; Thank you very much for your comments, they&nbsp;are extremely helpful and I will incorporate&nbsp;the changes into the manuscript. &nbsp;Your point about whole genome amplification and the possibilty that it could have preferentially amplified off-target DNA is, of course correct and I will adapt the manuscript to reflect this possibility rather than stating definitively that there was no miracidium present. In hindsight, I wish&nbsp;I had carried out qPCR on a high-copy target prior to sequencing to ensure that the sample was positive&nbsp;for miracidia,&nbsp;but unfortunately this was not done.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-239\/v1#referee-comment-6184","order":5,"name":"referee-comment-6184","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [218492]; European Research Council [SCHISTO_PERSIST_680088]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":6,"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"}]}}