{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T07:09:01Z","timestamp":1793862541075,"version":"4.6.1"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012194","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,10,3]],"date-time":"2024-10-03T00:00:00Z","timestamp":1727913600000}}],"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2024,9,23]],"date-time":"2024-09-23T00:00:00Z","timestamp":1727049600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1116450"],"award-info":[{"award-number":["OPP1116450"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["K24 AI144048"],"award-info":[{"award-number":["K24 AI144048"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Experience America Research Grant from Fulbright Taiwan"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>While there has been significant progress in controlling falciparum malaria in the Lao People\u2019s Democratic Republic (PDR), sporadic cases persist in southern provinces where the extent and patterns of transmission remain largely unknown. To assess parasite transmission in this area, 53 <jats:italic>Plasmodium falciparum<\/jats:italic> (Pf) positive cases detected through active test and treat campaigns from December 2017 to November 2018 were sequenced, targeting 204 highly polymorphic amplicons. Two R packages, <jats:italic>MOIRE<\/jats:italic> and <jats:italic>Dcifer<\/jats:italic>, were applied to assess the multiplicity of infections (MOI), effective MOI (eMOI), within-host parasite relatedness, and between-host parasite relatedness (<jats:inline-formula id=\"ppat.1012194.e001\"><jats:alternatives><jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" id=\"ppat.1012194.e001g\" mimetype=\"image\" position=\"anchor\" xlink:href=\"info:doi\/10.1371\/journal.ppat.1012194.e001\" xlink:type=\"simple\"\/><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\" display=\"inline\" id=\"M1\"><mml:mover accent=\"true\"><mml:mrow><mml:mi>r<\/mml:mi><mml:mi>b<\/mml:mi><\/mml:mrow><mml:mo>^<\/mml:mo><\/mml:mover><\/mml:math><\/jats:alternatives><\/jats:inline-formula>). Genomic data were integrated with survey data to characterize the temporal and spatial structures of identified clusters. The positive cases were mainly captured during the focal test and treat campaign conducted in 2018, and in the Pathoomphone area, which had the highest test positivity and forest activity. About 30% of the cases were polyclonal infections, with over half of theses (63%) showing within-host relatedness greater than 0.6, suggesting that cotransmission rather than superinfection was primarily responsible for maintaining polyclonality. A large majority of cases (81%) were infected by parasites genetically linked to one or more other cases. We identified five genetically distinct clusters in forest fringe villages within the Pathoomphone district, characterized by a high degree of genetic relatedness between parasites (mean <jats:inline-formula id=\"ppat.1012194.e002\"><jats:alternatives><jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" id=\"ppat.1012194.e002g\" mimetype=\"image\" position=\"anchor\" xlink:href=\"info:doi\/10.1371\/journal.ppat.1012194.e002\" xlink:type=\"simple\"\/><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\" display=\"inline\" id=\"M2\"><mml:mover accent=\"true\"><mml:mrow><mml:mi>r<\/mml:mi><mml:mi>b<\/mml:mi><\/mml:mrow><mml:mo>^<\/mml:mo><\/mml:mover><\/mml:math><\/jats:alternatives><\/jats:inline-formula> = 0.8). Four smaller clusters of 2\u20133 cases linked Moonlapamok and Pathoomphone districts, with an average <jats:inline-formula id=\"ppat.1012194.e003\"><jats:alternatives><jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" id=\"ppat.1012194.e003g\" mimetype=\"image\" position=\"anchor\" xlink:href=\"info:doi\/10.1371\/journal.ppat.1012194.e003\" xlink:type=\"simple\"\/><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\" display=\"inline\" id=\"M3\"><mml:mover accent=\"true\"><mml:mrow><mml:mi>r<\/mml:mi><mml:mi>b<\/mml:mi><\/mml:mrow><mml:mo>^<\/mml:mo><\/mml:mover><\/mml:math><\/jats:alternatives><\/jats:inline-formula> of 0.6, suggesting cross-district transmission. Most of the clustered cases occurred within 20 km and 2 months of each other, consistent with focal transmission. Transmission clusters identified in this study confirm the role of ongoing focal parasite transmission occurring within the forest or forest-fringe in the highly mobile population.<\/jats:p>","DOI":"10.1371\/journal.ppat.1012194","type":"journal-article","created":{"date-parts":[[2024,9,23]],"date-time":"2024-09-23T17:36:30Z","timestamp":1727112990000},"page":"e1012194","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Genomic epidemiology demonstrates spatially clustered, local transmission of Plasmodium falciparum in forest-going populations in southern Lao PDR"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7936-1313","authenticated-orcid":true,"given":"Ying-An","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric Neubauer","family":"Vickers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andres","family":"Aranda-Diaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inna","family":"Gerlovina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francois","family":"Rerolle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Dantzer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bouasy","family":"Hongvanthong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiao-Han","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew A.","family":"Lover","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas J.","family":"Hathaway","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Bennett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0287-9111","authenticated-orcid":true,"given":"Bryan","family":"Greenhouse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,9,23]]},"reference":[{"key":"ppat.1012194.ref001","author":"WHO","year":"2023","journal-title":"Mekong Malaria Elimination: epidemiology summary, volume 21, January\u2013March 2023."},{"issue":"1","key":"ppat.1012194.ref002","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1038\/s41598-024-52115-2","article-title":"Malaria risk stratification 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