{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T06:53:15Z","timestamp":1784357595140,"version":"3.55.0"},"update-to":[{"DOI":"10.1371\/journal.pntd.0010188","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T00:00:00Z","timestamp":1661817600000}}],"reference-count":108,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T00:00:00Z","timestamp":1660780800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["095778"],"award-info":[{"award-number":["095778"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>Populations within schistosomiasis control areas, especially those in Africa, are recommended to receive regular mass drug administration (MDA) with praziquantel (PZQ) as the main strategy for controlling the disease. The impact of PZQ treatment on schistosome genetics remains poorly understood, and is limited by a lack of high-resolution genetic data on the population structure of parasites within these control areas. We generated whole-genome sequence data from 174 individual miracidia collected from both children and adults from fishing communities on islands in Lake Victoria in Uganda that had received either annual or quarterly MDA with PZQ over four years, including samples collected immediately before and four weeks after treatment. Genome variation within and between samples was characterised and we investigated genomic signatures of natural selection acting on these populations that could be due to PZQ treatment. The parasite population on these islands was more diverse than found in nearby villages on the lake shore. We saw little or no genetic differentiation between villages, or between the groups of villages with different treatment intensity, but slightly higher genetic diversity within the pre-treatment compared to post-treatment parasite populations. We identified classes of genes significantly enriched within regions of the genome with evidence of recent positive selection among post-treatment and intensively treated parasite populations. The differential selection observed in post-treatment and pre-treatment parasite populations could be linked to any reduced susceptibility of parasites to praziquantel treatment.<\/jats:p>","DOI":"10.1371\/journal.pntd.0010188","type":"journal-article","created":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T17:57:49Z","timestamp":1660845469000},"page":"e0010188","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities"],"prefix":"10.1371","volume":"16","author":[{"given":"Tushabe John","family":"Vianney","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duncan J.","family":"Berger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen R.","family":"Doyle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geetha","family":"Sankaranarayanan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel","family":"Serubanja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prossy Kabuubi","family":"Nakawungu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fred","family":"Besigye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard E.","family":"Sanya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"Holroyd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona","family":"Allan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily L.","family":"Webb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison M.","family":"Elliott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5475-3583","authenticated-orcid":true,"given":"James A.","family":"Cotton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,18]]},"reference":[{"issue":"3","key":"pntd.0010188.ref001","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1017\/S0025727300022663","article-title":"The history of schistosomiasis research and policy for its control","volume":"20","author":"FR Sandbach","year":"1976","journal-title":"Med Hist"},{"issue":"7","key":"pntd.0010188.ref002","doi-asserted-by":"crossref","first-page":"e2865","DOI":"10.1371\/journal.pntd.0002865","article-title":"The global burden of disease study 2010: interpretation and implications for the neglected tropical diseases","volume":"8","author":"PJ Hotez","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"issue":"2","key":"pntd.0010188.ref003","doi-asserted-by":"crossref","first-page":"91","DOI":"10.2471\/BLT.06.030353","article-title":"Impact of a national helminth control programme on infection and morbidity in Ugandan schoolchildren","volume":"85","author":"NB Kabatereine","year":"2007","journal-title":"Bull World Health Organ"},{"issue":"10","key":"pntd.0010188.ref004","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1016\/j.ijpara.2011.06.002","article-title":"Schistosoma mansoni population structure and persistence after praziquantel treatment in two villages of Bahia, Brazil","volume":"41","author":"RE Blanton","year":"2011","journal-title":"Int J Parasitol"},{"issue":"4","key":"pntd.0010188.ref005","article-title":"Low Praziquantel Treatment Coverage for Schistosoma mansoni in Mayuge District, Uganda, Due to the Absence of Treatment Opportunities, Rather Than Systematic Non-Compliance","volume":"3","author":"M Adriko","year":"2018","journal-title":"Trop Med Infect Dis"},{"issue":"1","key":"pntd.0010188.ref006","article-title":"A Call for Systems Epidemiology to Tackle the Complexity of Schistosomiasis, Its Control, and Its Elimination.","volume":"4","author":"SJ Krauth","year":"2019","journal-title":"Trop Med Infect Dis"},{"issue":"10","key":"pntd.0010188.ref007","doi-asserted-by":"crossref","first-page":"e0005982","DOI":"10.1371\/journal.pntd.0005982","article-title":"Perceptions about interventions to control schistosomiasis among the Lake Victoria island communities of Koome, Uganda.","volume":"11","author":"RE Sanya","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0010188.ref008","unstructured":"Ending the neglect to attain the Sustainable Development Goals: a road map for neglected tropical diseases 2021\u221220302020."},{"issue":"9","key":"pntd.0010188.ref009","first-page":"1151","article-title":"Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration","volume":"63","author":"T Crellen","year":"2016","journal-title":"Clin Infect Dis"},{"issue":"4","key":"pntd.0010188.ref010","doi-asserted-by":"crossref","first-page":"ofaa091","DOI":"10.1093\/ofid\/ofaa091","article-title":"Does Intensive Treatment Select for Praziquantel Resistance in High-Transmission Settings? Parasitological Trends and Treatment Efficacy Within a Cluster-Randomized Trial.","volume":"7","author":"JV Tushabe","year":"2020","journal-title":"Open Forum Infect Dis."},{"issue":"3","key":"pntd.0010188.ref011","doi-asserted-by":"crossref","first-page":"e0009189","DOI":"10.1371\/journal.pntd.0009189","article-title":"Efficacy of praziquantel has been maintained over four decades (from 1977 to 2018): A systematic review and meta-analysis of factors influence its efficacy.","volume":"15","author":"M Fukushige","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"2","key":"pntd.0010188.ref012","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1016\/S1473-3099(16)30475-3","article-title":"Human schistosomiasis in the post mass drug administration era","volume":"17","author":"F Mutapi","year":"2017","journal-title":"Lancet Infect Dis"},{"issue":"12","key":"pntd.0010188.ref013","doi-asserted-by":"crossref","first-page":"e2596","DOI":"10.1371\/journal.pntd.0002596","article-title":"Praziquantel treatment decreases Schistosoma mansoni genetic diversity in experimental infections","volume":"7","author":"R Coeli","year":"2013","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref014","doi-asserted-by":"crossref","first-page":"61","DOI":"10.4269\/ajtmh.1995.53.61","article-title":"Short report: diminished susceptibility to praziquantel in a Senegal isolate of Schistosoma mansoni","volume":"53","author":"PG Fallon","year":"1995","journal-title":"Am J Trop Med Hyg"},{"issue":"8","key":"pntd.0010188.ref015","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.3109\/13880209.2014.970289","article-title":"Evaluation of a method for induction of praziquantel resistance in Schistosoma mansoni.","volume":"53","author":"WM Lotfy","year":"2015","journal-title":"Pharm Biol."},{"issue":"1","key":"pntd.0010188.ref016","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.molbiopara.2009.04.007","article-title":"Schistosoma mansoni P-glycoprotein levels increase in response to praziquantel exposure and correlate with reduced praziquantel susceptibility","volume":"167","author":"SM Messerli","year":"2009","journal-title":"Mol Biochem Parasitol"},{"key":"pntd.0010188.ref017","doi-asserted-by":"crossref","first-page":"594","DOI":"10.3389\/fmicb.2016.00594","article-title":"Morphological Characteristics of Schistosoma mansoni PZQ-Resistant and -Susceptible Strains Are Different in Presence of Praziquantel.","volume":"7","author":"A Pinto-Almeida","year":"2016","journal-title":"Front Microbiol"},{"issue":"4","key":"pntd.0010188.ref018","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.AME-0009-2019","article-title":"Population Structure and Dynamics of Helminthic Infection: Schistosomiasis.","volume":"7","author":"RE Blanton","year":"2019","journal-title":"Microbiol Spectr"},{"issue":"5","key":"pntd.0010188.ref019","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.02582-16","article-title":"Praziquantel for Schistosomiasis: Single-Drug Metabolism Revisited, Mode of Action, and Resistance","volume":"61","author":"N Vale","year":"2017","journal-title":"Antimicrob Agents Chemother"},{"issue":"49","key":"pntd.0010188.ref020","doi-asserted-by":"crossref","first-page":"18873","DOI":"10.1074\/jbc.AC119.011093","article-title":"The anthelmintic drug praziquantel activates a schistosome transient receptor potential channel","volume":"294","author":"SK Park","year":"2019","journal-title":"J Biol Chem"},{"issue":"625","key":"pntd.0010188.ref021","doi-asserted-by":"crossref","first-page":"eabj9114","DOI":"10.1126\/scitranslmed.abj9114","article-title":"Genetic analysis of praziquantel response in schistosome parasites implicates a transient receptor potential channel","volume":"13","author":"W Le Clec\u2019h","year":"2021","journal-title":"Sci Transl Med"},{"issue":"1_Suppl","key":"pntd.0010188.ref022","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4269\/ajtmh.19-0827","article-title":"Parasite Population Genetic Contributions to the Schistosomiasis Consortium for Operational Research and Evaluation within Sub-Saharan Africa","volume":"103","author":"JP Webster","year":"2020","journal-title":"Am J Trop Med Hyg"},{"issue":"12","key":"pntd.0010188.ref023","doi-asserted-by":"crossref","first-page":"e2561","DOI":"10.1371\/journal.pntd.0002561","article-title":"New insights into the molecular epidemiology and population genetics of Schistosoma mansoni in Ugandan pre-school children and mothers","volume":"7","author":"M Betson","year":"2013","journal-title":"PLoS Negl Trop Dis"},{"issue":"2","key":"pntd.0010188.ref024","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.actatropica.2012.08.009","article-title":"DNA \u2019barcoding\u2019 of Schistosoma mansoni across sub-Saharan Africa supports substantial within locality diversity and geographical separation of genotypes.","volume":"128","author":"BL Webster","year":"2013","journal-title":"Acta Trop"},{"key":"pntd.0010188.ref025","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1046\/j.1471-8278.2001.00042.x","article-title":"Isolation and characterization of polymorphic microsatellite markers in Schistosoma mansoni from Africa","volume":"1","author":"L Blair","year":"2001","journal-title":"Mol Ecol Notes"},{"key":"pntd.0010188.ref026","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1046\/j.1471-8278.2001.00053.x","article-title":"Microsatellite loci in the human blood fluke Schistosoma mansoni and their utility for other schistosome species","volume":"1","author":"J Curtis","year":"2001","journal-title":"Mol Ecol Notes"},{"issue":"7","key":"pntd.0010188.ref027","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1046\/j.1365-294x.2000.00939-4.x","article-title":"Isolation of microsatellite markers in the digenetic trematode Schistosoma mansoni from Guadeloupe island","volume":"9","author":"P Durand","year":"2000","journal-title":"Mol Ecol"},{"key":"pntd.0010188.ref028","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1111\/j.1471-8286.2007.02031.x","article-title":"Isolation and characterization of the first polymorphic microsatellite markers for Schistosoma haematobium and their application in multiplex reactions of larval stages","volume":"8","author":"R Golan","year":"2008","journal-title":"Mol Ecol Resour"},{"issue":"11","key":"pntd.0010188.ref029","doi-asserted-by":"crossref","first-page":"e340","DOI":"10.1371\/journal.pntd.0000340","article-title":"Population genetics of Schistosoma japonicum within the Philippines suggest high levels of transmission between humans and dogs","volume":"2","author":"JW Rudge","year":"2008","journal-title":"PLoS Negl Trop Dis"},{"issue":"2","key":"pntd.0010188.ref030","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.actatropica.2012.09.014","article-title":"Population genetic structure of Schistosoma mansoni and Schistosoma haematobium from across six sub-Saharan African countries: implications for epidemiology, evolution and control","volume":"128","author":"CM Gower","year":"2013","journal-title":"Acta Trop"},{"issue":"Pt 4","key":"pntd.0010188.ref031","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1017\/S0031182006001685","article-title":"Development and application of an ethically and epidemiologically advantageous assay for the multi-locus microsatellite analysis of Schistosoma mansoni","volume":"134","author":"CM Gower","year":"2007","journal-title":"Parasitology"},{"key":"pntd.0010188.ref032","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/1756-3305-4-131","article-title":"Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma","volume":"4","author":"SP Lawton","year":"2011","journal-title":"Parasit Vectors"},{"issue":"4","key":"pntd.0010188.ref033","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1645\/GE-1895.1","article-title":"Analysis of Schistosoma mansoni population structure using total fecal egg sampling","volume":"95","author":"WA Blank","year":"2009","journal-title":"J Parasitol"},{"issue":"3\u20134","key":"pntd.0010188.ref034","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.ijpara.2007.07.011","article-title":"Genetic diversity and population structuring of Schistosoma mansoni in a Brazilian village","volume":"38","author":"EA Thiele","year":"2008","journal-title":"Int J Parasitol"},{"issue":"8","key":"pntd.0010188.ref035","doi-asserted-by":"crossref","first-page":"e0003998","DOI":"10.1371\/journal.pntd.0003998","article-title":"Reconstructing Colonization Dynamics of the Human Parasite Schistosoma mansoni following Anthropogenic Environmental Changes in Northwest Senegal.","volume":"9","author":"F Van den Broeck","year":"2015","journal-title":"PLoS Negl Trop Dis."},{"key":"pntd.0010188.ref036","doi-asserted-by":"crossref","first-page":"104727","DOI":"10.1016\/j.meegid.2021.104727","article-title":"Population genetics of African Schistosoma species","volume":"89","author":"O Rey","year":"2021","journal-title":"Infect Genet Evol"},{"issue":"5","key":"pntd.0010188.ref037","doi-asserted-by":"crossref","first-page":"e0009396","DOI":"10.1371\/journal.pntd.0009396","article-title":"Revisiting density-dependent fecundity in schistosomes using sibship reconstruction","volume":"15","author":"MI Neves","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"4","key":"pntd.0010188.ref038","doi-asserted-by":"crossref","first-page":"951","DOI":"10.4269\/ajtmh.2010.10-0283","article-title":"Genetic consequences of mass human chemotherapy for Schistosoma mansoni: population structure pre- and post-praziquantel treatment in Tanzania","volume":"83","author":"AJ Norton","year":"2010","journal-title":"Am J Trop Med Hyg"},{"issue":"11","key":"pntd.0010188.ref039","doi-asserted-by":"crossref","first-page":"e897","DOI":"10.1371\/journal.pntd.0000897","article-title":"Observed reductions in Schistosoma mansoni transmission from large-scale administration of praziquantel in Uganda: a mathematical modelling study.","volume":"4","author":"MD French","year":"2010","journal-title":"PLoS Negl Trop Dis"},{"issue":"10","key":"pntd.0010188.ref040","doi-asserted-by":"crossref","first-page":"e3221","DOI":"10.1371\/journal.pntd.0003221","article-title":"No apparent reduction in schistosome burden or genetic diversity following four years of school-based mass drug administration in mwea, central kenya, a heavy transmission area","volume":"8","author":"AE Lelo","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref041","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1186\/s13071-017-2533-6","article-title":"Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme.","volume":"10","author":"CM Gower","year":"2017","journal-title":"Parasit Vectors"},{"issue":"1","key":"pntd.0010188.ref042","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1186\/s13071-019-3860-6","article-title":"Two-year longitudinal survey reveals high genetic diversity of Schistosoma mansoni with adult worms surviving praziquantel treatment at the start of mass drug administration in Uganda.","volume":"12","author":"CL Faust","year":"2019","journal-title":"Parasit Vectors"},{"issue":"13","key":"pntd.0010188.ref043","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1017\/S0031182018000811","article-title":"Whole genome amplification and exome sequencing of archived schistosome miracidia","volume":"145","author":"W Le Clec\u2019h","year":"2018","journal-title":"Parasitology"},{"issue":"10","key":"pntd.0010188.ref044","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1093\/molbev\/msz154","article-title":"Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites","volume":"36","author":"RN Platt","year":"2019","journal-title":"Mol Biol Evol"},{"key":"pntd.0010188.ref045","first-page":"465783","article-title":"Genomic analysis of a parasite invasion: colonization of the Americas by the blood fluke, Schistosoma mansoni.","author":"RN Platt","year":"2021","journal-title":"bioRxiv"},{"issue":"1","key":"pntd.0010188.ref046","doi-asserted-by":"crossref","first-page":"e0005292","DOI":"10.1371\/journal.pntd.0005292","article-title":"Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia","volume":"11","author":"JA Shortt","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref047","doi-asserted-by":"crossref","first-page":"6884","DOI":"10.1038\/s41598-021-86287-y","article-title":"Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts","volume":"11","author":"JA Shortt","year":"2021","journal-title":"Sci Rep"},{"issue":"1","key":"pntd.0010188.ref048","doi-asserted-by":"crossref","first-page":"e1455","DOI":"10.1371\/journal.pntd.0001455","article-title":"A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni","volume":"6","author":"AV Protasio","year":"2012","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref049","doi-asserted-by":"crossref","first-page":"e1007513","DOI":"10.1371\/journal.ppat.1007513","article-title":"Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium","volume":"15","author":"H Oey","year":"2019","journal-title":"PLoS Pathog"},{"issue":"9","key":"pntd.0010188.ref050","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giz108","article-title":"High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing","volume":"8","author":"AJ Stroehlein","year":"2019","journal-title":"Gigascience"},{"issue":"8","key":"pntd.0010188.ref051","doi-asserted-by":"crossref","first-page":"e0007612","DOI":"10.1371\/journal.pntd.0007612","article-title":"An improved genome assembly of the fluke Schistosoma japonicum","volume":"13","author":"F Luo","year":"2019","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref052","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41588-018-0262-1","article-title":"Comparative genomics of the major parasitic worms","volume":"51","author":"C. International Helminth Genomes","year":"2019","journal-title":"Nat Genet"},{"issue":"12","key":"pntd.0010188.ref053","doi-asserted-by":"crossref","first-page":"e0010062","DOI":"10.1371\/journal.pntd.0010062","article-title":"Morphological and genomic characterisation of the Schistosoma hybrid infecting humans in Europe reveals admixture between Schistosoma haematobium and Schistosoma bovis","volume":"15","author":"J Kincaid-Smith","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0010188.ref054","first-page":"456314","article-title":"Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system","author":"SK Buddenborg","year":"2021","journal-title":"bioRxiv"},{"issue":"1","key":"pntd.0010188.ref055","doi-asserted-by":"crossref","first-page":"4776","DOI":"10.1038\/s41467-021-24958-0","article-title":"Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration","volume":"12","author":"DJ Berger","year":"2021","journal-title":"Nat Commun"},{"key":"pntd.0010188.ref056","doi-asserted-by":"crossref","first-page":"17345","DOI":"10.1038\/srep17345","article-title":"Exploring molecular variation in Schistosoma japonicum in China.","volume":"5","author":"ND Young","year":"2015","journal-title":"Sci Rep"},{"key":"pntd.0010188.ref057","doi-asserted-by":"crossref","first-page":"20954","DOI":"10.1038\/srep20954","article-title":"Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection","volume":"6","author":"T Crellen","year":"2016","journal-title":"Sci Rep"},{"issue":"1","key":"pntd.0010188.ref058","doi-asserted-by":"crossref","first-page":"e0009020","DOI":"10.1371\/journal.pntd.0009020","article-title":"Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum)","volume":"15","author":"ZL Nikolakis","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0010188.ref059","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1038\/s41467-019-10121-3","article-title":"Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns","volume":"10","author":"AC Shetty","year":"2019","journal-title":"Nat Commun"},{"issue":"10","key":"pntd.0010188.ref060","doi-asserted-by":"crossref","first-page":"e1007065","DOI":"10.1371\/journal.pgen.1007065","article-title":"Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent","volume":"13","author":"AR Taylor","year":"2017","journal-title":"PLoS Genet"},{"key":"pntd.0010188.ref061","doi-asserted-by":"crossref","first-page":"42","DOI":"10.12688\/wellcomeopenres.16168.1","article-title":"An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.","volume":"6","author":"MalariaGen","year":"2021","journal-title":"Wellcome Open Res."},{"key":"pntd.0010188.ref062","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/s13063-015-0702-5","article-title":"The Lake Victoria Island Intervention Study on Worms and Allergy-related diseases (LaVIISWA): study protocol for a randomised controlled trial","volume":"16","author":"M Nampijja","year":"2015","journal-title":"Trials"},{"issue":"10","key":"pntd.0010188.ref063","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1093\/cid\/ciy761","article-title":"The Impact of Intensive Versus Standard Anthelminthic Treatment on Allergy-related Outcomes, Helminth Infection Intensity, and Helminth-related Morbidity in Lake Victoria Fishing Communities, Uganda: Results From the LaVIISWA Cluster-randomized Trial","volume":"68","author":"RE Sanya","year":"2019","journal-title":"Clin Infect Dis"},{"key":"pntd.0010188.ref064","doi-asserted-by":"crossref","first-page":"7035025","DOI":"10.1155\/2017\/7035025","article-title":"The Efficacy of Single-Dose versus Double-Dose Praziquantel Treatments on Schistosoma mansoni Infections: Its Implication on Undernutrition and Anaemia among Primary Schoolchildren in Two On-Shore Communities, Northwestern Tanzania.","volume":"2017","author":"DZ Munisi","year":"2017","journal-title":"Biomed Res Int"},{"issue":"6","key":"pntd.0010188.ref065","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.4269\/ajtmh.17-0368","article-title":"Defining Persistent Hotspots: Areas That Fail to Decrease Meaningfully in Prevalence after Multiple Years of Mass Drug Administration with Praziquantel for Control of Schistosomiasis","volume":"97","author":"N Kittur","year":"2017","journal-title":"Am J Trop Med Hyg"},{"issue":"3","key":"pntd.0010188.ref066","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1093\/cid\/ciz859","article-title":"The Effect of Helminth Infections and Their Treatment on Metabolic Outcomes: Results of a Cluster-Randomized Trial","volume":"71","author":"RE Sanya","year":"2020","journal-title":"Clin Infect Dis"},{"key":"pntd.0010188.ref067","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v084.i06","article-title":"tmap: Thematic Maps in R","volume":"84","author":"M. Tennekes","year":"2018","journal-title":"Journal of Statistical Software"},{"key":"pntd.0010188.ref068","doi-asserted-by":"crossref","first-page":"439","DOI":"10.32614\/RJ-2018-009","article-title":"Simple Features for R: Standardized Support for Spatial Vector Data.","volume":"10","author":"E. Pebesma","year":"2018","journal-title":"The R Journal"},{"issue":"3","key":"pntd.0010188.ref069","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/0035-9203(75)90126-1","article-title":"A simple and rapid technique for quantitative estimation of helminth eggs in human and animal excreta with special reference to Schistosoma sp","volume":"69","author":"RJ Pitchford","year":"1975","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"pntd.0010188.ref070","doi-asserted-by":"crossref","first-page":"826","DOI":"10.3389\/fgene.2019.00826","article-title":"Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing.","volume":"10","author":"SR Doyle","year":"2019","journal-title":"Front Genet"},{"issue":"7779","key":"pntd.0010188.ref071","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/s41586-019-1672-7","article-title":"The landscape of somatic mutation in normal colorectal epithelial cells","volume":"574","author":"H Lee-Six","year":"2019","journal-title":"Nature"},{"key":"pntd.0010188.ref072","unstructured":"Picard toolkit. Broad Institute; 2018."},{"issue":"15","key":"pntd.0010188.ref073","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"issue":"4","key":"pntd.0010188.ref074","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/genetics\/61.4.893","article-title":"The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations","volume":"61","author":"M. Kimura","year":"1969","journal-title":"Genetics"},{"key":"pntd.0010188.ref075","article-title":"The igraph software package for complex network research","author":"G Csardi","year":"2006","journal-title":"InterJournal."},{"issue":"5","key":"pntd.0010188.ref076","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1111\/1755-0998.12665","article-title":"Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond","volume":"17","author":"J. Huisman","year":"2017","journal-title":"Mol Ecol Resour"},{"issue":"7164","key":"pntd.0010188.ref077","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/nature06250","article-title":"Genome-wide detection and characterization of positive selection in human populations","volume":"449","author":"PC Sabeti","year":"2007","journal-title":"Nature"},{"issue":"6","key":"pntd.0010188.ref078","doi-asserted-by":"crossref","first-page":"R71","DOI":"10.1186\/gb-2009-10-6-r71","article-title":"Genomic linkage map of the human blood fluke Schistosoma mansoni","volume":"10","author":"CD Criscione","year":"2009","journal-title":"Genome Biol"},{"issue":"5","key":"pntd.0010188.ref079","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1086\/521987","article-title":"Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering","volume":"81","author":"SR Browning","year":"2007","journal-title":"Am J Hum Genet"},{"issue":"10","key":"pntd.0010188.ref080","doi-asserted-by":"crossref","first-page":"2824","DOI":"10.1093\/molbev\/msu211","article-title":"selscan: an efficient multithreaded program to perform EHH-based scans for positive selection","volume":"31","author":"ZA Szpiech","year":"2014","journal-title":"Mol Biol Evol"},{"issue":"W1","key":"pntd.0010188.ref081","doi-asserted-by":"crossref","first-page":"W191","DOI":"10.1093\/nar\/gkz369","article-title":"g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).","volume":"47","author":"U Raudvere","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pntd.0010188.ref082","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/j.pt.2014.08.004","article-title":"Models for measuring anthelmintic drug efficacy for parasitologists","volume":"30","author":"M Walker","year":"2014","journal-title":"Trends Parasitol"},{"key":"pntd.0010188.ref083","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets.","volume":"4","author":"CC Chang","year":"2015","journal-title":"Gigascience"},{"issue":"20","key":"pntd.0010188.ref084","doi-asserted-by":"crossref","first-page":"3243","DOI":"10.1093\/bioinformatics\/btx410","article-title":"Panoptes: web-based exploration of large scale genome variation data","volume":"33","author":"P Vauterin","year":"2017","journal-title":"Bioinformatics"},{"key":"pntd.0010188.ref085","doi-asserted-by":"crossref","first-page":"E1","DOI":"10.1111\/j.1749-6632.2012.06748.x","article-title":"The genetics of sex chromosomes: evolution and implications for hybrid incompatibility","volume":"1256","author":"NA Johnson","year":"2012","journal-title":"Ann N Y Acad Sci"},{"key":"pntd.0010188.ref086","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/s13071-016-1312-0","article-title":"New approaches to measuring anthelminthic drug efficacy: parasitological responses of childhood schistosome infections to treatment with praziquantel.","volume":"9","author":"M Walker","year":"2016","journal-title":"Parasit Vectors"},{"issue":"5","key":"pntd.0010188.ref087","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1371\/journal.pmed.0030102","article-title":"Incorporating a rapid-impact package for neglected tropical diseases with programs for HIV\/AIDS, tuberculosis, and malaria","volume":"3","author":"PJ Hotez","year":"2006","journal-title":"PLoS Med."},{"issue":"5","key":"pntd.0010188.ref088","first-page":"65","article-title":"Prevention and control of schistosomiasis: a current perspective","volume":"2014","author":"MT Inobaya","year":"2014","journal-title":"Res Rep Trop Med"},{"issue":"11","key":"pntd.0010188.ref089","doi-asserted-by":"crossref","first-page":"3821","DOI":"10.1128\/IAI.00590-12","article-title":"Schistosoma mansoni infection impairs antimalaria treatment and immune responses of rhesus macaques infected with mosquito-borne Plasmodium coatneyi","volume":"80","author":"AA Semenya","year":"2012","journal-title":"Infect Immun"},{"issue":"6","key":"pntd.0010188.ref090","doi-asserted-by":"crossref","first-page":"e0006484","DOI":"10.1371\/journal.pntd.0006484","article-title":"Schistosomiasis in Africa: Improving strategies for long-term and sustainable morbidity control","volume":"12","author":"MD French","year":"2018","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0010188.ref091","doi-asserted-by":"crossref","first-page":"635869","DOI":"10.3389\/fimmu.2021.635869","article-title":"Schistosomiasis Morbidity Hotspots: Roles of the Human Host, the Parasite and Their Interface in the Development of Severe Morbidity","volume":"12","author":"PA Mawa","year":"2021","journal-title":"Front Immunol"},{"issue":"6164","key":"pntd.0010188.ref092","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1126\/science.1243106","article-title":"Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites","volume":"342","author":"CL Valentim","year":"2013","journal-title":"Science"},{"issue":"9936","key":"pntd.0010188.ref093","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1016\/S0140-6736(13)61949-2","article-title":"Human schistosomiasis","volume":"383","author":"DG Colley","year":"2014","journal-title":"Lancet"},{"issue":"1","key":"pntd.0010188.ref094","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.molbiopara.2008.11.007","article-title":"Towards an understanding of the mechanism of action of praziquantel","volume":"164","author":"AD Aragon","year":"2009","journal-title":"Mol Biochem Parasitol"},{"issue":"1","key":"pntd.0010188.ref095","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40249-018-0391-x","article-title":"Pharmacological and immunological effects of praziquantel against Schistosoma japonicum: a scoping review of experimental studies.","volume":"7","author":"SH Xiao","year":"2018","journal-title":"Infect Dis Poverty"},{"key":"pntd.0010188.ref096","doi-asserted-by":"crossref","first-page":"e12357","DOI":"10.1111\/lre.12357","article-title":"A GIS-based approach for delineating suitable areas for cage fish culture in a lake.","volume":"26","author":"CM Aura","year":"2021","journal-title":"Lakes and Reservoirs"},{"issue":"1\u20132","key":"pntd.0010188.ref097","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s11010-008-9833-2","article-title":"Expression of ATP-binding cassette multidrug transporters in the giant liver fluke Fasciola gigantica and their possible involvement in the transport of bile salts and anthelmintics","volume":"317","author":"S Kumkate","year":"2008","journal-title":"Mol Cell Biochem"},{"issue":"6","key":"pntd.0010188.ref098","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1097\/QCO.0b013e328318978f","article-title":"Praziquantel: mechanisms of action, resistance and new derivatives for schistosomiasis.","volume":"21","author":"MJ Doenhoff","year":"2008","journal-title":"Curr Opin Infect Dis"},{"issue":"14","key":"pntd.0010188.ref099","doi-asserted-by":"crossref","first-page":"4871","DOI":"10.1007\/s00216-013-6872-7","article-title":"Immobilized purine nucleoside phosphorylase from Schistosoma mansoni for specific inhibition studies","volume":"405","author":"MC de Moraes","year":"2013","journal-title":"Anal Bioanal Chem"},{"issue":"1","key":"pntd.0010188.ref100","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/s42003-020-01377-3","article-title":"Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm","volume":"3","author":"SR Doyle","year":"2020","journal-title":"Commun Biol."},{"issue":"1","key":"pntd.0010188.ref101","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/s12864-019-5592-6","article-title":"Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus","volume":"20","author":"SR Doyle","year":"2019","journal-title":"BMC Genomics"},{"key":"pntd.0010188.ref102","first-page":"465712","article-title":"Genomic landscape of drug response reveals novel mediators of anthelmintic resistance.","author":"SR Doyle","year":"2021","journal-title":"bioRxiv"},{"issue":"6398","key":"pntd.0010188.ref103","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1126\/science.aar6609","article-title":"Eradication genomics-lessons for parasite control","volume":"361","author":"JA Cotton","year":"2018","journal-title":"Science"},{"key":"pntd.0010188.ref104","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/s13071-015-0766-9","article-title":"The roles of water, sanitation and hygiene in reducing schistosomiasis: a review.","volume":"8","author":"JE Grimes","year":"2015","journal-title":"Parasit Vectors"},{"issue":"4","key":"pntd.0010188.ref105","doi-asserted-by":"crossref","first-page":"e0003657","DOI":"10.1371\/journal.pntd.0003657","article-title":"Historical perspective: snail control to prevent schistosomiasis.","volume":"9","author":"CH King","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"issue":"10","key":"pntd.0010188.ref106","doi-asserted-by":"crossref","first-page":"e1007881","DOI":"10.1371\/journal.ppat.1007881","article-title":"Oxamniquine resistance alleles are widespread in Old World Schistosoma mansoni and predate drug deployment.","volume":"15","author":"FD Chevalier","year":"2019","journal-title":"PLoS Pathog"},{"issue":"4","key":"pntd.0010188.ref107","doi-asserted-by":"crossref","first-page":"2335","DOI":"10.1534\/genetics.104.036947","article-title":"Soft sweeps: molecular population genetics of adaptation from standing genetic variation","volume":"169","author":"J Hermisson","year":"2005","journal-title":"Genetics"},{"issue":"7","key":"pntd.0010188.ref108","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1586\/14787210.2013.811931","article-title":"Advocacy, policies and practicalities of preventive chemotherapy campaigns for African children with schistosomiasis","volume":"11","author":"JR Stothard","year":"2013","journal-title":"Expert Rev Anti Infect Ther"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0010188","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T00:00:00Z","timestamp":1661817600000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0010188","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T01:31:10Z","timestamp":1727832670000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0010188"}},"subtitle":[],"editor":[{"given":"Mar\u00eda-Gloria","family":"Bas\u00e1\u00f1ez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,8,18]]},"references-count":108,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,8,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0010188","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pntd.0010188","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,18]]}}}