{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:20:18Z","timestamp":1792790418215,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,30]]},"group-title":"Genomics","reference-count":78,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Bill & Melinda Gates Foundation","award":["INV-035751"],"award-info":[{"award-number":["INV-035751"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Bill & Melinda Gates Foundation","award":["INV-037316"],"award-info":[{"award-number":["INV-037316"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Bill & Melinda Gates Foundation","award":["INV-081860"],"award-info":[{"award-number":["INV-081860"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Bill & Melinda Gates Foundation","award":["INV-069975"],"award-info":[{"award-number":["INV-069975"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institutes of Health","award":["U2RTW012116"],"award-info":[{"award-number":["U2RTW012116"]}]},{"name":"National Institutes of Health","award":["U19AI089674"],"award-info":[{"award-number":["U19AI089674"]}]},{"name":"National Institutes of Health","award":["K23AI166009"],"award-info":[{"award-number":["K23AI166009"]}]},{"name":"National Institutes of Health","award":["K24AI144048"],"award-info":[{"award-number":["K24AI144048"]}]},{"name":"National Institutes of Health","award":["R01 AI173557"],"award-info":[{"award-number":["R01 AI173557"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Uganda has one of the world\u2019s highest malaria burdens, but parasite population structure and connectivity have not been characterized nationally with whole-genome data. We analyzed 249 monoclonal\n                  <jats:italic>Plasmodium falciparum<\/jats:italic>\n                  genomes from 26 sentinel sites across Uganda in 2023 and compared them with publicly available genomes from five neighboring countries. Genetic diversity was high and differentiation low in Uganda, but identity-by-descent detected limited structure. This was most pronounced in the low-transmission southwest, where parasites shared ancestry and recent relatedness with isolates from western Tanzania. Selection scans identified signals at loci associated with resistance to artemisinins and their partner drugs, and to chloroquine and antifolates. The strongest signal was at PfPX1 where the PIN haplotype (L1222P, M1701I, D1705N) reached 70% prevalence nationwide, but selection was carried by PIN haplotypes that had additionally acquired D384A, largely confined to northern and eastern Uganda. A second substitution at the same codon, D384Y, formed a haplotype shared across the Tanzanian border. PfKelch13 variants were partitioned across multiple backgrounds, consistent with repeated independent emergence, and C469Y was enriched on the PfPX1 D384A-PIN background. These genomes provide a 2023 baseline for tracking potential mediators of drug resistance and support coordinated genomic surveillance across Uganda and its neighbors.\n                <\/jats:p>","DOI":"10.64898\/2026.09.27.754784","type":"posted-content","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T03:55:37Z","timestamp":1790826937000},"source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome characterization of\n                  <i>Plasmodium falciparum<\/i>\n                  population structure and drug resistance across Uganda and neighboring countries"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6380-4714","authenticated-orcid":false,"given":"Shahiid","family":"Kiyaga","sequence":"first","affiliation":[{"name":"Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda"},{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"The African Center of Excellence in Bioinformatics and Data Intensive Sciences, Kampala, Uganda"},{"name":"The Infectious Diseases Institute, Makerere University, Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6621-0586","authenticated-orcid":false,"given":"Monica","family":"Mbabazi","sequence":"additional","affiliation":[{"name":"Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda"},{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2002-8911","authenticated-orcid":false,"given":"Thomas","family":"Katairo","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, Uganda"},{"name":"Liverpool School of Tropical Medicine (LSTM), Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0489-4692","authenticated-orcid":false,"given":"Victor","family":"Asua","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"Institute for Tropical Medicine, University of T\u00fcbingen, T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2258-194X","authenticated-orcid":false,"given":"Francis D.","family":"Semakuba","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9786-7294","authenticated-orcid":false,"given":"Bienvenu","family":"Nsengimaana","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6469-6516","authenticated-orcid":false,"given":"Stephen","family":"Tukwasibwe","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, Uganda"},{"name":"Department of Medical Biochemistry, Makerere University College of Health Sciences, Kampala, Uganda"},{"name":"Uganda Christian University, Mukono, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0819-3889","authenticated-orcid":false,"given":"Innocent","family":"Wiringilimaana","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9581-0857","authenticated-orcid":false,"given":"Jackie","family":"Nakasaanya","sequence":"additional","affiliation":[{"name":"Infectious Diseases Research Collaboration, Kampala, Uganda"},{"name":"National Malaria Reference and Research Laboratory (NMRRL), Central Public Health Laboratories (CPHL), Kampala, 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