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Following an outbreak of\n                  <jats:italic>Plasmodium falciparum<\/jats:italic>\n                  infection in Sabah Malaysia in 2019, 98 samples were sequenced to search for adaptations driving the outbreak. The genomic data revealed evidence of clonal expansion of a strain carrying multiple copies of the chloroquine resistance transporter gene (\n                  <jats:italic>pfcrt<\/jats:italic>\n                  ) in 86 cases. A TaqMan qPCR assay was developed to quantify\n                  <jats:italic>pfcrt<\/jats:italic>\n                  copy number, confirming the\n                  <jats:italic>in silico<\/jats:italic>\n                  evidence of duplication. Whilst point mutations in\n                  <jats:italic>pfcrt<\/jats:italic>\n                  have been associated with resistance to chloroquine and other drugs, copy number amplification has not been widely explored as a resistance mechanism. We investigated the genetic architecture of the duplication, revealing a wildtype haplotype (3D7 reference-type with 76K variant) and a novel mutant (with 76T mutation). Application of the TaqMan assay in 43\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  cases from neighbouring Palawan Island, the Philippines, identified a further two cases with\n                  <jats:italic>pfcrt<\/jats:italic>\n                  duplication. Assessment of the global genomic data in the MalariaGEN Pf8 repository identified a further 86 cases, including 73 (85%) from West Africa with evidence of\n                  <jats:italic>pfcrt<\/jats:italic>\n                  duplication. Amongst 47 monoclonal MalariaGEN cases, majority (95%) comprised wild type and mutant variants at codon 76. Our study reveals a potential previously unconsidered antimalarial resistance mechanism for\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  and provides an assay for surveillance in other populations.\n                <\/jats:p>","DOI":"10.64898\/2026.06.18.732750","type":"posted-content","created":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T04:30:18Z","timestamp":1781929818000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>Pfcrt<\/i>\n                  copy number amplification detected in a\n                  <i>Plasmodium falciparum<\/i>\n                  outbreak"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-9299-5715","authenticated-orcid":false,"given":"Anjana","family":"Rai","sequence":"first","affiliation":[{"name":"Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiyun","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK"},{"name":"Wellcome Sanger Institute, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2436-8283","authenticated-orcid":false,"given":"Hidayat","family":"Trimarsanto","sequence":"additional","affiliation":[{"name":"Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2804-8298","authenticated-orcid":false,"given":"Ashley","family":"Osborne","sequence":"additional","affiliation":[{"name":"Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern 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Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia"},{"name":"Department of Medicine, Queen Elizabeth Hospital II, Kota Kinabalu, Sabah, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"June Haidee","family":"Acu\u00f1a-Lariosa","sequence":"additional","affiliation":[{"name":"Parasitology Department, National Reference Laboratory for Malaria and Other Parasites, Research Institute for Tropical Medicine, Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7013-9188","authenticated-orcid":false,"given":"Maria Lourdes M","family":"Macalinao","sequence":"additional","affiliation":[{"name":"Parasitology Department, National Reference Laboratory for Malaria and Other Parasites, Research Institute for Tropical Medicine, Philippines"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Luchavez","sequence":"additional","affiliation":[{"name":"Parasitology Department, 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Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6753-8938","authenticated-orcid":false,"given":"David","family":"Fidock","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5023-0176","authenticated-orcid":false,"given":"Dominic P","family":"Kwiatkowski","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas M","family":"Anstey","sequence":"additional","affiliation":[{"name":"Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 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