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While such deletions have been reported in other malaria-endemic countries, their presence and diagnostic impact in Malawi remain unknown. This study aimed to determine the prevalence of\n                      <jats:italic>pfhrp2\/pfhrp3<\/jats:italic>\n                      gene deletions in Malawi and their effect on the diagnostic accuracy of HRP2-based RDTs relative to light microscopy and qPCR.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A cross-sectional study was conducted between December 2020 and June 2021, enrolling 1582 participants from referral hospitals in Mzuzu (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u20091186) and Lilongwe (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009396). Malaria diagnosis was performed using RDTs, microscopy, and qPCR. A total of 391\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      positive samples were analyzed for\n                      <jats:italic>pfhrp2\/pfhrp3<\/jats:italic>\n                      gene deletions using multiplex qPCR. Diagnostic accuracy metrics, such as sensitivity and specificity, were calculated with 95% confidence intervals. Spearman correlation was applied to assess associations involving log-transformed parasitemia, unpaired\n                      <jats:italic>t<\/jats:italic>\n                      -tests were used to compare diagnostic methods, and Mann\u2013Whitney tests were used to compare symptomatic and asymptomatic groups.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Malaria prevalence was higher in Lilongwe (45.2%) than in Mzuzu (22.9%). Infections in Lilongwe were predominantly asymptomatic (94.2%), whereas Mzuzu had mostly symptomatic cases (97.1%) (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.0002). RDTs demonstrated higher sensitivity of\u00a078.5% (95%\n                      <jats:italic>CI<\/jats:italic>\n                      : 74.6\u201382.1%) than microscopy 64.8% (95%\n                      <jats:italic>CI<\/jats:italic>\n                      : 60.3\u201369.1), but slightly lower specificity, with 93.6% (95%\n                      <jats:italic>CI<\/jats:italic>\n                      : 92.0\u201395.0%) for RDT compared to 95.4% (95%\n                      <jats:italic>CI<\/jats:italic>\n                      : 94.0\u201396.6%) for microscopy. Dual\n                      <jats:italic>pfhrp2\/3<\/jats:italic>\n                      gene deletions were found in 24 (15.0%) isolates from Lilongwe and 24 (10.4%) from Mzuzu. All dual-deleted samples were false negative by RDT but were positive by microscopy and qPCR.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study is the first to report\n                      <jats:italic>pfhrp2\/3<\/jats:italic>\n                      gene deletions in Malawi. The presence of these deletions may compromise the performance of HRP2-based RDTs, indicating the need to reassess diagnostic strategies in affected regions.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40249-025-01368-8","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T12:50:20Z","timestamp":1760014220000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["First report of pfhrp2 and pfhrp3 gene deletions compromising HRP2-based malaria rapid diagnostic tests in Malawi"],"prefix":"10.1186","volume":"14","author":[{"given":"Johnsy Mary","family":"Louis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernest","family":"Mazigo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hojong","family":"Jun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wang-Jong","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jadidan Hada","family":"Syahada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fadhila","family":"Fitriana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fauzi","family":"Muh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanjoo","family":"Chun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Won Sun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Se Jin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunghun","family":"Na","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eun-Teak","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0836-6675","authenticated-orcid":false,"given":"Jin-Hee","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"1368_CR1","doi-asserted-by":"publisher","first-page":"264","DOI":"10.12688\/wellcomeopenres.19390.1","volume":"8","author":"D Mategula","year":"2023","unstructured":"Mategula D, Gichuki J, Chipeta MG, Chirombo J, Kalonde PK, Gumbo A, et al. 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