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Here, we assessed\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      infection rates, resistance alleles and profiles in\n                      <jats:italic>Anopheles funestus<\/jats:italic>\n                      s.s. populations across Kenyan malaria-endemic regions separated by the RV.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Anopheles funestus<\/jats:italic>\n                      s.s. populations in western, coastal and Kerio Valley (KV, within the RV) were genotyped for key resistance markers using polymerase chain reaction (PCR).\n                      <jats:italic>Taq<\/jats:italic>\n                      Man assay combined with nested PCR were used to screen the samples for\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      sporozoite infection and association with resistance alleles and genotype frequencies assessed using Fisher\u2019s exact test or Pearson\u2019s chi-square test. Following established WHO guidelines, phenotypic resistance using F1 progeny was also assessed using diagnostic, intensity and piperonyl butoxide (PBO)-synergistic assays.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The 4.3kb-SV (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009336) and\n                      <jats:italic>G454A-Cyp9k1<\/jats:italic>\n                      (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009445) alleles were nearly fixed in western Kenya but declined towards the RV and coast, whereas L119F-GSTe2 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009392) increased across a west-KV-coast gradient with a novel haplotype distinct from known African variants detected at the coast. There were lower odds of\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      infection in mosquitoes with L119F-GSTe2-RR than RS genotype (\n                      <jats:italic>OR<\/jats:italic>\n                      0.2,\n                      <jats:italic>P<\/jats:italic>\n                      \u2009=\u20090.046). Likewise, mosquitoes harboring the R allele of the 4.3 kb marker had higher\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      infection rates than the S allele (\n                      <jats:italic>OR<\/jats:italic>\n                      5.7,\n                      <jats:italic>P<\/jats:italic>\n                      \u2009=\u20090.049).\n                      <jats:italic>An. funestus<\/jats:italic>\n                      populations exhibited a high degree of pyrethroid resistance with intensity higher in KV compared to western Kenya, a traditional malaria hotspot. Pre-exposure to PBO increased mortality for type II (deltamethrin, alpha-cypermethrin), than I (permethrin) pyrethroids, yet mortality remained lower in KV, suggesting non-P450-mediated resistance.\n                      <jats:italic>An. funestus<\/jats:italic>\n                      mosquitoes from the coast showed extreme permethrin resistance (&lt;\u200910% mortality at 10\u2009\u00d7\u2009dose). Resistance to dichlorodiphenyltrichloroethane was widespread, while all populations remained fully susceptible to bendiocarb, pirimiphos-methyl, clothianidin, and chlorfenapyr.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Region-specific selection may drive varying resistance profiles in\n                      <jats:italic>An. funestus<\/jats:italic>\n                      across Kenyan malaria-endemic regions separated by the Rift Valley, with implications for malaria transmission and insecticide resistance management.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40249-026-01458-1","type":"journal-article","created":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T14:27:20Z","timestamp":1778855240000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Signature of resistance gene evolution and pyrethroid resistance escalation in the major malaria vector Anopheles funestus across Kenyan malaria-endemic regions separated by the Rift Valley"],"prefix":"10.1186","volume":"15","author":[{"given":"David P.","family":"Tchouassi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amine M.","family":"Mustapha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilbert","family":"Rotich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trizah K.","family":"Milugo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brenda","family":"Musimbi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ambrose","family":"Oruni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos S. 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