{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T10:02:54Z","timestamp":1784628174634,"version":"3.55.0"},"posted":{"date-parts":[[2026,7,17]]},"group-title":"Microbiology","reference-count":71,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["1R21AI180663-01A1"],"award-info":[{"award-number":["1R21AI180663-01A1"]}]},{"DOI":"10.13039\/100006975","name":"Indiana Clinical and Translational Sciences Institute","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100006975","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Bangladesh has greatly reduced malaria transmission, but persistent\n                  <jats:italic>Plasmodium falciparum<\/jats:italic>\n                  transmission in the Chittagong Hill Tracts (CHT), bordering Myanmar, remains a concern for elimination. Emerging artemisinin resistance could threaten remaining control efforts, making it important to identify determinants of reduced artemisinin susceptibility in CHT parasites. We combined long-term\n                  <jats:italic>in vitro<\/jats:italic>\n                  dihydroartemisinin (DHA) selection, whole-genome sequencing, functional genetics, and analysis of contemporaneous clinical isolates to define artemisinin-response variation in CHT\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  . Starting with a 2018 patient-isolated, artemisinin-sensitive CHT clone, three independent cultures were exposed over 18 months to 27 cycles of stepwise DHA pressure up to 1600 nM. This generated CHT-R lines with elevated RSA survival relative to parental\/sibling controls (4.0\u20136.5% versus &lt;1%; 7\u201311-fold increase) and faster post-DHA recovery than CHT-S-sib (5.2 \u00b1 0.3 versus 10.1 \u00b1 0.57 days). Whole-genome sequencing identified convergent disruption of PF3D7_0606000, encoding KIC1 (Kelch13 Interacting Candidate1), a protein linked to the Kelch13-associated endocytic compartment; no\n                  <jats:italic>pfkelch13<\/jats:italic>\n                  mutations emerged. Independent DHA-selected lines acquired distinct stop-gain or frameshift mutations predicted to truncate KIC1, and targeted\n                  <jats:italic>pfkic1<\/jats:italic>\n                  disruption in parental CHT-S increased RSA survival and accelerated recovery, functionally validating KIC1 as a contributor to reduced artemisinin susceptibility. To link the\n                  <jats:italic>in vitro<\/jats:italic>\n                  selection findings to naturally circulating parasites, we tested whether\n                  <jats:italic>pfkic1<\/jats:italic>\n                  variation was associated with artemisinin response in an independent set of CHT isolates. We integrated newly generated RSA measurements and whole-genome variation from lab adapted field isolates all carrying wild-type\n                  <jats:italic>pfkelch13<\/jats:italic>\n                  , with patient clearance values from our CHT artemether-lumefantrine efficacy study. Among 22 isolates, RSA survival ranged from 0.00 to 6.44%, with 12 exceeding the 1%\n                  <jats:italic>in vitro<\/jats:italic>\n                  ART-R threshold and was associated with PC\n                  <jats:sub>50<\/jats:sub>\n                  , the time required to clear 50% of the initial parasite density, but not parasite clearance half-life (PCt\n                  <jats:sub>1\/2<\/jats:sub>\n                  ). In this field-isolate dataset, targeted\n                  <jats:italic>pfkic1<\/jats:italic>\n                  gene-score analysis and elastic-net modeling provided supportive evidence that natural variation at the\n                  <jats:italic>pfkic1<\/jats:italic>\n                  locus is associated with PC\n                  <jats:sub>50<\/jats:sub>\n                  and RSA survival; an exploratory genome-wide gene-score scan nominated additional candidate loci for future study. Together, these findings identify KIC1 as a functionally validated determinant of reduced artemisinin susceptibility in a Bangladeshi parasite background and suggest that artemisinin-response variation in CHT parasites may involve perturbation of the Kelch13-associated endocytic pathway beyond canonical\n                  <jats:italic>pfkelch13<\/jats:italic>\n                  mutations.\n                <\/jats:p>","DOI":"10.64898\/2026.07.17.738940","type":"posted-content","created":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T04:20:12Z","timestamp":1784348412000},"source":"Crossref","is-referenced-by-count":0,"title":["Experimental evolution and functional genetics identify KIC1 as a determinant of reduced artemisinin susceptibility in Bangladeshi\n                  <i>Plasmodium falciparum<\/i>"],"prefix":"10.64898","author":[{"given":"Maisha Khair","family":"Nima","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA"},{"name":"Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nirjhar","family":"Bhattacharyya","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA"},{"name":"Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saiful Arefeen","family":"Sazed","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching Swe","family":"Phru","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8330-5499","authenticated-orcid":false,"given":"Mohammad Shafiul","family":"Alam","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael T","family":"Ferdig","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA"},{"name":"Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7080-494X","authenticated-orcid":false,"given":"Angana","family":"Mukherjee","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA"},{"name":"Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072102300952000_2026.07.17.738940v1.1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0808859"},{"key":"2026072102300952000_2026.07.17.738940v1.2","doi-asserted-by":"publisher","DOI":"10.1056\/nejmc0805011"},{"key":"2026072102300952000_2026.07.17.738940v1.3","doi-asserted-by":"publisher","DOI":"10.1056\/nejmoa1314981"},{"key":"2026072102300952000_2026.07.17.738940v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw388"},{"key":"2026072102300952000_2026.07.17.738940v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu491"},{"key":"2026072102300952000_2026.07.17.738940v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(15)70032-0"},{"key":"2026072102300952000_2026.07.17.738940v1.7","doi-asserted-by":"crossref","unstructured":"Tun KM , Jeeyapant A , Imwong M , Thein M , Aung SSM , Hlaing TM , et al. 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