{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T02:55:15Z","timestamp":1771556115142,"version":"3.50.1"},"reference-count":28,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011880","name":"Acad\u00e9mie de recherche et d'enseignement sup\u00e9rieur","doi-asserted-by":"publisher","award":["Grant PFS2020-Rwanda"],"award-info":[{"award-number":["Grant PFS2020-Rwanda"]}],"id":[{"id":"10.13039\/501100011880","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Parasitol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Malaria remains a major public health challenge across sub-Saharan Africa, with Plasmodium falciparum responsible for the vast majority of cases and deaths. In Rwanda, although control measures have led to significant progress, malaria continues to be endemic, with urban centers like Kigali experiencing continuous transmission. With the recent rollout of malaria vaccines such as RTS,S and R21, understanding the genetic variability of vaccine-targeted antigens is essential for anticipating and enhancing vaccine performance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study investigated the genetic diversity of the Plasmodium falciparum circumsporozoite protein (Pfcsp) gene among 245 clinical isolates collected between October 2021 and June 2023 at King Faisal Hospital, a referral center in Kigali, Rwanda. PCR amplification of the csp locus was performed, and the resulting amplicons were sequenced using Oxford Nanopore Technology (ONT) employing the R10.4 flow cell chemistry, allowing for high-resolution haplotype reconstruction and detection of polymorphic sites across the gene.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>A total of 48 distinct haplotypes were identified, indicating high haplotype diversity (Hd = 0.8899) but moderate nucleotide diversity (p = 0.00834), suggesting immune-driven balancing selection. The N-terminal region was highly conserved across isolates, including full conservation of the KLKQP motif, reinforcing its functional importance in hepatocyte invasion. In contrast, the central repeat region exhibited substantial variability in NANP\/ NVNP tetrapeptide repeat numbers, and the C-terminal region, particularly the Th2R and Th3R epitopes showed extensive polymorphism. Notably, fewer than 1% of sequences matched the 3D7 vaccine strain, and several key amino acid positions associated with vaccine escape showed high mutation frequencies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Our findings suggest that the genetic divergence of circulating csp variants in Kigali could be a factor influencing vaccine performance, underscoring the importance of ongoing molecular surveillance to guide eventual vaccine implementation in Rwanda and other endemic regions<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpara.2025.1679131","type":"journal-article","created":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T06:10:42Z","timestamp":1762236642000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Genetic polymorphism of Plasmodium falciparum circumsporozoite protein in Kigali, Rwanda"],"prefix":"10.3389","volume":"4","author":[{"given":"Sandra Noukimi","family":"Fankem","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Bosco","family":"Mbonimpa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edgar Mutebwa","family":"Kalimba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariama Telly","family":"Diallo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob","family":"Souopgui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.1016\/S0140-6736(23)02276-6","article-title":"Malaria community welcomes WHO vaccine approval","volume":"402","author":"Adepoju","year":"2023","journal-title":"Lancet"},{"key":"B2","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1093\/postmj\/qgae086","article-title":"A new era in malaria prevention: a comparative look at RTS,S\/AS01 and R21\/Matrix-M vaccines","volume":"100","author":"Al-obeidee","year":"2024","journal-title":"Postgrad. Med. J."},{"key":"B3","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1186\/s12936-020-03510-3","article-title":"Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana","volume":"19","author":"Amegashie","year":"2020","journal-title":"Malar. J."},{"key":"B4","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature15535","article-title":"The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015","volume":"526","author":"Bhatt","year":"2015","journal-title":"Nature"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1038\/srep46621","article-title":"Enhancing protective immunity to malaria with a highly immunogenic virus-like particle vaccine","volume":"7","author":"Collins","year":"2017","journal-title":"Sci. Rep."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"B7","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.pt.2018.11.008","article-title":"Important extracellular interactions between plasmodium sporozoites and host cells required for infection","volume":"35","author":"Dundas","year":"2019","journal-title":"Trends Parasitol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/S0140-6736(15)60721-8","article-title":"Efficacy and safety of RTS,S\/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial","volume":"386","year":"2015","journal-title":"Lancet"},{"key":"B9","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/s0166-6851(02)00216-5","article-title":"A study of genetic diversity in the gene encoding the circumsporozoite protein (CSP) of Plasmodium falciparum from different transmission areas\u2013XVI. Asembo Bay Cohort Project","volume":"125","author":"Escalante","year":"2002","journal-title":"Mol. Biochem. Parasitol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"2365","DOI":"10.1038\/s41564-023-01516-6","article-title":"Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana","volume":"8","author":"Girgis","year":"2023","journal-title":"Nat. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1093\/infdis\/171.6.1576","article-title":"Safety, immunogenicity, and efficacy of a recombinantly produced Plasmodium falciparum circumsporozoite protein-hepatitis B surface antigen subunit vaccine","volume":"171","author":"Gordon","year":"1995","journal-title":"J. Infect. Dis."},{"key":"B12","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s12936-020-03315-4","article-title":"Genetic polymorphism of Plasmodium falciparum circumsporozoite protein on Bioko Island, Equatorial Guinea and global comparative analysis","volume":"19","author":"Huang","year":"2020","journal-title":"Malar. J."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1080\/21645515.2019.1669415","article-title":"RTS,S\/AS01 vaccine (Mosquirix\u2122): an overview","volume":"16","author":"Laurens","year":"2019","journal-title":"Hum. Vaccines Immunother."},{"key":"B15","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.3389\/fpara.2024.1346017","article-title":"Genetic variation of the Plasmodium falciparum circumsporozoite protein in parasite isolates from Homabay County in Kenya","volume":"3","author":"Maina","year":"2024","journal-title":"Front. Parasitol."},{"key":"B17","unstructured":"Malaria cases on the rise in Rwanda"},{"key":"B18","doi-asserted-by":"publisher","first-page":"14985","DOI":"10.1038\/s41598-025-00140-0","article-title":"Unveiling mismatch of RTS S AS01 and R21 Matrix M malaria vaccines haplotype among Ethiopian Plasmodium falciparum clinical isolates","volume":"15","author":"Mandefro","year":"2025","journal-title":"Sci. Rep."},{"key":"B19","unstructured":"Rwanda rolls out new malaria strategy after recording 87,000 cases in March\n          \n          \n            \n              Mbabazi\n              J.\n            \n          \n          \n          2025"},{"key":"B20","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1186\/s12936-021-03971-0","article-title":"Assessment of genetic diversity of Plasmodium falciparum circumsporozoite protein in Sudan: the RTS,S leading malaria vaccine candidate","volume":"20","author":"Mohamed","year":"2021","journal-title":"Malar. J."},{"key":"B21","doi-asserted-by":"publisher","first-page":"2025","DOI":"10.1056\/NEJMoa1505819","article-title":"Genetic diversity and protective efficacy of the RTS,S\/AS01 malaria vaccine","volume":"373","author":"Neafsey","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"B22","doi-asserted-by":"publisher","first-page":"7092","DOI":"10.1074\/jbc.M106862200","article-title":"Binding and invasion of liver cells by plasmodium falciparum sporozoites: essential involvement of the amino terminus of circumsporozoite protein *","volume":"277","author":"Rathore","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B23","doi-asserted-by":"publisher","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP 6: DNA sequence polymorphism analysis of large data sets","volume":"34","author":"Rozas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1093\/cid\/ciab357","article-title":"Exposure to diverse plasmodium falciparum genotypes shapes the risk of symptomatic malaria in incident and persistent infections: A longitudinal molecular epidemiologic study in Kenya","volume":"73","author":"Sumner","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"B25","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s12936-025-05278-w","article-title":"Half-decade of scaling up malaria control: malaria trends and impact of interventions from 2018 to 2023 in Rwanda","volume":"24","author":"Umugwaneza","year":"2025","journal-title":"Malar. J."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.8603","article-title":"Amplicon_sorter: A tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences","volume":"12","author":"Vierstraete","year":"2022","journal-title":"Ecol. Evol."},{"key":"B27","unstructured":"WHO recommends R21\/Matrix-M vaccine for malaria prevention in updated advice on immunization"},{"key":"B28","unstructured":"World malaria report\n          \n          \n          \n          2024"}],"container-title":["Frontiers in Parasitology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpara.2025.1679131\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T06:10:45Z","timestamp":1762236645000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpara.2025.1679131\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,4]]},"references-count":28,"alternative-id":["10.3389\/fpara.2025.1679131"],"URL":"https:\/\/doi.org\/10.3389\/fpara.2025.1679131","relation":{},"ISSN":["2813-2424"],"issn-type":[{"value":"2813-2424","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,4]]},"article-number":"1679131"}}