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This ongoing allelic diversity influences the development of naturally acquired immunity and it can inform vaccine efficacy. To investigate the diversity and infection variability, <jats:italic>Plasmodium falciparum<\/jats:italic> merozoite surface protein 1 (<jats:italic>Pf<\/jats:italic>MSP1), a crucial protein for parasite invasion and immune response, was assessed in parasites isolated from children in the Junju cohort, Kilifi County, who experienced at least 10 febrile malaria episodes over a span of 5 years.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>\n              <jats:italic>Pfmsp1<\/jats:italic> C-terminal region (<jats:italic>Pf<\/jats:italic>msp1<jats:sub>19<\/jats:sub>) was genotyped using PCR followed by capillary sequencing in blood samples collected from the children. Sequenced reads were trimmed and aligned to the <jats:italic>P. falciparum<\/jats:italic> 3D7 reference genome. Single nucleotide polymorphisms in the <jats:italic>Pf<\/jats:italic>msp1<jats:sub>19<\/jats:sub> region were identified from the alignment and grouped to distinct microhaplotypes whose changing frequency over time were examined across the multiple infection episodes. In addition, the variability of infections in the population was assessed using nucleotide and haplotype diversity indices.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>A total of eleven microhaplotypes were observed across all malaria episodes. There were 3 prevalent microhaplotypes, E-KSNG-L, Q-KSNG-L, and Q-KSNG-F in the population. Conversely, microhaplotypes such as Q-KNNG-L, E-KSSR-L, E-KNNG-L, E-KSSG-L, E-TSSR-L (3D7), Q-TSSR-L, E-TSSG-L, and E-KSNG-F were rare and maintained at low frequencies. High allelic replacements were observed, however some individuals experienced consecutive re-infections with the same microhaplotype. Notably, <jats:italic>Pf<\/jats:italic>MSP1<jats:sub>19<\/jats:sub> allelic diversity as measured by haplotype diversity was stable, while nucleotide diversity decreased over time with decreasing parasitemia. Parasite <jats:italic>Pf<\/jats:italic>MSP1<jats:sub>19<\/jats:sub> allelic diversity remained stable over the multiple malaria episodes, despite declining parasitaemia levels. In addition, there are reveal dynamic <jats:italic>Pf<\/jats:italic>MSP1<jats:sub>19<\/jats:sub> allelic replacements across parasite infection episodes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Allelic diversity was stable over time in individuals, based on this limited polymorphic region and small sample size, suggesting that there are no significant shifts in allele frequencies or replacements due to alleles being maintained under balancing selection. The dominant alleles in the population are those frequently observed in these children with multiple malaria episodes, further suggesting that early exposure to dominant alleles does not shift their frequency in the population or prevent repeat infection with the same alleles in subsequent infections. However, a blood stage merozoite vaccine is likely to require a multi-allelic formulation.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s12936-025-05378-7","type":"journal-article","created":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T07:36:18Z","timestamp":1745825778000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Stable Plasmodium falciparum merozoite surface protein-1 allelic diversity despite decreasing parasitaemia in children with multiple malaria infections"],"prefix":"10.1186","volume":"24","author":[{"given":"Reuben M.","family":"Yaa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelvin M.","family":"Kimenyi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry Antonio","family":"Palasciano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Obiero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L. 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