Abstract
<jats:p> The <jats:italic>Plasmodium falciparum</jats:italic> <jats:italic>PIMMS43</jats:italic> gene encodes an ookinete protein that is important for mosquito infection. Here, large indel variants within the coding sequence are identified, and frequencies in natural infections of humans and mosquitoes investigated. Comparing long-read genome sequences in a small panel of <jats:italic>P. falciparum</jats:italic> strains and related species revealed a 150 bp deletion in the central part of the gene in several strains including the standard 3D7 reference genome. Mapping of short-read genome sequence data from 524 <jats:italic>P. falciparum</jats:italic> infections from nine different countries to full-length <jats:italic>PIMMS43</jats:italic> showed the 150 bp deletion and an alternative 90 bp deletion to be common structural variants. Across African populations, the 150 bp deletion had a mean allele frequency of 32%, and the 90 bp deletion a mean frequency of 12%, with significant geographical variation. Targeted genotyping of 30 oocysts from naturally infected mosquitoes in Tanzania by nested PCR showed overall deletion variant frequencies similar to those seen in human infections in the same country. Although sample size was limited, a difference in the variant frequencies in oocysts from <jats:italic>Anopheles gambiae</jats:italic> and <jats:italic>Anopheles funestus</jats:italic> suggests potential vector-specific selection. The findings highlight the importance of surveying structural genomic variation and its potential role in parasite adaptation. </jats:p>