Interchromosomal segmental duplication drives translocation and loss ofP. falciparumhistidine-rich protein 3 in Americas and Africa

Abstract

ABSTRACTMost malaria rapid diagnostic tests (RDTs) detect histidine-rich protein 2 (PfHRP2) and PfHRP3 encoded by thepfhrp2andpfhrp3genes. Deletions of bothpfhrp2andpfhrp3make parasites undetectable by RDTs. However, deletions have emerged in settings where RDT use is uncommon and can occur independent of each other, withpfhrp3deletion more frequent in many parasite populations. To improve our understanding of geographic patterns and mechanisms ofpfhrp3deletion, we analyzed 8,765 publicly available, whole-genome-sequencedP. falciparumfield samples. Twopfhrp3deletion patterns predominated: 1) chromosome 13 loss centromeric topfhrp3extending to the chromosome end with duplication of chromosome 11’s subtelomeric region (Americas/Africa; Pattern 13-11++) and 2) deletion of chromosome 13 starting at varied locations centromeric topfhrp3(Asia; Pattern 13-). Pattern 13-11++’s centromeric boundary fell within the largest (15kb) segmental duplication in the core genome containing ribosomal genes. Long-read sequencing ofpfhrp3-deleted isolates from Honduras (HB3) and Sudan (SD01) confirmed 13-11 hybrid chromosomes. The majority of isolates had the same haplotype (lack of variation between copies) along their chr. 11 and chr. 13-11 hybrid shared regions, suggesting intrastrain (self) meiotic recombination as the primary mechanism generating 13-11++. Together, our findings demonstrate thatpfhrp3deletion in the Americas and Africa often results from duplication-mediated non-homologous recombination, which drives translocation and creation of a hybrid 13-11 chromosome lackingpfhrp3. Furthermore, this suggests specific conditions including low transmission are needed for emergence, a finding that can inform refined surveillance strategies.SIGNIFICANCE STATEMENTMost cases ofPlasmodium falciparummalaria are diagnosed using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2 (HRP2) and HRP3. RDT effectiveness is threatened by the emergence of parasites that escape detection owing to deletion of thepfhrp2andpfhrp3genes. However, these deletions have been difficult to detect and study, and we lack understanding of their causes. Using whole-genome short and long-read sequencing, we found that duplication-mediated non-homologous recombination leading to translocation and a hybrid chromosome may be responsible forpfhrp3deletion in the Americas and Africa, suggesting that the deletion occurs frequently and can only emerge under specific conditions. Defining these conditions will provide avenues for improved control and surveillance.