Cryptic absence and genetic variation of Plasmodium falciparum PfHRP2 and PfHRP3 from isolates in Papua, Indonesia.

The rising prevalence of histidine-rich protein 2 (PfHRP2) gene deletions (pfhrp2-) poses a threat to the accuracy of PfHRP2-based rapid diagnostic tests (RDTs). However, evidence of this deletion is scarce in Indonesia. We examined the prevalence of pfhrp2 and its paralogue histidine-rich protein 3 (PfHRP3) gene deletions (pfhrp3-) in blood samples collected from a study assessing three PfHRP2-based RDTs conducted between December 2022 and April 2023 in Timika, Papua. Out of 2157 symptomatic-patients enrolled, 566 P. falciparum mono-infection cases were included for pfhrp2/3 exon 2 genotyping. We detected nine samples (1.59%, 95% CI 0.73-3.00%) with pfhrp2-/pfhrp3-, of which eight were PfHRP2-RDTs positive. Of three pfhrp2- samples (0.53%, 95% CI 0.11-1.54%), one was PfHRP2-RDTs positive. In contrast, 201 samples (35.51%, 95% CI 31.57-39.61%) had pfhrp3-, five of which were pfhrp2 + but PfHRP2-RDT negative; however, four exhibited low parasitemia. Five PfHRP2-RDTs negative samples with pfhrp2 + /pfhrp3 + were sequenced alongside two pfhrp2 + with PfHRP2-RDTs positive samples. We found more repeat-type variations in pfhrp2 compared to pfhrp3. Seven unique repeat types in pfhrp2 and one unique repeat type in pfhrp3 amino acid sequences were characterized in single or multiple copies per sample. These results demonstrated the low prevalence of pfhrp2- 2.12% (95% CI 1.10-3.67%) suggesting PfHRP2-based RDTs remain suitable for malaria diagnosis in Timika, Papua, Indonesia.