High Prevalence of Pfhrp2/3 Gene Deletions and Major Threat to Malaria Control Programs in Ethiopia

Background: Rapid diagnostic tests (RDTs) targeting pfhistidine-rich protein 2 (Pfhrp2) are widely used for diagnosis of Plasmodium falciparum infections in resource-limited malaria endemic countries. However, test results are affected by deletions of the Pfhrp2, Pfhrp3, and flanking genes and associated negative results from rapid diagnostic devices were previously reported. Therefore, the aim of this study was to reveal the existing genetic profile of Pfhrp2 and Pfhrp3 genes of P. falciparum-infected patients in northwestern Ethiopia. Methods: A total number of 302 blood samples were collected from children at Chilga (Aykel, Negade Bahir), and Sanja health centers in northwestern Ethiopia. Thirty-three (10.9%) samples tested positive for P. falciparum malaria. The Pfhrp2, Pfhrp3, and flanking genes (MAL7P1_228 and MAL7P1_230 for Pfhrp2, and MAL13P1_475 and MAL13P1_485 for Pfhrp3) were amplified using standard nested-PCR. Results: Pfhrp2 and both of its flanking genes were found to be present in 12 (36.4%) out of the 33 samples. Twenty-one (63.6%) samples tested negative for the Pfhrp2 gene and 19 samples (57.6%) tested positive for at least one of the flanking genes. Five (15.2%) samples gave positive results for the Pfhrp3 gene and both of its flanking genes, whereas 16 (48.5%) tested negative for all three. Conclusions: Our study provides widespread deletions in the Pfhrp2 and Pfhrp3 genes in Ethiopia, thereby confirming anecdotal reports of diagnostic failure with Pfhrp2-based RDTs in the region. The implications of our finding for the current diagnostic paradigm, which relies on the detection of P. falciparum by Pfhrp2-based RDTs in remote areas, may need rethinking.