High Prevalence of 2/3 Gene Deletions and Major Threat to Malaria Control Programs in Ethiopia.

Rapid diagnostic tests (RDTs) targeting histidine-rich protein 2 (2) are widely used for diagnosis of infections in resource-limited malaria endemic countries. However, test results are affected by deletions of the , , 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 2 and 3 genes of -infected patients in northwestern Ethiopia. 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 malaria. The 2, 3, and flanking genes (MAL7P1_228 and MAL7P1_230 for 2, and MAL13P1_475 and MAL13P1_485 for 3) were amplified using standard nested-PCR. 2 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 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 3 gene and both of its flanking genes, whereas 16 (48.5%) tested negative for all three. Our study provides widespread deletions in the 2 and 3 genes in Ethiopia, thereby confirming anecdotal reports of diagnostic failure with 2-based RDTs in the region. The implications of our finding for the current diagnostic paradigm, which relies on the detection of by 2-based RDTs in remote areas, may need rethinking.