First detection of pfhrp2 and pfhrp3 gene deletions in Niger Republic: a retrospective sub-analysis of biological samples

Rapid diagnostic tests (RDTs) based on histidine-rich protein 2 (HRP2) are the main diagnostic tool for malaria in Niger and many countries in sub-Saharan Africa. However, deletions of the P. falciparum hrp2 and hrp3 genes can compromise RDT performance, and pose a threat to diagnostic accuracy. Although these deletions were reported in several regions of Africa, Asia and South America, no molecular data on pfhrp2/3 were previously available for Niger. The present study is a retrospective sub-analysis of biological samples derived from a therapeutic efficacy study (TES) conducted in Niger in 2022. Antigen profiling was performed using a multiplex bead-based assay to identify samples with weak or undetectable HRP2 signal. Species confirmation was conducted by PET-PCR, and pfhrp2 /3 exon 2 genotyping was performed using one-step PCR. Among the 375 P. falciparum mono-infection isolates analyzed, pfhrp2 deletions were found in 3% (11/375; 95% CI 1–5%), pfhrp3 deletions in 11% (41/375; 95% CI 8–14%), and double deletions in 1% (5/375; 95% CI 0–2%). These figures likely represent a conservative estimate, as the true prevalence may be higher due to the antigen pre-screening and the selection bias inherent in the original study design. This is the first molecular evidence of Pfhrp2 and Pfhrp3 deletions in P. falciparum in Niger. The observed pfhrp2 deletion rate is a significant molecular finding; however, further evidence is needed to determine if the rate of false-negative RDTs caused by these deletions reaches the 5% threshold set by WHO for a national RDT policy revision.