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The majority of
Plasmodium falciparum
malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the
pfhrp2
and/or
pfhrp3
genes (
pfhrp2/3
) raise concern about existing malaria diagnostic strategies. We previously identified
pfhrp2
-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT;
pfhrp2/3
genotyping and species-specific PCR assays; a bead-based immunoassay for
Plasmodium
antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative
pfhrp2/3
deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with
P. falciparum
was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen’s kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to
pfhrp2/3
-deleted
P. falciparum
was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.