BackgroundMalaria rapid diagnostic tests have become a primary and critical tool for malaria diagnosis in malaria-endemic countries where PfHRP2-based RDTs are widely used. However, in the last decade, the accuracy of PfHRP2-based RDTs has been challenged by the emergence of P. falciparum strains harbouring deletions of the pfhrp2 gene, resulting in false-negative results. In DR. Congo, little is known about the prevalence of the pfhrp2 gene deletion among P. falciparum isolates infecting symptomatic patients, especially in low to moderate transmission areas where pfhrp2 deletion parasites are assumed to emerge and spread. Here we determine the local prevalence and factors associated with pfhrp2 gene deletions among symptomatic malaria patients in the Kwilu province of the Democratic Republic of Congo, a low to moderate malaria transmission area.MethodsWe used secondary data from a prospective health facility-based cross-sectional study conducted on 684 individuals of all ages, seeking healthcare with symptoms suggestive of malaria from October to December 2018 in 34 randomly selected health facilities. Sociodemographic, malaria prevention and treatment practices, and clinical variables were collected using a pre-tested structured questionnaire. Patients’ medical records were used to collect additional clinical data. Blood was collected for microscopy, PfHRP2-RDT, and spotted onto Whatman filter paper for downstream genetic analysis. Genomic DNA was extracted and used to perform PCR assays for the detection and confirmation of pfhrp2 gene deletions. Data were entered and analysed using STATA15. Fischer’s exact and the Kruskal-Wallis tests were applied to look for associations between exposures and the pfhrp2 gene deletion with a level of statistical significance set at p < 0.05. ResultsThe overall prevalence of the pfhrp2 gene deletion was 9.2% (95% CI 6.7% – 12.1%). The deletion of the pfhrp2 gene was associated with health zone of origin (p=0.012) and age (p=0.019). Among false-negative PfHRP2-RDT results, only 9.9% were due to pfhrp2 gene deletion.ConclusionP. falciparum isolates with pfhrp2 gene deletions are relatively common among symptomatic patients in Kwilu province. Further investigations are needed to provide enough evidence for policy change. Meanwhile, the use of RDTs targeting PfHRP2 and pLDH antigens could limit the spread of deleted isolates.