Background Malaria remains a major public health concern, especially in the tropics and subtropics where disproportionately high disease burden occurs annually. The World Health Organization recommends parasitological confirmation of suspected malaria cases by either Giemsa stained microscopy or rapid diagnostic tests (RDT) before treatment. The most sensitive RDT used for malaria diagnosis targets histidine-rich protein 2 (HRP2), an antigen unique to Plasmodium falciparum. HRP2 based RDTs also detect histidine-rich protein 3 (HRP3), a structural homolog sharing multiple epitopes with HRP-2. This notwithstanding, there are reports of the deletion of the pfhrp2/pfhrp3 gene and it impact on performance. To improve on the detection of the deletion, this study aimed to investigate the prevalence of pfhrp2/pfhrp3 gene deletion using novel digital PCR (dPCR) in Southern Ghana. The dPCR assay provides absolute quantification of the target gene without a need for a calibration curve.

Methods Community-based cross sectional study was conducted at three districts (i.e., Nkwanta South, Sekyere South and Ga South) in Southern Ghana. A total of 1134 whole blood samples were obtained from asymptomatic individuals in the aforementioned study sites.

Results After screening for Plasmodium falciparum with varATS multicopy gene, 304 samples were selected from Nkwanta South (54.6%, n=166), Ga South (28.3%, n=86) and Sekyere South (17.1%, n=52) and were typed for the presence/absence of the target gene using digital PCR. The assay detected deletion in pfhrp3 gene with 0.3%(n=300) of the isolates examined reported to have a deletion. Unlike pfhrp3, no deletion was observed with respect to pfhrp2.

Conclusion Our findings validate the novel dPCR assay as a is high-throughput and highly sensitive tool for molecular surveillance of pfhrp2/pfhrp3 gene deletion in Ghana.