Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT, and a highly sensitive quantitative PCR and the implication of submicroscopic infections

Abstract Background: The World Health Organization recommends parasitological confirmation of all suspected malaria cases by microscopy or rapid diagnostic tests (RDTs) before treatment. These conventional tools are widely used for point-of-care diagnosis in spite of their poor sensitivity at low parasite density. Several studies have compared the diagnostic accuracy of microscopy and RDT using standard 18S rRNA PCR as reference with varying outcomes. Here, we present for the first time in Ghana, the accuracy of diagnosis of microscopy and RDT using highly sensitive varATS qPCR as reference in a clinical setting.Methods: 1,040 febrile patients were recruited from two primary health care centers in the Ashanti Region of Ghana and tested for malaria by microscopy, RDT, and varATS qPCR. The sensitivity, specificity, and predictive values were assessed using qPCR as gold standard.Results: Parasite prevalence was 17.5%, 24.5%, and 42.1% by microscopy, RDT, and varATS qPCR respectively. Using qPCR as the standard, RDT was more sensitive (55.7% vs 39.3%), marginally less specific (98.2% vs 98.3%), and had higher positive (95.7% vs 94.5%) and negative predictive values (75.3% vs 69.0%) than microscopy. Parasite prevalence and density was higher among the 5-14 age group than the <5, 15-30, and >30 age groups across all the tests.Conclusions: RDT outperformed microscopy for the diagnosis of P. falciparum malaria in the study area. However, both diagnostic methods missed over 40% of infections that were detected by varATS qPCR. Novel tools are needed to ensure prompt diagnosis of all clinical malaria cases.