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Background   Plasmodium falciparum,  the most dominant species in sub-Saharan Africa, causes the most severe clinical malaria manifestations. In resource-limited Ghana, where malaria and HIV geographically overlap, histidine-rich protein 2 (HRP2)-based rapid diagnostic test (RDT) is a faster, easier and cheaper alternative to clinical gold standard light microscopy. However, mutations in parasite  hrp2  gene may result in missed infections, which have severe implications for malaria control.    Methods  The performance of a common HRP2-based RDT and expert light microscopy in HIV-positive and HIV-negative children under 5 years old was compared with PCR as laboratory gold standard. Finger-prick capillary blood was tested with First Response ®  Malaria Ag  P. falciparum  (HRP2). Giemsa-stained thick and thin blood films were examined with ≥ 200 high power fields and parasites counted per 200 white blood cells. Nested PCR species identification of  P. falciparum  was performed and resolved on agarose gel. False negatives from RDT were further tested for deleted  pfhrp2/3  and flanking genes, using PCR. The study was performed in two anti-retroviral therapy clinics in Accra and Atibie.    Results  Out of 401 participants enrolled, 150 were HIV positive and 251 HIV negative. Malaria was more prevalent in children without HIV. Microscopy had a higher sensitivity [100% (99–100)] than RDT [83% (53.5–100)]. Parasites with  pfhrp2/3  deletions contributed to missed infections from RDT false negatives.    Conclusion  Circulation of malaria parasites with  pfrhp2/3  deletions in this population played a role in missed infections with RDT. This ought to be addressed if further strides in malaria control are to be made.    Electronic supplementary material  The online version of this article (10.1186/s12936-018-2231-7) contains supplementary material, which is available to authorized users.

Plasmodium falciparum diagnostic tools in HIV-positive under-5-year-olds in two ART clinics in Ghana: are there missed infections?