Molecular Surveillance Reveals The Presence Ofpfhrp2andpfhrp3gene Deletions Inplasmodium Falciparumparasite Populations In Uganda, 2017-2019

Background Histidine-rich protein-2 (HRP2)-based rapid diagnostic tests (RDTs) are the only RDTs recommended for malaria diagnosis in Uganda. However, the emergence ofPlasmodium falciparumhistidine rich protein 2 and 3 (pfhrp2andpfhrp3)gene deletions threatens their usefulness as malaria diagnostic and surveillance tools. Thepfhrp2andpfhrp3gene deletions surveillance was conducted inP. falciparumparasite populations in Uganda. Methods Three-hundred (n = 300)P. falciparumisolates collected from cross-sectional malaria surveys in symptomatic individuals in 48 districts of eastern and western Uganda were analysed for the presence ofpfhrp2andpfhrp3genes. Presence of parasite DNA was confirmed by PCR amplification of the18s rRNAgene, msp1andmsp2single copy genes. Presence or absence of deletions was confirmed by amplification of exon1 and exon2 ofpfhrp2andpfhrp3using gene specific PCR. Results Overall,pfhrp2andpfhrp3gene deletions were detected in 29/300 (9.7%, 95% CI 6.6-13.6%) parasite isolates. Thepfhrp2gene was deleted in 10/300 (3.3%, 95% CI 1.6-6.0%) isolates,pfhrp3in 9/300 (3.0%, 95% CI 1.4-5.6%) while bothpfhrp2andpfhrp3were deleted in 10/300 (3.3%, 95% CI 1.6-6.0%) parasite isolates. Proportion ofpfhrp2/3deletions was higher in the eastern 14.7% (95% CI 9.7-20.0%) compared to the western region 3.1% (95% CI 0.8-7.7%), p = 0.001. Geographical location was associated with gene deletions aOR 6.25 (2.02-23.55), p = 0.003. Conclusions This is the first large-scale survey reporting the presence ofpfhrp2/3gene deletions inP. falciparumisolates in Uganda. Roll out of RDTs for malaria diagnosis should take into consideration the existence ofpfhrp2/3gene deletions particularly in areas where they were detected. Periodicpfhrp2/3surveys are recommended to inform future decisions for deployment of alternative RDTs.