Histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in Plasmodium falciparum isolates from select sites in Brazil and Bolivia

Abstract

More than 80% of available malaria rapid diagnostic tests (RDTs) are based on the detection of histidine-rich protein-2 (PfHRP2) for diagnosis of Plasmodium falciparum malaria. Recent studies have shown the genes that code for this protein and its paralog, histidine-rich protein-3 (PfHRP3), are absent in parasites from the Peruvian Amazon Basin. Lack of PfHRP2 protein through deletion of the pfhrp2 gene leads to false-negative RDT results for P. falciparum. We have evaluated the extent of pfhrp2 and pfhrp3 gene deletions in a convenience sample of 198 isolates from six sites in three states across the Brazilian Amazon Basin (Acre, Rondonia and Para) and 25 isolates from two sites in Bolivia collected at different times between 2010 and 2012. Pfhrp2 and pfhrp3 gene and their flanking genes on chromosomes 7 and 13, respectively, were amplified from 198 blood specimens collected in Brazil. In Brazil, the isolates collected in Acre state, located in the western part of the Brazilian Amazon, had the highest percentage of deletions for pfhrp2 25 (31.2%) of 79, while among those collected in Rondonia, the prevalence of pfhrp2 gene deletion was only 3.3% (2 out of 60 patients). In isolates from Para state, all parasites were pfhrp2-positive. In contrast, we detected high proportions of isolates from all 3 states that were pfhrp3-negative ranging from 18.3% (11 out of 60 samples) to 50.9% (30 out of 59 samples). In Bolivia, only one of 25 samples (4%) tested had deleted pfhrp2 gene, while 68% (17 out of 25 samples) were pfhrp3-negative. Among the isolates tested, P. falciparum pfhrp2 gene deletions were present mainly in those from Acre State in the Brazilian Amazon. These results indicate it is important to reconsider the use of PfHRP2-based RDTs in the western region of the Brazilian Amazon and to implement appropriate surveillance systems to monitor pfhrp2 gene deletions in this and other parts of the Amazon region.

Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis

“…However, this approach may be compromised by the emergence of P. falciparum parasites with deleted pfhrp2. South America was the first region to report the occurrence of false negative RDT results due to this gene deletion (Gamboa et al, 2010;Akinyi et al, 2013;Abdallah et al, 2015;Akinyi Okoth et al, 2015;Murillo Solano et al, 2015;Rachid Viana et al, 2017). Similar evidence was followed by more recent studies from Africa (Dolo et al, 2012;Wurtz et al, 2013;Parr et al, 2016;Beshir et al, 2017) and Asia (Kumar et al, 2013;Li et al, 2015;Bharti et al, 2016).…”

“…Meta-analysis was then performed on the remaining ten studies. These studies consisted of data from Bolivia (Rachid Viana et al, 2017), Brazil (Rachid Viana et al, 2017), Colombia (Murillo Solano et al, 2015;Dorado et al, 2016), French Guiana (Trouvay et al, 2013), Guyana , Honduras (Abdallah et al, 2015), Peru (Gamboa et al, 2010), and Suriname (Akinyi Okoth et al, 2015) in South America, and from Eritrea (Menegon et al, 2017;Berhane et al, 2018), Ghana (Amoah et al, 2016), and Kenya (Beshir et al, 2017) in Africa .…”

“…Initial evidence of deletion was confirmed by PCR amplification of pfhrp2 and pfhrp3 and their flanking regions to infer the extent of the respective deletions. To test the quality of DNA in the samples and confirm the gene deletions, further PCR amplification was carried out in other genes, such as the merozoite surface protein-1 or -2 genes (Gamboa et al, 2010;Murillo Solano et al, 2015;Dorado et al, 2016;Beshir et al, 2017;Rachid Viana et al, 2017). However, the recommended antigen analysis based on re-testing the samples with a different pfhrp2-based RDT or using an enzyme-linked immunosorbent assay to quantify the levels of the pfhrp2 protein (Cheng et al, 2014) in a sample was only performed in three studies (Gamboa et al, 2010;Dorado et al, 2016;Rachid Viana et al, 2017).…”

“…The meta-analysis provided global estimates for the mean frequency of pfhrp2 and pfhrp3 deletions, respectively, though it has some caveats. Firstly, the studies considered different populations, such as asymptomatic children (Amoah et al, 2016;Beshir et al, 2017), children and adults (Menegon et al, 2017), or symptomatic patients (Abdallah et al, 2015;Dorado et al, 2016;Rachid Viana et al, 2017). Secondly, some studies referred to historical samples available from the respective populations (Trouvay et al, 2013) or to data passively collected from health centres or clinics (Akinyi Okoth et al, 2015).…”

A novel metabarcoded DNA sequencing tool for the detection of Plasmodium species in malaria positive patients

“…Several factors potentially affect the accuracy and false-negative results of RDT including the interpretation of the test strip colour change, the density of malaria infection in the host, improper storage/handling of the kit and poor test performance (Echeverry et al, 2016). Besides this, other major factors such cross-reactivity of HRP2 with histidine-rich protein 3 (a structural homolog with significant sequence similarity) and deletions in the HRP2 locus in P. falciparum isolates may account for false-negative results (Akinyi Okoth et al, 2015; Rachid Viana et al, 2017).…”