London School of Hygiene & Tropical Medicine Malaria Centre

Markers in some malaria diagnosis tests are deleted in certain strains of malaria parasite - are these tests still effective?

07 November 2017
Blog | Publication

Evidence of deletion of Plasmodium falciparum histidine-rich proteins in Kenya


Malaria parasites with gene deletions that affect a key target of rapid diagnostic tests (RDTs) are circulating in East Africa. A report of this new finding, from research conducted by Malaria Centre members, is published today in Scientific Reports. The researchers identified Plasmodium falciparum parasites from eastern and western Kenya that have deletions of genes called pfhrp2 and pfhrp3, which code for histidine-rich proteins 2 (HRP2) and 3 (HRP3).


Malaria RDTs based on detection of HRP2 are widely used in clinical care in malaria-endemic areas, including much of sub-Saharan Africa. Recently, concern has grown that deletions of the pfhrp2 and pfhrp3 genes could affect the performance of HRP2-based RDTs. Pfhrp2 and pfhrp3 deletions have been reported in South America and India, and recently in some African countries. The true extent of parasites with this genetic profile is not known in Africa, which bears by far the largest proportion of the global P. falciparum burden.


Malaria parasites with deletions may still be detectable 


The report being published today confirms the presence of pfhrp deletions in parasites that infect humans in Kenya. Importantly, this study also indicates that pfhrp2-deleted parasites may be detectable by HRP2-based RDT at higher parasite densities, possibly due to the presence of intact pfhrp3.


Dr Khalid Beshir, a study co-leader at London School of Hygiene and Tropical Medicine (LSHTM), said: “We now have a high throughput DNA extraction and genotyping system that can rapidly detect parasites strains carrying such mutations. One significant finding of the study is that the pfhrp2-deleted parasite strains can still give signal in HRP2-based RDT if the parasitaemia is high and if pfhrp3 is not deleted. The high throughput technology can be used for efficient future research and surveillance for samples from Africa.”

Images, top: high throughput robotic DNA extraction and genotyping system. Credit Dr Khalid B Beshir. Figure, bottom left: algorithm to determine histidine-rich protein deletion. Figure, bottom right: plot map of samples from genomic data showing gene deletion. Figures replicated with permission of the author.

But how common are these malaria parasites?


The study processed more than 200 samples from children in Kenya. A rigorous series of molecular testing, based on guidance from the WHO, revealed that 10% of malaria parasites had pfhrp2 deletions and another 1% had deletion in pfhrp3. The researchers also used genomic data from Kenya, open to the scientific community, to screen for deletion of the genes and found out that both deletions are present in a small percentage. Dr Nuno Sepulveda, a co-author also at LSHTM, said: “Our study is the perfect example of combining a field work approach with invaluable genomic resources open to the scientific community. The availability of parasite genomic data from other endemic countries will prompt us to extend our analysis into a global scale in order to better understand the true spread of the pfhrp2 and pfhrp3 deletions worldwide.” 


Dr Heidi Hopkins, a study co-leader and Associate Professor at LSHTM, said, “It is reassuring that in this relatively small study, pfhrp2 deletions in Kenya don’t appear to be affecting the accuracy of malaria RDTs. However, our results confirm the need for a more systematic approach to establish the prevalence and distribution of pfhrp2 and pfhrp3 deletions, and to monitor the potential implications for diagnostic strategies in malaria-endemic areas.“ 


The researchers are currently analyzing parasite samples from Ghana, Tanzania and Uganda, to investigate whether pfhrp2 and pfhrp3 deletions are present, and to integrate molecular data with microscopy and RDT results to assess any effect on RDT performance in those areas.