Plasmodium falciparum parasites with histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in two endemic regions of Kenya

Khalid B Beshir,Nuno Sepúlveda,Colin Sutherland,Jetske Gudrun De Boer,Julian Mwanguzi,Ailie Robinson,Jameel Bharmal,Heidi Hopkins,Jane Cunningham,Annette Obukosia Busula

doi:10.1038/s41598-017-15031-2

Abstract

Deletions of the Plasmodium falciparum hrp2 and hrp3 genes can affect the performance of HRP2-based malaria rapid diagnostic tests (RDTs). Such deletions have been reported from South America, India and Eritrea. Whether these parasites are widespread in East Africa is unknown. A total of 274 samples from asymptomatic children in Mbita, western Kenya, and 61 genomic data from Kilifi, eastern Kenya, were available for analysis. PCR-confirmed samples were investigated for the presence of pfhrp2 and pfhrp3 genes. In samples with evidence of deletion, parasite presence was confirmed by amplifying three independent genes. We failed to amplify pfhrp2 from 25 of 131 (19.1%) PCR-confirmed samples. Of these, only 8 (10%) samples were microscopic positive and were classified as pfhrp2-deleted. Eight microscopically-confirmed pfhrp2-deleted samples with intact pfhrp3 locus were positive by HRP2-based RDT. In addition, one PCR-confirmed infection showed a deletion at the pfhrp3 locus. One genomic sample lacked pfhrp2 and one lacked pfhrp3. No sample harbored parasites lacking both genes. Parasites lacking pfhrp2 are present in Kenya, but may be detectable by HRP-based RDT at higher parasitaemia, possibly due to the presence of intact pfhrp3. These findings warrant further systematic study to establish prevalence and diagnostic significance.

Highlights

Antigen-detecting rapid diagnostic tests (RDTs) play a key role in malaria control successes in many parts of the world, and the global availability and scale of use of RDTs has increased dramatically over the last 10 years[1]
The minimum parasite density reported by microscopy was 80 parasites/μL, suggesting that this was the threshold for detection by the field microscopist
Eight of 89 (9%) samples analyzed from western Kenya were pfhrp2-deleted; and genomic data from eastern Kenya identified a genome with no coverage for the pfhrp[2] gene or flanking regions

Summary

Introduction

Antigen-detecting RDTs play a key role in malaria control successes in many parts of the world, and the global availability and scale of use of RDTs has increased dramatically over the last 10 years[1]. In one study in western Kenya, HRP2-based RDT gave false-negative results in 5–10% and 25–30% of samples compared to microscopy and PCR respectively[7]. Such results have been ascribed to varying thresholds of detection for the different tests. Concerns have been raised that such false-negative results may reflect presence of parasites with pfhrp[2] gene deletions or mutations. In the past few years, reports have emerged of pfhrp[2] mutations or deletions in Africa and India[9,10,11,12] leading to false-negative RDT results. Guidelines have recently been issued for study design and molecular assays to assess gene mutations[16]

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Conclusion