Sequence variation in Plasmodium falciparum Histidine Rich Proteins 2 and 3 in Indian isolates: Implications for Malaria Rapid Diagnostic Test Performance

Neeru Singh,Venkatachalam Udhayakumar,Shrikant Nema,Himanshu Singh Chandel,Praveen Kumar Bharti,Amreen Ahmad,Sri Krishna

doi:10.1038/s41598-017-01506-9

Abstract

Commercial malaria rapid diagnostic tests (RDTs) detect P. falciparum histidine rich protein 2 (PfHRP2) and cross react with PfHRP3, a structural homologue. Here, we analysed natural variations in PfHRP2 and PfHRP3 sequences from Indian isolates and correlated these variations with RDT reactivity. A total 1392 P. falciparum positive samples collected from eight endemic states were PCR amplified for Pfhrp2 and Pfhrp3 genes and were sequenced. The deduced protein sequences were analysed for repeat variations and correlated with RDT reactivity. Out of 1392 PCR amplified samples, a single sample was Pfhrp2 negative and two samples were Pfhrp3 negative. Complete Pfhrp2 and Pfhrp3 sequences were obtained for 769 samples and 750 samples, respectively. A total of 16 distinct repeat motifs were observed for Pfhrp2 and 11 for Pfhrp3, including some new repeat types. No correlation was found between variations in the size of Pfhrp2 repeat types 2 and 7, nor between any combinations of repeat motifs, and performance of a commercial RDT at low parasite densities. The findings suggest that sequence diversity in Pfhrp2 and Pfhrp3 genes in Indian isolates is not likely to negatively influence performance of currently used PfHRP2 RDTs.

Highlights

Commercial malaria rapid diagnostic tests (RDTs) detect P. falciparum histidine rich protein 2 (PfHRP2) and cross react with PfHRP3, a structural homologue
This prediction was not confirmed in a subsequent study that included a large sample size (PfHRP2 in 458 isolates from 38 countries), the possibility remains that some of the variation in this protein may impact the performance of RDTs, especially when the parasite density is
We reported that among 1521 microscopically confirmed P. falciparum parasites screened from eight malaria endemic states, 50 isolates were not detected by RDTs, 36 of them had deleted Pfhrp[2] and 27 of them had deleted Pfhrp[310]

Summary

Introduction

Commercial malaria rapid diagnostic tests (RDTs) detect P. falciparum histidine rich protein 2 (PfHRP2) and cross react with PfHRP3, a structural homologue. By analysing a limited number of parasite isolate sequences with their corresponding RDT reactivity patterns at various densities, Baker et al reported that the combined number of type 2 (AHHAHHAD) x type 7 (AHHAAD) repeats (cut off

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