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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.

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