Molecular surveillance reveals the presence of pfhrp2 and pfhrp3 gene deletions in Plasmodium falciparum parasite populations in Uganda, 2017-2019

Agaba B. Bosco, Karen Anderson, Karryn Gresty, Christiane Prosser, David Smith, Joaniter I. Nankabirwa, Sam Nsobya, Adoke Yeka, Jimmy Opigo, Samuel Gonahasa, Rhoda Namubiru, Emmanuel Arinaitwe, Paul Mbaka, John Kissa, Sungho Won, Bora Lee, Chae Seung Lim, Charles Karamagi, Jane Cunningham, Joan K. NakayagaMoses R. Kamya, Qin Cheng

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17 Citations (Scopus)


Background: Histidine-rich protein-2 (HRP2)-based rapid diagnostic tests (RDTs) are the only RDTs recommended for malaria diagnosis in Uganda. However, the emergence of Plasmodium falciparum histidine rich protein 2 and 3 (pfhrp2 and pfhrp3) gene deletions threatens their usefulness as malaria diagnostic and surveillance tools. The pfhrp2 and pfhrp3 gene deletions surveillance was conducted in P. falciparum parasite populations in Uganda. Methods: Three-hundred (n = 300) P. falciparum isolates collected from cross-sectional malaria surveys in symptomatic individuals in 48 districts of eastern and western Uganda were analysed for the presence of pfhrp2 and pfhrp3 genes. Presence of parasite DNA was confirmed by PCR amplification of the 18s rRNA gene, msp1 and msp2 single copy genes. Presence or absence of deletions was confirmed by amplification of exon1 and exon2 of pfhrp2 and pfhrp3 using gene specific PCR. Results: Overall, pfhrp2 and pfhrp3 gene deletions were detected in 29/300 (9.7%, 95% CI 6.6-13.6%) parasite isolates. The pfhrp2 gene was deleted in 10/300 (3.3%, 95% CI 1.6-6.0%) isolates, pfhrp3 in 9/300 (3.0%, 95% CI 1.4-5.6%) while both pfhrp2 and pfhrp3 were deleted in 10/300 (3.3%, 95% CI 1.6-6.0%) parasite isolates. Proportion of pfhrp2/3 deletions was higher in the eastern 14.7% (95% CI 9.7-20.0%) compared to the western region 3.1% (95% CI 0.8-7.7%), p = 0.001. Geographical location was associated with gene deletions aOR 6.25 (2.02-23.55), p = 0.003. Conclusions: This is the first large-scale survey reporting the presence of pfhrp2/3 gene deletions in P. falciparum isolates in Uganda. Roll out of RDTs for malaria diagnosis should take into consideration the existence of pfhrp2/3 gene deletions particularly in areas where they were detected. Periodic pfhrp2/3 surveys are recommended to inform future decisions for deployment of alternative RDTs.

Original languageEnglish
Article number300
JournalMalaria Journal
Issue number1
Publication statusPublished - 2020 Aug 26

Bibliographical note

Funding Information:
Funding for parasite gene deletion analysis was supported by the US Armed Forces Health Surveillance Branch (AFHSB) Global Emerging Infections Surveillance (GEIS) section and the Fogarty International Center of the National Institutes of Health under Award Number D43TW010526. JIN is supported by the Fogarty International Center (Emerging Global Leader Award grant number K43TW010365). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.

Publisher Copyright:
© 2020 The Author(s).


  • Deoxyribonucleic acid
  • Gene deletion
  • Histidine rich protein 2
  • Histidine rich protein 3
  • Malaria rapid diagnostic tests
  • Microscopy
  • Plasmodium falciparum

ASJC Scopus subject areas

  • Parasitology
  • Infectious Diseases


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