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Apinjoh TO, Tangi LN, Oriero EC, Drammeh S, Ntui-Njock VN, Etoketim B, Chi HF, Kwi PN, Njie B, Oboh MA, Achidi EA, Amambua-Ngwa A. Histidine-rich protein (hrp) 2-based RDT false-negatives and Plasmodium falciparum hrp 2 and 3 gene deletions in low, seasonal and intense perennial transmission zones in Cameroon: a cross - sectional study. BMC Infect Dis 2024; 24:1080. [PMID: 39350071 PMCID: PMC11443727 DOI: 10.1186/s12879-024-09935-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND False negative rapid diagnostic tests (RDTs) accruing to the non-detection of Plasmodium falciparum histidine-rich protein 2/3 (Pfhrp2/3) is threatening the diagnosis and management of malaria. Although regular monitoring is necessary to gauge the level of efficacy of the tool, studies in Cameroon remain limited. This study assessed Plasmodium spp. prevalence and Pfhrp2/3 gene deletions across ecological and transmission zones in Cameroon. METHODS This is a cross-sectional, multi-site, community- and hospital- based study, in 21 health facilities and 14 communities covering all five ecological settings in low seasonal (LS) and intense perennial (IPT) malaria transmission zones between 2019 and 2021. Participants were screened for malaria parasite using Pfhrp2 RDT and light microscopic examination of thick peripheral blood smears. DNA was extracted from dried blood spot using chelex®-100 and P. falciparum confirmed using varATS real-time quantitative Polymerase Chain Reaction (qPCR), P. malariae and P. ovale by real-time qPCR of Plasmepsin gene, and P. vivax using a commercial kit. Isolates with amplified Pfcsp and Pfama-1 genes were assayed for Pfhrp 2/3 gene deletions by conventional PCR. RESULTS A total of 3,373 participants enrolled, 1,786 Plasmodium spp. infected, with 77.4% P. falciparum. Discordant RDT and qPCR results (False negatives) were reported in 191 (15.7%) P. falciparum mono-infected samples from LS (29%, 42) and IPT (13.9%, 149). The Pfhrp2+/Pfhrp3 + genotype was most frequent, similar between LS (5.5%, 8/145) and IPT (6.0%, 65/1,076). Single Pfhrp2 and Pfhrp3 gene deletions occurred in LS (0.7%, 1/145 each) and IPT (3.6%, 39/1,076 vs. 2.9%, 31/1,076), respectively. Whilst a single sample harboured Pfhrp2-/Pfhrp3- genotype in LS, 2.4% (26/1,076) were double deleted at IPT. Pfhrp2+/Pfhrp3- (0.3%, 3/1,076) and Pfhrp2-/Pfhrp3+ (1.2%, 13/1,076) genotypes were only observed in IPT. Pfhrp2, Pfhrp3 deletions and Pfhrp2-/Pfhrp3- genotype accounted for 78.8% (26), 69.7% (23) and 63.6% (21) RDT false negatives, respectively. CONCLUSION Plasmodium falciparum remains the most dominant and widely distributed Plasmodium species across transmission and ecological zones in Cameroon. Although the low prevalence of Pfhrp2/3 gene deletions supports the continued use of HRP2-based RDTs for routine malaria diagnosis, the high proportion of false-negatives due to gene deleted parasites necessitates continued surveillance to inform control and elimination efforts.
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Affiliation(s)
- Tobias Obejum Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon.
- Department of Chemical and Biological Engineering, The University of Bamenda, Bambili, Cameroon.
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
| | - Livinus Ngu Tangi
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Eniyou Cheryll Oriero
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Sainabou Drammeh
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Blessed Etoketim
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Hanesh Fru Chi
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Pilate Nkineh Kwi
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Bekai Njie
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mary Aigbiremo Oboh
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Eric Akum Achidi
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.611954. [PMID: 39314390 PMCID: PMC11418992 DOI: 10.1101/2024.09.09.611954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He ) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST ) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends ( He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
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Molina-de la Fuente I, Pacheco MA, García L, González V, Riloha M, Oki C, Benito A, Escalante AA, Berzosa P. Evolution of pfhrp2 and pfhrp3 deletions in Equatorial Guinea between the pre- and post-RDT introduction. Malar J 2024; 23:215. [PMID: 39026276 PMCID: PMC11264669 DOI: 10.1186/s12936-024-05036-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Pfhrp2 and pfhrp3 deletions are threatening Plasmodium falciparum malaria diagnosis by rapid diagnostic tests (RDT) due to false negatives. This study assesses the changes in the frequencies of pfhrp2 and pfhrp3 deletions (pfhrp2Del and pfhrp3Del, respectively) and the genes in their flaking regions, before and after RDT introduction in Equatorial Guinea. METHODS A total of 566 P. falciparum samples were genotyped to assess the presence of pfhrp2 and pfhrp3 deletions and their flanking genes. The specimens were collected 18 years apart from two provinces of Equatorial Guinea, North Bioko (Insular Region) and Litoral Province (Continental Region). Orthologs of pfhrp2 and pfhrp3 genes from other closely related species were used to compare sequencing data to assess pfhrp2 and pfhrp3 evolution. Additionally, population structure was studied using seven neutral microsatellites. RESULTS This study found that pfhrp2Del and pfhrp3Del were present before the introduction of RDT; however, they increased in frequency after their use, reaching more than 15%. Haplotype networks suggested that pfhrp2Del and pfhrp3Del emerged multiple times. Exon 2 of pfhrp2 and pfhrp3 genes had high variability, but there were no significant changes in amino acid sequences. CONCLUSIONS Baseline sampling before deploying interventions provides a valuable context to interpret changes in genetic markers linked to their efficacy, such as the dynamic of deletions affecting RDT efficacy.
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Affiliation(s)
- Irene Molina-de la Fuente
- Biomedicine and biotechnology Department, University of Alcalá, Ctra.Madrid-Barcelona Km.33,600, 28871, Alcalá de Henares, Spain.
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Luz García
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Vicenta González
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Matilde Riloha
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Consuelo Oki
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Agustín Benito
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Pedro Berzosa
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
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Bally DR, Santos SDS, Arregue DC, de Mattos MK, Suárez-Mutis MC. High Frequency of Deletions in the pfhrp2 and pfhrp3 Genes of Plasmodium falciparum in the Middle Rio Negro Region of the Brazilian Amazon. Trop Med Infect Dis 2024; 9:149. [PMID: 39058191 PMCID: PMC11281371 DOI: 10.3390/tropicalmed9070149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Several countries are reporting natural populations of P. falciparum with deletions in the pfhrp2/3 genes that can lead to false-negative results in rapid diagnostic tests. To investigate the prevalence of deletion in the pfhrp2/3 genes in the Rio Negro basin in the Brazilian Amazon and identify whether there is clinical differentiation between individuals infected by these parasites, clinical samples collected from 2003 to 2016 were analyzed from symptomatic and asymptomatic P. falciparum-infected individuals. The molecular deletion of pfhrp2 and pfhrp3 genes was evaluated using the protocols recommended by the WHO. From 82 samples used, 28 (34.2%) had a single deletion in pfhrp2, 19 (23.2%) had a single deletion in pfhrp3, 15 (18.3%) had a double deletion (pfhrp2/3), and 20 (24.4%) did not have a deletion in either gene. In total, 29.3% of individuals had an asymptomatic plasmodial infection and were 3.64 times more likely to have parasites with a double deletion (pfhrp2/3) than patients with clinical malaria (p = 0.02). The high prevalence of parasites with pfhrp2/3 deletions shows the need to implement a surveillance program in this area. Deletions in parasites may be associated with the clinical pattern of the disease in this area. More studies must be carried out to elucidate these findings.
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Affiliation(s)
- Daniela Romero Bally
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (D.R.B.); (S.d.S.S.); (D.C.A.); (M.K.d.M.)
- Post-Graduation Program in Tropical Medicine, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Simone da Silva Santos
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (D.R.B.); (S.d.S.S.); (D.C.A.); (M.K.d.M.)
| | - Diego Calafate Arregue
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (D.R.B.); (S.d.S.S.); (D.C.A.); (M.K.d.M.)
| | - Mariana Kelly de Mattos
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (D.R.B.); (S.d.S.S.); (D.C.A.); (M.K.d.M.)
| | - Martha C. Suárez-Mutis
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (D.R.B.); (S.d.S.S.); (D.C.A.); (M.K.d.M.)
- Post-Graduation Program in Tropical Medicine, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro 21040-900, Brazil
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5
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Gatton ML, Smith D, Pasay C, Anderson K, Mihreteab S, Valdivia HO, Sanchez JF, Beshir KB, Cunningham J, Cheng Q. Comparison of prevalence estimates of pfhrp2 and pfhrp3 deletions in Plasmodium falciparum determined by conventional PCR and multiplex qPCR and implications for surveillance and monitoring. Int J Infect Dis 2024; 144:107061. [PMID: 38631508 DOI: 10.1016/j.ijid.2024.107061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVES The accuracy of malaria rapid diagnostic tests is threatened by Plasmodium falciparum with pfhrp2/3 deletions. This study compares gene deletion prevalence determined by multiplex real time polymerase chain reaction (qPCR) and conventional polymerase chain reaction (cPCR) using existing samples with clonality previously determined by microsatellite genotyping. METHODS Multiplex qPCR was used to estimate prevalence of pfhrp2/3 deletions in three sets of previously collected patient samples from Eritrea and Peru. The qPCR was validated by multiplex digital polymerase chain reaction. Sample classification was compared with cPCR, and receiver operating characteristic curve analysis was used to determine the optimal ΔCq threshold that aligned the results of the two assays. RESULTS qPCR classified 75% (637 of 849) of samples as single, and 212 as mixed-pfhrp2/3 genotypes, with a positive association between clonality and proportion of mixed-pfhrp2/3 genotype samples. The sample classification agreement between cPCR and qPCR was 75.1% (95% confidence interval [CI] 68.6-80.7%) and 47.8% (95% CI 38.9-56.9%) for monoclonal and polyclonal infections. The qPCR prevalence estimates of pfhrp2/3 deletions showed almost perfect (κ = 0.804, 95% CI 0.714-0.895) and substantial agreement (κ = 0.717, 95% CI 0.562-0.872) with cPCR for Peru and 2016 Eritrean samples, respectively. For 2019 Eritrean samples, the prevalence of double pfhrp2/3 deletions was approximately two-fold higher using qPCR. The optimal threshold for matching the assay results was ΔCq = 3. CONCLUSIONS Multiplex qPCR and cPCR produce comparable estimates of gene deletion prevalence when monoclonal infections dominate; however, qPCR provides higher estimates where multi-clonal infections are common.
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Affiliation(s)
- Michelle L Gatton
- Centre for Immunology and Infection Control, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
| | - David Smith
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Cielo Pasay
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Karen Anderson
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Selam Mihreteab
- National Malaria Control Program, Ministry of Health, Asmara, Eritrea
| | - Hugo O Valdivia
- U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Juan F Sanchez
- U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Jane Cunningham
- Faculty of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Qin Cheng
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
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Watson OJ, Tran TNA, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.21.23297352. [PMID: 37905102 PMCID: PMC10615018 DOI: 10.1101/2023.10.21.23297352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the thirteen years since the first report of pfhrp2-deleted parasites in 2010, the World Health Organization (WHO) has found that 40 of 47 countries surveyed worldwide have reported pfhrp2/3 gene deletions. Due to a high prevalence of pfhrp2/3 deletions causing false-negative HRP2 RDTs, in the last five years, Eritrea, Djibouti and Ethiopia have switched or started switching to using alternative RDTs, that target pan-specific-pLDH or P. falciparum specific-pLDH alone of in combination with HRP2. However, manufacturing of alternative RDTs has not been brought to scale and there are no WHO prequalified combination tests that use Pf-pLDH instead of HRP2 for P. falciparum detection. For these reasons, the continued spread of pfhrp2/3 deletions represents a growing public health crisis that threatens efforts to control and eliminate P. falciparum malaria. National malaria control programmes, their implementing partners and test developers desperately seek pfhrp2/3 deletion data that can inform their immediate and future resource allocation. In response, we use a mathematical modelling approach to evaluate the global risk posed by pfhrp2/3 deletions and explore scenarios for how deletions will continue to spread in Africa. We incorporate current best estimates of the prevalence of pfhrp2/3 deletions and conduct a literature review to estimate model parameters known to impact the selection of pfhrp2/3 deletions for each malaria endemic country. We identify 20 countries worldwide to prioritise for surveillance and future deployment of alternative RDT, based on quickly selecting for pfhrp2/3 deletions once established. In scenarios designed to explore the continued spread of deletions in Africa, we identify 10 high threat countries that are most at risk of deletions both spreading to and subsequently being rapidly selected for. If HRP2-based RDTs continue to be relied on for malaria case management, we predict that the major route for pfhrp2 deletions to spread is south out from the current hotspot in the Horn of Africa, moving through East Africa over the next 20 years. We explore the variation in modelled timelines through an extensive parameter sensitivity analysis and despite wide uncertainties, we identify three countries that have not yet switched RDTs (Senegal, Zambia and Kenya) that are robustly identified as high risk for pfhrp2/3 deletions. These results provide a refined and updated prediction model for the emergence of pfhrp2/3 deletions in an effort to help guide pfhrp2/3 policy and prioritise future surveillance efforts and innovation.
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Affiliation(s)
- Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert J Zupko
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tasmin Symons
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | | | | | - Susan Rumisha
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Paulina A Dzianach
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Isaac Kim
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | | | - Lucy Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Peter Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Australia
| | - Azra Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
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Kattenberg JH, Fernandez-Miñope C, van Dijk NJ, Llacsahuanga Allcca L, Guetens P, Valdivia HO, Van geertruyden JP, Rovira-Vallbona E, Monsieurs P, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay. Microbiol Spectr 2023; 11:e0096022. [PMID: 36840586 PMCID: PMC10101074 DOI: 10.1128/spectrum.00960-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 02/24/2023] Open
Abstract
Molecular surveillance for malaria has great potential to support national malaria control programs (NMCPs). To bridge the gap between research and implementation, several applications (use cases) have been identified to align research, technology development, and public health efforts. For implementation at NMCPs, there is an urgent need for feasible and cost-effective tools. We designed a new highly multiplexed deep sequencing assay (Pf AmpliSeq), which is compatible with benchtop sequencers, that allows high-accuracy sequencing with higher coverage and lower cost than whole-genome sequencing (WGS), targeting genomic regions of interest. The novelty of the assay is its high number of targets multiplexed into one easy workflow, combining population genetic markers with 13 nearly full-length resistance genes, which is applicable for many different use cases. We provide the first proof of principle for hrp2 and hrp3 deletion detection using amplicon sequencing. Initial sequence data processing can be performed automatically, and subsequent variant analysis requires minimal bioinformatic skills using any tabulated data analysis program. The assay was validated using a retrospective sample collection (n = 254) from the Peruvian Amazon between 2003 and 2018. By combining phenotypic markers and a within-country 28-single-nucleotide-polymorphism (SNP) barcode, we were able to distinguish different lineages with multiple resistance haplotypes (in dhfr, dhps, crt and mdr1) and hrp2 and hrp3 deletions, which have been increasing in recent years. We found no evidence to suggest the emergence of artemisinin (ART) resistance in Peru. These findings indicate a parasite population that is under drug pressure but is susceptible to current antimalarials and demonstrate the added value of a highly multiplexed molecular tool to inform malaria strategies and surveillance systems. IMPORTANCE While the power of next-generation sequencing technologies to inform and guide malaria control programs has become broadly recognized, the integration of genomic data for operational incorporation into malaria surveillance remains a challenge in most countries where malaria is endemic. The main obstacles include limited infrastructure, limited access to high-throughput sequencing facilities, and the need for local capacity to run an in-country analysis of genomes at a large-enough scale to be informative for surveillance. In addition, there is a lack of standardized laboratory protocols and automated analysis pipelines to generate reproducible and timely results useful for relevant stakeholders. With our standardized laboratory and bioinformatic workflow, malaria genetic surveillance data can be readily generated by surveillance researchers and malaria control programs in countries of endemicity, increasing ownership and ensuring timely results for informed decision- and policy-making.
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Affiliation(s)
| | - Carlos Fernandez-Miñope
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Norbert J. van Dijk
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Lidia Llacsahuanga Allcca
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pieter Guetens
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | | | - Eduard Rovira-Vallbona
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Pieter Monsieurs
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
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8
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Sabin S, Jones S, Patel D, Subramaniam G, Kelley J, Aidoo M, Talundzic E. Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer. Sci Rep 2023; 13:2893. [PMID: 36801925 PMCID: PMC9938884 DOI: 10.1038/s41598-022-26935-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/22/2022] [Indexed: 02/20/2023] Open
Abstract
The prevalence of Plasmodium falciparum hrp2 (pfhrp2)-deleted parasites threatens the efficacy of the most used and sensitive malaria rapid diagnostic tests and highlights the need for continued surveillance for this gene deletion. While PCR methods are adequate for determining pfhrp2 presence or absence, they offer a limited view of its genetic diversity. Here, we present a portable sequencing method using the MinION. Pfhrp2 amplicons were generated from individual samples, barcoded, and pooled for sequencing. To overcome potential crosstalk between barcodes, we implemented a coverage-based threshold for pfhrp2 deletion confirmation. Amino acid repeat types were then counted and visualized with custom Python scripts following de novo assembly. We evaluated this assay using well-characterized reference strains and 152 field isolates with and without pfhrp2 deletions, of which 38 were also sequenced on the PacBio platform to provide a standard for comparison. Of 152 field samples, 93 surpassed the positivity threshold, and of those samples, 62/93 had a dominant pfhrp2 repeat type. PacBio-sequenced samples with a dominant repeat-type profile from the MinION sequencing data matched the PacBio profile. This field-deployable assay can be used alone for surveilling pfhrp2 diversity or as a sequencing-based addition to the World Health Organization's existing deletion surveillance protocol.
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Affiliation(s)
- Susanna Sabin
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Sophie Jones
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Williams Consulting, Catonsville, MD, USA
| | - Dhruviben Patel
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Williams Consulting, Catonsville, MD, USA
| | - Gireesh Subramaniam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Julia Kelley
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Aidoo
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
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9
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Bendezu J, Torres K, Villasis E, Incardona S, Bell D, Vinetz J, Gamboa D. Geographical distribution and genetic characterization of pfhrp2 negative Plasmodium falciparum parasites in the Peruvian Amazon. PLoS One 2022; 17:e0273872. [PMID: 36413547 PMCID: PMC9681099 DOI: 10.1371/journal.pone.0273872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
Malaria rapid diagnostic tests (RDTs) have been evaluated in the Peruvian Amazon region and their performance has been variable. This region is known for being the first with documented evidence of wild Plasmodium falciparum parasites lacking pfhrp2 and pfhrp3 genes, leading to false-positive results with HRP2-based RDTs. In our attempt to further characterize the deletion pattern of these genes and their evolutionary relationship, 93 P. falciparum samples, collected in different communities from the Peruvian Amazon region between 2009 and 2010, were analyzed in this study. Genomic DNA was used to amplify 18S rRNA, pfmsp2 and pfglurp to confirm the diagnosis and DNA quality, respectively; pfhrp2, pfhrp3, and their flanking genes were amplified by PCR to assess the pattern of the gene deletions. In addition, microsatellite analysis were performed using seven neutral microsatellites (MS) and five microsatellite loci flanking pfhrp2. The data showed the absence of pfhrp3 gene in 53.76% (50/93) of the samples, reflecting a higher frequency than the proportion of pfhrp2 gene deletions (33.33%; 31/93). Among the flanking genes, the highest frequency of deletion was observed in the PF3D7_0831900 gene (78.49%; 73/93) for pfhrp2. MS marker analysis showed the presence of 8 P. falciparum lineages. The lineage Bv1 was the most prevalent among parasites lacking pfhrp2 and pfhrp3 genes. Additionally, using MS flanking pfhrp2 gene, the haplotypes α and δ were found to be the most abundant in this region. This study confirms the presence in this area of field isolates with deletions in either pfhrp2, pfhrp3, or both genes, along with their respective flanking regions. Our data suggest that some pfhrp2/pfhrp3 deletion haplotypes, in special the lineage Bv1, are widely dispersed within the Peruvian Amazon. The persistence of these haplotypes ensures a proportion of P.falciparum parasites lacking the pfhrp2/pfhrp3 genes in this area, which ultimately leads to false-negative results on PfHRP2-detecting malaria RDTs. However, additional studies are needed to not only confirm this hypothesis but also to further delineate the origin and genetic basis for the pfhrp2- and pfhrp3 gene deletions in wild P. falciparum parasites.
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Affiliation(s)
- Jorge Bendezu
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Escuela Universitaria de Posgrado, Universidad Nacional Federico Villareal, Lima, Peru
| | - Katherine Torres
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt” Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elizabeth Villasis
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt” Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - David Bell
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Joseph Vinetz
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States of America
| | - Dionicia Gamboa
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt” Universidad Peruana Cayetano Heredia, Lima, Peru
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10
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Valdivia HO, Anderson K, Smith D, Pasay C, Salas CJ, Braga G, Lucas CM, Lizewski SE, Joya CA, Kooken JM, Sanchez JF, Cheng Q. Spatiotemporal dynamics of Plasmodium falciparum histidine-rich protein 2 and 3 deletions in Peru. Sci Rep 2022; 12:19845. [PMID: 36400806 PMCID: PMC9674673 DOI: 10.1038/s41598-022-23881-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Peru was the first country where pfhrp2 and pfhrp3 gene deletions were detected despite the fact that rapid diagnostics tests are not commonly used for confirmatory malaria diagnosis. This context provides a unique scenario to study the dynamics of pfhrp2 and pfhrp3 gene deletions without apparent RDTs selection pressure. In this study we characterized the presence of pfhrp2 and pfhrp3 genes on 325 P. falciparum samples collected in Iquitos and surrounding communities between 2011 and 2018 in order to understand the dynamics of gene deletion prevalence, potential associations with clinical symptomatology and parasite genetic background. P. falciparum presence was confirmed by microscopy and PCR of 18 s rRNA, pfmsp1 and pfmsp2. Gene deletions were assessed by amplification of exon1 and exon2 of pfhrp2 and pfhrp3 using gene specific PCRs. Confirmation of absence of HRP2 expression was assessed by ELISA of HRP2 and pLDH. Genotyping of 254 samples were performed using a panel of seven neutral microsatellite markers. Overall, pfhrp2 and pfhrp3 dual gene deletions were detected in 67% (217/324) parasite samples. Concordance between pfhrp2 deletion and negligible HRP2 protein levels was observed (Cohen's Kappa = 0.842). Prevalence of gene deletions was heterogeneous across study sites (adjusted p < 0.005) but there is an overall tendency towards increase through time in the prevalence of dual pfhrp2/3-deleted parasites between 2011 (14.3%) and 2016 (88.39%) stabilizing around 65% in 2018. Dual deletions increase was associated with dominance of a single new parasite haplotype (H8) which rapidly spread to all study sites during the 8 study years. Interestingly, participants infected with dual pfhrp2/3-deleted parasites had a significantly lower parasitemias than those without gene deletions in this cohort. Our study showed the increase of pfhrp2/3 deletions in the absence of RDTs pressure and a clonal replacement of circulating lines in the Peruvian Amazon basin. These results suggest that other factors linked to the pfhrp2/3 deletion provide a selective advantage over non-deleted strains and highlight the need for additional studies and continuing surveillance.
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Affiliation(s)
- Hugo O. Valdivia
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Karen Anderson
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - David Smith
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Cielo Pasay
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Carola J. Salas
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Greys Braga
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Carmen M. Lucas
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Stephen E. Lizewski
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Christie A. Joya
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Jennifer M. Kooken
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.507680.c0000 0001 2230 3166Walter Reed Army Institute for Research, Silver Spring, USA
| | - Juan F. Sanchez
- grid.415929.20000 0004 0486 6610U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Qin Cheng
- Australia Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia ,grid.1049.c0000 0001 2294 1395QIMR-Berghofer Medical Research Institute, Brisbane, Australia
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11
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Molina-de la Fuente I, Yimar M, García L, González V, Amor A, Anegagrie M, Benito A, Martínez J, Moreno M, Berzosa P. Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia. Malar J 2022; 21:287. [PMID: 36209103 PMCID: PMC9548178 DOI: 10.1186/s12936-022-04306-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Although rapid diagnostic tests (RDTs) play a key role in malaria-control strategies, their efficacy has been threatened by deletion and genetic variability of the genes pfhrp2/3. This study aims to characterize the deletion, genetic patterns and diversity of these genes and their implication for malaria RDT effectiveness, as well as their genetic evolution in the Amhara region of Ethiopia. Methods The study included 354 isolates from symptomatic patients from the Amhara region of Ethiopia who tested positive by microscopy. Exon 1–2 and exon 2 of genes pfhrp2 and -3 were amplified, and exon 2 was sequenced to analyse the genetic diversity, phylogenetic relationship and epitope availability. Results The deletion frequency in exon 1–2 and exon 2 was 22 and 4.6% for pfhrp2, and 68 and 18% for pfhrp3, respectively. Double deletion frequency for pfhrp2 and pfhrp3 was 1.4%. High genetic diversity, lack of clustering by phylogenetic analysis and evidence of positive selection suggested a diversifying selection for both genes. The amino-acid sequences, classified into different haplotypes, varied widely in terms of frequency of repeats, with novel amino-acid changes. Aminoacidic repetition type 2 and type 7 were the most frequent in all the sequences. The most frequent epitopes among protein sequences were those recognized by MAbs 3A4 and C1-13. Conclusion Deletions and high amino acidic variation in pfhrp2 and pfhrp3 suggest their possible impact on RDT use in the Amhara region, and the high genetic diversity of these genes could be associated with a diversifying selection in Ethiopia. Surveillance of these genes is, therefore, essential to ensure the effectiveness of public health interventions in this region. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04306-3.
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Affiliation(s)
- Irene Molina-de la Fuente
- Department of Biomedicine and Biotechnology, School of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid, Spain. .,Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain. .,Public Health and Epidemiology Research Group, School of Medicine, University of Alcalá, Alcalá de Henares, Madrid, Spain.
| | - Mulat Yimar
- College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Luz García
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Vicenta González
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Arancha Amor
- Mundo Sano Foundations, Institute of Health Carlos III, Madrid, Spain
| | - Melaku Anegagrie
- Mundo Sano Foundations, Institute of Health Carlos III, Madrid, Spain
| | - Agustín Benito
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Javier Martínez
- Department of Biomedicine and Biotechnology, School of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Marta Moreno
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Pedro Berzosa
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
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12
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Martiáñez-Vendrell X, Skjefte M, Sikka R, Gupta H. Factors Affecting the Performance of HRP2-Based Malaria Rapid Diagnostic Tests. Trop Med Infect Dis 2022; 7:265. [PMID: 36288006 PMCID: PMC9611031 DOI: 10.3390/tropicalmed7100265] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
The recent COVID-19 pandemic has profoundly impacted global malaria elimination programs, resulting in a sharp increase in malaria morbidity and mortality. To reduce this impact, unmet needs in malaria diagnostics must be addressed while resuming malaria elimination activities. Rapid diagnostic tests (RDTs), the unsung hero in malaria diagnosis, work to eliminate the prevalence of Plasmodium falciparum malaria through their efficient, cost-effective, and user-friendly qualities in detecting the antigen HRP2 (histidine-rich protein 2), among other proteins. However, the testing mechanism and management of malaria with RDTs presents a variety of limitations. This paper discusses the numerous factors (including parasitic, host, and environmental) that limit the performance of RDTs. Additionally, the paper explores outside factors that can hinder RDT performance. By understanding these factors that affect the performance of HRP2-based RDTs in the field, researchers can work toward creating and implementing more effective and accurate HRP2-based diagnostic tools. Further research is required to understand the extent of these factors, as the rapidly changing interplay between parasite and host directly hinders the effectiveness of the tool.
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Affiliation(s)
- Xavier Martiáñez-Vendrell
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands or
| | - Malia Skjefte
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Ruhi Sikka
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, UP, India
| | - Himanshu Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, UP, India
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13
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Kaaya RD, Amour C, Matowo JJ, Mosha FW, Kavishe RA, Beshir KB. Genetic Sequence Variation in the Plasmodium falciparum Histidine-Rich Protein 2 Gene from Field Isolates in Tanzania: Impact on Malaria Rapid Diagnosis. Genes (Basel) 2022; 13:1642. [PMID: 36140809 PMCID: PMC9498557 DOI: 10.3390/genes13091642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
Malaria rapid diagnosis test (RDT) is crucial for managing the disease, and the effectiveness of detection depends on parameters such as sensitivity and specificity of the RDT. Several factors can affect the performance of RDT. In this study, we focused on the pfhrp2 sequence variation and its impact on RDTs targeted by antigens encoded by Plasmodium falciparum histidine-rich protein 2 (pfhrp2). Field samples collected during cross-sectional surveys in Tanzania were sequenced to investigate the pfhrp2 sequence diversity and evaluate the impact on HRP2-based RDT performance. We observed significant mean differences in amino acid repeats between current and previous studies. Several new amino acid repeats were found to occur at different frequencies, including types AAY, AHHAHHAAN, and AHHAA. Based on the abundance of types 2 and 7 amino acid repeats, the binary predictive model was able to predict RDT insensitivity by about 69% in the study area. About 85% of the major epitopes targeted by monoclonal antibodies (MAbs) in RDT were identified. Our study suggested that the extensive sequence variation in pfhrp2 can contribute to reduced RDT sensitivity. The correlation between the different combinations of amino acid repeats and the performance of RDT in different malaria transmission settings should be investigated further.
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Affiliation(s)
- Robert D. Kaaya
- Faculty of Medicine, Kilimanjaro Christian Medical University College, Moshi P.O. Box 2240, Tanzania
- Pan-African Malaria Vector Research Consortium, Moshi P.O. Box 2240, Tanzania
| | - Caroline Amour
- Faculty of Medicine, Kilimanjaro Christian Medical University College, Moshi P.O. Box 2240, Tanzania
| | - Johnson J. Matowo
- Faculty of Medicine, Kilimanjaro Christian Medical University College, Moshi P.O. Box 2240, Tanzania
- Pan-African Malaria Vector Research Consortium, Moshi P.O. Box 2240, Tanzania
| | - Franklin W. Mosha
- Faculty of Medicine, Kilimanjaro Christian Medical University College, Moshi P.O. Box 2240, Tanzania
- Pan-African Malaria Vector Research Consortium, Moshi P.O. Box 2240, Tanzania
| | - Reginald A. Kavishe
- Faculty of Medicine, Kilimanjaro Christian Medical University College, Moshi P.O. Box 2240, Tanzania
| | - Khalid B. Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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14
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Sivaradjy M, Hamide A, Krishnamoorthy S, Rajkumari N, Mohan V, Sharmila FM. Assessment of Plasmodium falciparum histidine rich protein 2 and /3 ( pfhrp 2&/ pfhrp 3) gene deletion or mutation in Plasmodium falciparum positive blood samples in a tertiary care centre in South India. J Parasit Dis 2022; 46:729-743. [PMID: 36091262 PMCID: PMC9458806 DOI: 10.1007/s12639-022-01492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
Rapid diagnostic card tests (RDTs) enable timely and appropriate diagnosis of malaria especially in remote areas. Plasmodium falciparum histidine rich protein 2 (PFHRP2) is the most targeted antigen for the detection of Plasmodium falciparum infections by rapid diagnostic card test. Genetic mutations and gene deletions are important emerging factors for false-negative RDTs, which may delay the provision of life-saving treatment for the patients. Hence, we would like to evaluate for the existence of pfhrp2/3 gene deleted P. falciparum parasites in our health care setting. This study was conducted for a period of 2 years in a tertiary care centre in South India. Blood samples that are microscopically confirmed as P. falciparum but negative by RDT were assessed for the presence of pfhrp2, pfhrp3, and their flanking genes using conventional PCR. Follow up of the clinical outcomes were also done for these patients. Of the 63 positive samples collected (50 /63) 79.4% were P.vivax and (13/63) 20.6% were P.falciparum by PCR. Among the 13 P. falciparum positive samples, 4 samples (4/13), (95% CI -10.36% to 61.11%) were found to be RDT negative but microscopically positive.Pfhrp2,pfhrp3 and their flanking genes were amplified for these 4 samples. All 4 samples were found to be negative for both pfhrp2-2 & pfhrp2-3 exon regions and also varying patterns of flanking gene deletions were also noted.This study provides molecular evidence for the existence of pfhrp2 & pfhrp3 deleted P. falciparum parasites in a tertiary care centre in South India warranting periodic evaluation of pfhrp2 based RDT use. Only pfhrp2/3 RDT based decision on diagnosis of P.falciparum malaria should always be reconsidered especially in remote areas.
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Affiliation(s)
- Monika Sivaradjy
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
| | - Abdoul Hamide
- Department of Medicine, JIPMER, Dhanvantri nagar, Puducherry, India
| | | | - Nonika Rajkumari
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
| | - Vamsi Mohan
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
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15
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Marquart L, Webb L, O'Rourke P, Gatton ML, Hsiang MS, Kalnoky M, Jang IK, Ntuku H, Mumbengegwi DR, Domingo GJ, McCarthy JS, Britton S. The in-vivo dynamics of Plasmodium falciparum HRP2: implications for the use of rapid diagnostic tests in malaria elimination. Malar J 2022; 21:233. [PMID: 35922803 PMCID: PMC9351188 DOI: 10.1186/s12936-022-04245-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) that rely on the detection of Plasmodium falciparum histidine-rich protein 2 (PfHRP2) have become key tools for diagnosing P. falciparum infection. The utility of RDTs can be limited by PfHRP2 persistence, however it can be a potential benefit in low transmission settings where detection of persistent PfHRP2 using newer ultra-sensitive PfHRP2 based RDTs can serve as a surveillance tool to identify recent exposure. Better understanding of the dynamics of PfHRP2 over the course of a malaria infection can inform optimal use of RDTs. Methods A previously published mathematical model was refined to mimic the production and decay of PfHRP2 during a malaria infection. Data from 15 individuals from volunteer infection studies were used to update the original model and estimate key model parameters. The refined model was applied to a cohort of patients from Namibia who received treatment for clinical malaria infection for whom longitudinal PfHRP2 concentrations were measured. Results The refinement of the PfHRP2 dynamic model indicated that in malaria naïve hosts, P. falciparum parasites of the 3D7 strain produce 33.6 × 10−15 g (95% CI 25.0–42.1 × 10−15 g) of PfHRP2 in vivo per parasite replication cycle, with an elimination half-life of 1.67 days (95% CI 1.11–3.40 days). The refined model included these updated parameters and incorporated individualized body fluid volume calculations, which improved predictive accuracy when compared to the original model. The performance of the model in predicting clearance of PfHRP2 post treatment in clinical samples from six adults with P. falciparum infection in Namibia improved when using a longer elimination half-life of 4.5 days, with 14% to 67% of observations for each individual within the predicted range. Conclusions The updated mathematical model can predict the growth and clearance of PfHRP2 during the production and decay of a mono-infection with P. falciparum, increasing the understanding of PfHRP2 antigen dynamics. This model can guide the optimal use of PfHRP2-based RDTs for reliable diagnosis of P. falciparum infection and re-infection in endemic settings, but also for malaria surveillance and elimination programmes in low transmission areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04245-z.
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Affiliation(s)
- Louise Marquart
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .,University of Queensland, Brisbane, QLD, Australia.
| | - Lachlan Webb
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter O'Rourke
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Michelle S Hsiang
- Department of Pediatrics, University of Texas, Southwestern, Dallas, TX, USA.,Malaria Elimination Initiative, Institute for Global Health Services, University of California, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco, CA, USA
| | | | | | - Henry Ntuku
- Malaria Elimination Initiative, Institute for Global Health Services, University of California, San Francisco, CA, USA
| | | | | | - James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,University of Queensland, Brisbane, QLD, Australia
| | - Sumudu Britton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,University of Queensland, Brisbane, QLD, Australia
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Vera-Arias CA, Holzschuh A, Oduma CO, Badu K, Abdul-Hakim M, Yukich J, Hetzel MW, Fakih BS, Ali A, Ferreira MU, Ladeia-Andrade S, Sáenz FE, Afrane Y, Zemene E, Yewhalaw D, Kazura JW, Yan G, Koepfli C. High-throughput Plasmodium falciparum hrp2 and hrp3 gene deletion typing by digital PCR to monitor malaria rapid diagnostic test efficacy. eLife 2022; 11:72083. [PMID: 35762586 PMCID: PMC9246365 DOI: 10.7554/elife.72083] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 06/05/2022] [Indexed: 01/11/2023] Open
Abstract
Most rapid diagnostic tests for Plasmodium falciparum malaria target the Histidine-Rich Proteins 2 and 3 (HRP2 and HRP3). Deletions of the hrp2 and hrp3 genes result in false-negative tests and are a threat for malaria control. A novel assay for molecular surveillance of hrp2/hrp3 deletions was developed based on droplet digital PCR (ddPCR). The assay quantifies hrp2, hrp3, and a control gene with very high accuracy. The theoretical limit of detection was 0.33 parasites/µl. The deletion was reliably detected in mixed infections with wild-type and hrp2-deleted parasites at a density of >100 parasites/reaction. For a side-by-side comparison with the conventional nested PCR (nPCR) assay, 248 samples were screened in triplicate by ddPCR and nPCR. No deletions were observed by ddPCR, while by nPCR hrp2 deletion was observed in 8% of samples. The ddPCR assay was applied to screen 830 samples from Kenya, Zanzibar/Tanzania, Ghana, Ethiopia, Brazil, and Ecuador. Pronounced differences in the prevalence of deletions were observed among sites, with more hrp3 than hrp2 deletions. In conclusion, the novel ddPCR assay minimizes the risk of false-negative results (i.e., hrp2 deletion observed when the sample is wild type), increases sensitivity, and greatly reduces the number of reactions that need to be run.
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Affiliation(s)
| | - Aurel Holzschuh
- University of Notre Dame, Notre Dame, United States.,Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Colins O Oduma
- Kenya Medical Research Institute-Centre for Global Health Research, Kisumu, Kenya.,Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya
| | - Kingsley Badu
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, Zanzibar, United Republic of Tanzania
| | | | | | - Fabián E Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Yaw Afrane
- Department of Medical Microbiology, University of Ghana, Accra, Ghana
| | - Endalew Zemene
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - James W Kazura
- Case Western Reserve University, Cleveland, United States
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, Irvine, United States
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17
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Beshir KB, Parr JB, Cunningham J, Cheng Q, Rogier E. Screening strategies and laboratory assays to support Plasmodium falciparum histidine-rich protein deletion surveillance: where we are and what is needed. Malar J 2022; 21:201. [PMID: 35751070 PMCID: PMC9233320 DOI: 10.1186/s12936-022-04226-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
Rapid diagnostic tests (RDTs) detecting Plasmodium falciparum histidine-rich protein 2 (HRP2) have been an important tool for malaria diagnosis, especially in resource-limited settings lacking quality microscopy. Plasmodium falciparum parasites with deletion of the pfhrp2 gene encoding this antigen have now been identified in dozens of countries across Asia, Africa, and South America, with new reports revealing a high prevalence of deletions in some selected regions. To determine whether HRP2-based RDTs are appropriate for continued use in a locality, focused surveys and/or surveillance activities of the endemic P. falciparum population are needed. Various survey and laboratory methods have been used to determine parasite HRP2 phenotype and pfhrp2 genotype, and the data collected by these different methods need to be interpreted in the appropriate context of survey and assay utilized. Expression of the HRP2 antigen can be evaluated using point-of-care RDTs or laboratory-based immunoassays, but confirmation of a deletion (or mutation) of pfhrp2 requires more intensive laboratory molecular assays, and new tools and strategies for rigorous but practical data collection are particularly needed for large surveys. Because malaria diagnostic strategies are typically developed at the national level, nationally representative surveys and/or surveillance that encompass broad geographical areas and large populations may be required. Here is discussed contemporary assays for the phenotypic and genotypic evaluation of P. falciparum HRP2 status, consider their strengths and weaknesses, and highlight key concepts relevant to timely and resource-conscious workflows required for efficient diagnostic policy decision making.
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Affiliation(s)
- Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Diseases, Keppel Street, London, WC1E 7HT, UK
| | - Jonathan B Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30029, USA.
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18
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Eyong EM, Etutu SJM, Jerome FC, Nyasa RB, Kwenti TE, Moyeh MN. Plasmodium falciparum histidine-rich protein 2 and 3 gene deletion in the Mount Cameroon region. IJID REGIONS (ONLINE) 2022; 3:300-307. [PMID: 35755467 PMCID: PMC9216387 DOI: 10.1016/j.ijregi.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022]
Abstract
pfhrp2/3 gene deletions occur in parasite populations in the Mount Cameroon region pfhrp2-negative parasites are the more common in the Mount Cameroon region pfhrp2/3-negative parasites negatively impact malaria rapid diagnostic test success
Objective Plasmodium falciparum produces histidine-rich protein 2/3 (Pfhrp2/3) genes that accumulate to high levels in the bloodstream and serve as a diagnostic and prognostic marker for falciparum malaria. Pfhrp2/3 gene deletions may lead to false-negative rapid diagnostic test (RDT) results. We aimed to determine the prevalence of pfhrp2/3 gene deletions in P. falciparum isolates and the implications for RDT use in the Mount Cameroon region. Methods A cross-sectional hospital-based study with malaria diagnosis performed using microscopy, RDT and nested polymerase chain reaction (nPCR). In total, 324 P. falciparum microscopy positive individuals were enrolled and their samples confirmed positive for P. falciparum using 18SrRNA PCR. Samples that gave false-negative RDT results were analyzed to detect pfhrp2/3 exon 2 deletions. Results Of 324 positive microscopic and nPCR samples, 16 gave RDT false-negative results. Among the 324 P. falciparum positive isolates, exon 2 deletions were observed in 2.2% (7 of 324); 3 were negative for pfhrp2 gene, 2 for pfhrp3, and 2 for both pfhrp2 and pfhrp3 (double deletions). Conclusion P. falciparum isolates with pfhrp2/3 gene deletion were present in the parasite populations and may contribute to the RDT false-negative results in the Mount Cameroon region.
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Affiliation(s)
- Esum Mathias Eyong
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
| | - Sophie Jose Molua Etutu
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
| | - Fru-Cho Jerome
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
| | - Raymond Babila Nyasa
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
| | - Tebit Emmanuel Kwenti
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
| | - Marcel N Moyeh
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, P.O. Box 63, Buea, South West Region of Cameroon
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19
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Deletions of the Plasmodium falciparum histidine-rich protein 2/3 genes are common in field isolates from north-eastern Tanzania. Sci Rep 2022; 12:5802. [PMID: 35388127 PMCID: PMC8987040 DOI: 10.1038/s41598-022-09878-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/30/2022] [Indexed: 11/26/2022] Open
Abstract
Plasmodium falciparum parasites lacking histidine-rich protein 2 and 3 (pfhrp2/3) genes have been reported in several parts of the world. These deletions are known to compromise the effectiveness of HRP2-based malaria rapid diagnostic tests (HRP2-RDT). The National Malaria Control Programme (NMCP) in Tanzania adopted HRP2-RDTs as a routine tool for malaria diagnosis in 2009 replacing microscopy in many Health facilities. We investigated pfhrp2/3 deletions in 122 samples from two areas with diverse malaria transmission intensities in Northeastern Tanzania. Pfhrp2 deletion was confirmed in 1.6% of samples while pfhrp3 deletion was confirmed in 50% of samples. We did not find parasites with both pfhrp2 and pfhrp3 deletions among our samples. Results from this study highlight the need for systematic surveillance of pfhrp2/3 deletions in Tanzania to understand their prevalence and determine their impact on the performance of mRDT.
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20
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Kumari MS, Sharma S, Bhardwaj N, Kumar S, Ahmed MZ, Pande V, Anvikar AR. Pfhrp2/3 gene deletion and genetic variation in PfHRP2-based RDTs with P. falciparum positive samples from India and its implication on malaria control. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105232. [PMID: 35114396 DOI: 10.1016/j.meegid.2022.105232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Recent studies have documented Pfhrp2/3 gene deletion globally as one of the biological threats in the fight against malaria. For malaria diagnosis, PfHRP2 based RDTs are most widely used in India, and performance of these RDTs are affected by deleted Pfhrp2/3 gene in Plasmodium falciparum. This study was planned to confirm Pfhrp2/3 gene deletion incidences and genetic variation in PfHRP2-based RDT positive with P.falciparum malaria cases from India. METHODOLOGY Confirmed positive samples by PfHRP2-based RDTs as P. falciparum (n = 240) from six different endemic regions of India were validated by PCR to assure the actual infection. Two hundred forty samples qualified for DNA intactness by single-copy genes were subjected to amplification for the Pfhrp2/3 gene and its neighbouring gene (downstream and upstream) by PCR genotyping. Genetic variation in samples was analysed post-sequencing using Mega X software. Statistical analysis was performed to validate the genetic variation using Mann-Whitney Test. RESULTS RDT target region of Pfhrp2 gene (exon2) was found deleted in a single sample with presence of the Pfhrp3 exon2. Complete gene deletion of 4.2% was observed in the Pfhrp3 gene. Partial gene deletion was recorded for both pfhrp2 gene (exon2-0.4%, upstream 25.8% and downstream -9.1%) and Pfhrp3 gene (exon2-18.75%, upstream - 22.08% and downstream 13.3%). Eleven new unique types of amino acid repeat sequence and earlier reported amino acid repeat type was found in the Pfhrp2 gene, prompting high genetic variation. CONCLUSIONS This study suggests that parasites lacking Pfhrp2/3 gene and its neighbouring gene (downstream and upstream) are present in malaria endemic areas of India, resulting in false positive results by RDT. Systematic countrywide monitoring for malaria control and elimination of malaria is warranted in this regard.
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Affiliation(s)
- Ms Sarita Kumari
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India; Kumaun University, Sleepy Hallow, Nainital, Uttarakhand 263001, India
| | - Supriya Sharma
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India.
| | - Nitin Bhardwaj
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India; Kumaun University, Sleepy Hallow, Nainital, Uttarakhand 263001, India
| | - Sandeep Kumar
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India; Kumaun University, Sleepy Hallow, Nainital, Uttarakhand 263001, India
| | - Md Zohaib Ahmed
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India; Kumaun University, Sleepy Hallow, Nainital, Uttarakhand 263001, India
| | - Veena Pande
- Kumaun University, Sleepy Hallow, Nainital, Uttarakhand 263001, India
| | - Anupkumar R Anvikar
- National Institute of Malaria Research (ICMR), Sector - 8, Dwarka, New Delhi 110077, India.
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21
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Plasmodium falciparum histidine-rich protein 2 and 3 genes deletion in global settings (2010–2021): a systematic review and meta-analysis. Malar J 2022; 21:26. [PMID: 35093092 PMCID: PMC8800273 DOI: 10.1186/s12936-022-04051-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/17/2022] [Indexed: 01/10/2023] Open
Abstract
Background The usefulness of histidine-rich protein-2/3 (HRP2/3)-based rapid diagnostic tests of malaria due to Plasmodium falciparum has been threatened by the appearance of mutant PfHRP2/3 genes. This study was undertaken to determine the global pooled estimates of PfHRP2/3gene deletions. Methods Relevant publications were identified from electronic databases such as; PubMed, EMBASE, and MEDLINE online. Besides, all the relevant literatures were retrieved through Google and Google Scholar. STATA software was used for data analysis. The pooled estimates were calculated using random effect model. The summary estimates were presented using forest plots and tables. Results A total of 27 studies were included in the systematic review. However, only 24 and 17 studies were included for PfHRP2 and 3 gene deletion meta-analysis, respectively. The prevalence of PfHRP2 gene deletion across the individual studies ranged from the highest 100% to the lowest 0%. However, the meta-analysis result showed that the global pooled prevalence of PfHRP2 and PfHRP3 gene deletions were 21.30% and 34.50%, respectively. The pooled proportion of PfHRP2 gene deletion among false negative PfHRP2-based RDTs results was found to be 41.10%. The gene deletion status was higher in South America and followed by Africa. The pooled estimate of PfHRP2 gene deletion among studies, which did not follow the WHO PfHRP2/3 gene deletion analysis protocol was higher than their counter parts (21.3% vs 10.5%). Conclusions This review showed that there is a high pooled prevalence of PfHRP2/3 gene deletions in Plasmodium falciparum confirmed isolates and also a high proportion of their deletions among false-negative malaria cases using PfHRP2-based RDT results. Hence, malaria diagnosis based on PfHRP2-based rapid tests seems to be less sensitive and warrants further evaluation of PfHRP2/3 gene deletions.
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22
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Atroosh WM, Lau YL, Snounou G, Azzani M, Al-Mekhlafi HM. Plasmodium falciparum histidine rich protein 2 (pfhrp2): an additional genetic marker suitable for anti-malarial drug efficacy trials. Malar J 2022; 21:2. [PMID: 34983529 PMCID: PMC8725490 DOI: 10.1186/s12936-021-04014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022] Open
Abstract
Background Genotyping of the three Plasmodium falciparum polymorphic genes, msp1, msp2 and glurp, has been adopted as a standard strategy to distinguish recrudescence from new infection in drug efficacy clinical trials. However, the suitability of a particular gene is compromised in areas where its allelic variants distribution is significantly skewed, a phenomenon that might occur in isolated parasite populations or in areas of very low transmission. Moreover, observation of amplification bias has diminished the value of glurp as a marker. Methods The suitability of the polymorphic P. falciparum histidine-rich protein 2 (pfhrp2) gene was assessed to serve as an alternative marker using a PCR-sequencing or a PCR–RFLP protocol for genotyping of samples in drug efficacy clinical trials. The value of pfhrp2 was validated by side-by-side analyses of 5 admission-recrudescence sample pairs from Yemeni malaria patients. Results The outcome of the single pfhrp2 gene discrimination analysis has been found consistent with msp1, msp2 and glurp pool genotyping analysis for the differentiation of recrudescence from new infection. Conclusion The findings suggest that under the appropriate circumstances, pfhrp2 can serve as an additional molecular marker for monitoring anti-malarials efficacy. However, its use is restricted to endemic areas where only a minority of P. falciparum parasites lack the pfhrp2 gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04014-4.
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Affiliation(s)
- Wahib M Atroosh
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University of Aden, Aden, Yemen.
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Georges Snounou
- CEA-Université Paris Sud 11-INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA-HB), IDMIT Department, IBFJ, DRF, Fontenay-aux-Roses, France
| | - Meram Azzani
- Department of Community Medicine, Faculty of Medicine, MAHSA University, Bandar Saujana Putra, Selangor, Malaysia
| | - Hesham M Al-Mekhlafi
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen.,Medical Research Centre, Jazan University, Jazan, Kingdom of Saudi Arabia
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23
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Chaudhry A, Cunningham J, Cheng Q, Gatton ML. Modelling the epidemiology of malaria and spread of HRP2-negative Plasmodium falciparum following the replacement of HRP2-detecting rapid diagnostic tests. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000106. [PMID: 36962137 PMCID: PMC10021339 DOI: 10.1371/journal.pgph.0000106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Malaria rapid diagnostic tests (RDTs) are dominated by products which use histidine-rich protein 2 (HRP2) to detect Plasmodium falciparum. The emergence of parasites lacking the pfhrp2 gene can lead to high rates of false-negative results amongst these RDTs. One solution to restore the ability to correctly diagnose falciparum malaria is to switch to an RDT which is not solely reliant on HRP2. This study used an agent-based stochastic simulation model to investigate the impact on prevalence and transmission caused by switching the type of RDT used once false-negative rates reached pre-defined thresholds within the treatment-seeking symptomatic population. The results show that low transmission settings were the first to reach the false-negative switch threshold, and that lower thresholds were typically associated with better long-term outcomes. Changing the diagnostic RDT away from a HRP2-only RDT is predicted to restore the ability to correctly diagnose symptomatic malaria infections, but often did not lead to the extinction of HRP2-negative parasites from the population which continued to circulate in low density infections, or return to the parasite prevalence and transmission levels seen prior to the introduction of the HRP2-negative parasite. In contrast, failure to move away from HRP2-only RDTs leads to near fixation of these parasites in the population, and the inability to correctly diagnose symptomatic cases. Overall, these results suggest pfhrp2-deleted parasites are likely to become a significant component of P. falciparum parasite populations, and that long-term strategies are needed for diagnosis and surveillance which do not rely solely on HRP2.
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Affiliation(s)
- Alisha Chaudhry
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Diseases Institute, Brisbane, Australia
- ADFMIDI Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Michelle L Gatton
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
- Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, Australia
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24
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Mihreteab S, Anderson K, Pasay C, Smith D, Gatton ML, Cunningham J, Berhane A, Cheng Q. Epidemiology of mutant Plasmodium falciparum parasites lacking histidine-rich protein 2/3 genes in Eritrea 2 years after switching from HRP2-based RDTs. Sci Rep 2021; 11:21082. [PMID: 34702923 PMCID: PMC8548324 DOI: 10.1038/s41598-021-00714-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/15/2021] [Indexed: 12/02/2022] Open
Abstract
Eritrea was the first African country to complete a nationwide switch in 2016 away from HRP2-based RDTs due to high rates of false-negative RDT results caused by Plasmodium falciparum parasites lacking hrp2/hrp3 genes. A cross-sectional survey was conducted during 2019 enrolling symptomatic malaria patients from nine health facilities across three zones consecutively to investigate the epidemiology of P. falciparum lacking hrp2/3 after the RDT switch. Molecular analyses of 715 samples revealed the overall prevalence of hrp2-, hrp3-, and dual hrp2/3-deleted parasites as 9.4% (95%CI 7.4–11.7%), 41.7% (95% CI 38.1–45.3%) and 7.6% (95% CI 5.8–9.7%), respectively. The prevalence of hrp2- and hrp3-deletion is heterogeneous within and between zones: highest in Anseba (27.1% and 57.9%), followed by Gash Barka (6.4% and 37.9%) and Debub zone (5.2% and 43.8%). hrp2/3-deleted parasites have multiple diverse haplotypes, with many shared or connected among parasites of different hrp2/3 status, indicating mutant parasites have likely evolved from multiple and local parasite genetic backgrounds. The findings show although prevalence of hrp2/3-deleted parasites is lower 2 years after RDT switching, HRP2-based RDTs remain unsuitable for malaria diagnosis in Eritrea. Continued surveillance of hrp2/3-deleted parasites in Eritrea and neighbouring countries is required to monitor the trend.
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Affiliation(s)
- Selam Mihreteab
- National Malaria Control Program, Ministry of Health, Asmara, Eritrea.
| | - Karen Anderson
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Cielo Pasay
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - David Smith
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Michelle L Gatton
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Araia Berhane
- Communicable Diseases Control, Ministry of Health, Asmara, Eritrea
| | - Qin Cheng
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia. .,Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.
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25
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Alemayehu GS, Messele A, Blackburn K, Lopez K, Lo E, Janies D, Golassa L. Genetic variation of Plasmodium falciparum histidine-rich protein 2 and 3 in Assosa zone, Ethiopia: its impact on the performance of malaria rapid diagnostic tests. Malar J 2021; 20:394. [PMID: 34627242 PMCID: PMC8502267 DOI: 10.1186/s12936-021-03928-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/26/2021] [Indexed: 11/21/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are commonly used for the diagnosis of malaria caused by Plasmodium falciparum. However, false negative results of RDT caused by genetic variation of P. falciparum histidine-rich protein 2 and 3 genes (pfhrp2/3) threaten existing malaria case management and control efforts. The main objective of this study was to investigate the genetic variations of the pfhrp2/3 genes. Methods A cross-sectional study was conducted from malaria symptomatic individuals in 2018 in Assosa zone, Ethiopia. Finger-prick blood samples were collected for RDT and microscopic examination of thick and thin blood films. Dried blood spots (DBS) were used for genomic parasite DNA extraction and molecular detection. Amplification of parasite DNA was made by quantitative PCR. DNA amplicons of pfhrp2/3 were purified and sequenced. Results The PfHRP2 amino acid repeat type isolates were less conserved compared to the PfHRP3 repeat type. Eleven and eight previously characterized PfHRP2 and PfHRP3 amino acid repeat types were identified, respectively. Type 1, 4 and 7 repeats were shared by PfHRP2 and PfHRP3 proteins. Type 2 repeats were found only in PfHRP2, while types 16 and 17 were found only in PfHRP3 with a high frequency in all isolates. 18 novel repeat types were found in PfHRP2 and 13 novel repeat types were found in PfHRP3 in single or multiple copies per isolate. The positivity rate for PfHRP2 RDT was high, 82.9% in PfHRP2 and 84.3% in PfHRP3 sequence isolates at parasitaemia levels > 250 parasites/µl. Using the Baker model, 100% of the isolates in group A (If product of types 2 × type 7 repeats ≥ 100) and 73.7% of the isolates in group B (If product of types 2 × type 7 repeats 50–99) were predicted to be detected by PfHRP2 RDT at parasitaemia level > 250 parasite/μl. Conclusion The findings of this study indicate the presence of different PfHRP2 and PfHRP3 amino acid repeat including novel repeats in P. falciparum from Ethiopia. These results indicate that there is a need to closely monitor the performance of PfHRP2 RDT associated with the genetic variation of the pfhrp2 and pfhrp3 gene in P. falciparum isolates at the country-wide level. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03928-3.
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Affiliation(s)
| | - Alebachew Messele
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
| | - Kayla Blackburn
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Karen Lopez
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.,School of Data Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel Janies
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Lemu Golassa
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
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26
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441 DOI: 10.12688/wellcomeopenres.16168.1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
| |
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27
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441.2 DOI: 10.12688/wellcomeopenres.16168.2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
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Prabhu SR, Ware AP, Saadi AV. Erythrocyte miRNA regulators and malarial pathophysiology. INFECTION GENETICS AND EVOLUTION 2021; 93:105000. [PMID: 34252617 DOI: 10.1016/j.meegid.2021.105000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022]
Abstract
Pathophysiology of Plasmodium falciparum and Plasmodium vivax in malaria vis a vis host and the parasite genome interactions has been deciphered recently to present the biology of cerebral malaria, severe anaemia and placental malaria. Small non-coding RNAs have exhibited their potential to be considered as indicators and regulators of diseases. The malarial pathologies and their associated mechanisms mediated by miRNAs and their role in haematopoiesis and red cell-related disorders are elucidated. Evidence of miRNA carrying exosome-like vesicles released during infection, delivering signals to endothelial cells enhancing gene expression, resulting in parasite sequestration and complications leading to pathologies of cerebral malaria are important breakthroughs. Pregnancy malaria showed Plasmodium surface antigen promoted erythrocyte sequestration in the placental intervillous space, provoking disease development and assorted complications. Syncytiotrophoblast-derived microparticles during pregnancy and fetus development may predict pathophysiological progression on account of their altered miRNA cargoes in malaria.
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Affiliation(s)
- Sowmya R Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Akshay P Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Molina-de la Fuente I, Pastor A, Herrador Z, Benito A, Berzosa P. Impact of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions on malaria control worldwide: a systematic review and meta-analysis. Malar J 2021; 20:276. [PMID: 34158065 PMCID: PMC8220794 DOI: 10.1186/s12936-021-03812-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background Deletion of pfhrp2 and/or pfhrp3 genes cause false negatives in malaria rapid diagnostic test (RDT) and threating malaria control strategies. This systematic review aims to assess the main methodological aspects in the study of pfhrp2 and pfhrp3 gene deletions and its global epidemiological status, with special focus on their distribution in Africa; and its possible impact in RDT. Methods The systematic review was conducted by examining the principal issues of study design and methodological workflow of studies addressing pfhrp2 deletion. Meta-analysis was applied to represent reported prevalences of pfhrp2 and pfhrp3 single and double deletion in the World Health Organization (WHO) region. Pooled-prevalence of deletions was calculated using DerSimonnian-Laird random effect model. Then, in-deep analysis focused on Africa was performed to assess possible variables related with these deletions. Finally, the impact of these deletions in RDT results was analysed combining reported information about RDT sensitivity and deletion prevalences. Results 49 articles were included for the systematic review and 37 for the meta-analysis, 13 of them placed in Africa. Study design differs significantly, especially in terms of population sample and information reported, resulting in high heterogeneity between studies that difficulties comparisons and merged conclusions. Reported prevalences vary widely in all the WHO regions, significantly higher deletion were reported in South-Central America, following by Africa and Asia. Pfhrp3 deletion is more prevalent (43% in South-Central America; 3% in Africa; and 1% in Asia) than pfhrp2 deletion (18% in South-Central America; 4% in Africa; and 3% in Asia) worldwide. In Africa, there were not found differences in deletion prevalence by geographical or population origin of samples. The prevalence of deletion among false negatives ranged from 0 to 100% in Africa, but in Asia and South-Central America was only up to 90% and 48%, respectively, showing substantial relation between deletions and false negatives. Conclusion The concerning prevalence of pfhrp2, pfhrp3 and pfhrp2/3 gene deletions, as its possible implications in malaria control, highlights the importance of regular and systematic surveillance of these deletions. This review has also outlined that a standardized methodology could play a key role to ensure comparability between studies to get global conclusions. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03812-0.
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Affiliation(s)
- Irene Molina-de la Fuente
- Department of Biomedicine and Biotechnology, School of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid, Spain. .,Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, 28029, Madrid, Spain. .,Public Health and Epidemiology Research Group, School of Medicine, University of Alcalá, 28871, Alcalá de Henares, Madrid, Spain.
| | - Andrea Pastor
- Public Health and Epidemiology Research Group, School of Medicine, University of Alcalá, 28871, Alcalá de Henares, Madrid, Spain
| | - Zaida Herrador
- National Centre of Epidemiology, Institute of Health Carlos III, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET in Spanish), Madrid, Spain
| | - Agustín Benito
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET in Spanish), Madrid, Spain
| | - Pedro Berzosa
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, 28029, Madrid, Spain.,Network Biomedical Research on Tropical Diseases (RICET in Spanish), Madrid, Spain
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Prosser C, Gresty K, Ellis J, Meyer W, Anderson K, Lee R, Cheng Q. Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions in Strains from Nigeria, Sudan, and South Sudan. Emerg Infect Dis 2021; 27:471-479. [PMID: 33496220 PMCID: PMC7853540 DOI: 10.3201/eid2702.191410] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Deletion of histidine-rich protein genes pfhrp2/3 in Plasmodium falciparum causes infections to go undetected by HRP2-based malaria rapid diagnostic tests. We analyzed P. falciparum malaria cases imported to Australia (n = 210, collected 2010–2018) for their pfhrp2/3 status. We detected gene deletions in patients from 12 of 25 countries. We found >10% pfhrp2-deletion levels in those from Nigeria (13.3%, n = 30), Sudan (11.2%, n = 39), and South Sudan (17.7%, n = 17) and low levels of pfhrp3 deletion from Sudan (3.6%) and South Sudan (5.9%). No parasites with pfhrp2/3 double deletions were detected. Microsatellite typing of parasites from Nigeria, Sudan, and South Sudan revealed low relatedness among gene-deleted parasites, indicating independent emergences. The gene deletion proportions signify a risk of false-negative HRP2-RDT results. This study’s findings warrant surveillance to determine whether the prevalence of gene-deleted parasites justifies switching malaria rapid diagnostic tests in Nigeria, Sudan, and South Sudan.
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31
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Agaba BB, Anderson K, Gresty K, Prosser C, Smith D, Nankabirwa JI, Nsobya S, Yeka A, Namubiru R, Arinaitwe E, Mbaka P, Kissa J, Lim CS, Karamagi C, Nakayaga JK, Kamya MR, Cheng Q. Genetic diversity and genetic relatedness in Plasmodium falciparum parasite population in individuals with uncomplicated malaria based on microsatellite typing in Eastern and Western regions of Uganda, 2019-2020. Malar J 2021; 20:242. [PMID: 34059047 PMCID: PMC8165787 DOI: 10.1186/s12936-021-03763-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/11/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genetic diversity and parasite relatedness are essential parameters for assessing impact of interventions and understanding transmission dynamics of malaria parasites, however data on its status in Plasmodium falciparum populations in Uganda is limited. Microsatellite markers and DNA sequencing were used to determine diversity and molecular characterization of P. falciparum parasite populations in Uganda. METHODS A total of 147 P. falciparum genomic DNA samples collected from cross-sectional surveys in symptomatic individuals of 2-10 years were characterized by genotyping of seven highly polymorphic neutral microsatellite markers (n = 85) and genetic sequencing of the Histidine Rich Protein 2 (pfhrp2) gene (n = 62). ArcGIS was used to map the geographical distribution of isolates while statistical testing was done using Student's t-test or Wilcoxon's rank-sum test and Fisher's exact test as appropriate at P ≤ 0.05. RESULTS Overall, 75.5% (95% CI 61.1-85.8) and 24.5% (95% CI14.2-38.9) of parasites examined were of multiclonal (mixed genotype) and single clone infections, respectively. Multiclonal infections occurred more frequently in the Eastern region 73.7% (95% CI 48.8-89.1), P < 0.05. Overall, multiplicity of infection (MOI) was 1.9 (95% CI 1.7-2.1), P = 0.01 that was similar between age groups (1.8 vs 1.9), P = 0.60 and regions (1.9 vs 1.8), P = 0.43 for the < 5 and ≥ 5 years and Eastern and Western regions, respectively. Genomic sequencing of the pfhrp2 exon2 revealed a high level of genetic diversity reflected in 96.8% (60/62) unique sequence types. Repeat type AHHAAAHHATD and HRP2 sequence Type C were more frequent in RDT-/PCR + samples (1.9% vs 1.5%) and (13% vs 8%), P < 0.05 respectively. Genetic relatedness analysis revealed small clusters of gene deleted parasites in Uganda, but no clustering with Eritrean parasites. CONCLUSION High level of genetic diversity of P. falciparum parasites reflected in the frequency of multiclonal infections, multiplicity of infection and variability of the pfhrp2 gene observed in this study is consistent with the high malaria transmission intensity in these settings. Parasite genetic analysis suggested spontaneous emergence and clonal expansion of pfhrp2 deleted parasites that require close monitoring to inform national malaria diagnosis and case management policies.
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Affiliation(s)
- Bosco B Agaba
- College of Health Sciences, Makerere University, Kampala, Uganda.
- National Malaria Control Division, Kampala, Uganda.
| | - Karen Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Karryn Gresty
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Christiane Prosser
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - David Smith
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
| | - Joaniter I Nankabirwa
- College of Health Sciences, Makerere University, Kampala, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Sam Nsobya
- College of Health Sciences, Makerere University, Kampala, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Adoke Yeka
- College of Health Sciences, Makerere University, Kampala, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Rhoda Namubiru
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Paul Mbaka
- World Health Organization Country Office, Kampala, Uganda
| | - John Kissa
- National Health Information Division, Ministry of Health, Kampala, Uganda
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Health Sciences, Korea University, Seoul, South Korea
| | - Charles Karamagi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joan K Nakayaga
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses R Kamya
- College of Health Sciences, Makerere University, Kampala, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Qin Cheng
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
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Prevalence of Plasmodium falciparum isolates lacking the histidine rich protein 2 gene among symptomatic malaria patients in Kwilu Province of the Democratic Republic of Congo. Infect Dis Poverty 2021; 10:77. [PMID: 34034827 PMCID: PMC8146217 DOI: 10.1186/s40249-021-00860-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
Background Malaria rapid diagnostic tests have become a primary and critical tool for malaria diagnosis in malaria-endemic countries where Plasmodium falciparum Histidine Rich Protein 2-based rapid diagnostic tests (PfHRP2-based RDTs) are widely used. However, in the last decade, the accuracy of PfHRP2-based RDTs has been challenged by the emergence of P. falciparum strains harbouring deletions of the P. falciparum histidine rich protein 2 (pfhrp2) gene, resulting in false-negative results. In the Democratic Republic of Congo (D.R. Congo), little is known about the prevalence of the pfhrp2 gene deletion among P. falciparum isolates infecting symptomatic patients, especially in low to moderate transmission areas where pfhrp2 deletion parasites are assumed to emerge and spread. Here we determine the local prevalence and factors associated with pfhrp2 gene deletions among symptomatic malaria patients in the Kwilu Province of the D.R. Congo. Methods We used secondary data from a prospective health facility-based cross-sectional study conducted in 2018. Blood was collected for microscopy, PfHRP2-RDT, and spotted onto Whatman filter paper for downstream genetic analysis. Genomic DNA was extracted and used to perform PCR assays for the detection and confirmation of pfhrp2 gene deletions. Fischer’s exact and the Kruskal–Wallis tests were applied to look for associations between potential explanatory variables and the pfhrp2 gene deletion with a level of statistical significance set at P < 0.05. Results Of the 684 enrolled symptomatic patients, 391 (57.7%) were female. The majority (87.7%) reported the presence of mosquito breeding sites within the household’s compound, and fever was the most reported symptom (81.6%). The overall prevalence of the pfhrp2 gene deletion was 9.2% (95% CI: 6.7%–12.1%). The deletion of the pfhrp2 gene was associated with health zone of origin (P = 0.012) and age (P = 0.019). Among false-negative PfHRP2-RDT results, only 9.9% were due to pfhrp2 gene deletion. Conclusions P. falciparum isolates with pfhrp2 gene deletions are relatively common among symptomatic patients in Kwilu province. Further investigations are needed to provide enough evidence for policy change. Meanwhile, the use of RDTs targeting PfHRP2 and parasite lactate dehydrogenase (pLDH) antigens could limit the spread of deleted isolates. Graphic Abstract ![]()
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Kong A, Wilson SA, Ah Y, Nace D, Rogier E, Aidoo M. HRP2 and HRP3 cross-reactivity and implications for HRP2-based RDT use in regions with Plasmodium falciparum hrp2 gene deletions. Malar J 2021; 20:207. [PMID: 33926477 PMCID: PMC8086288 DOI: 10.1186/s12936-021-03739-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 01/29/2023] Open
Abstract
Background The Plasmodium falciparum antigen histidine rich protein 2 (HRP2) is a preferred target for malaria rapid diagnostic tests (RDTs) because of its abundant production by the parasite and thermal stability. As a result, a majority of RDTs procured globally target this antigen. However, previous reports from South America and recent reports from sub-Saharan Africa and Asia indicate that certain P. falciparum parasites have deletions of the gene coding for HRP2. The HRP2 antigen is paralogous to another P. falciparum antigen HRP3 and some antibodies to HRP2 cross-react with HRP3. Multiple parasites have been described with deletions of one or both hrp2 and hrp3 genes. It is unclear how the various combinations of hrp2 and hrp3 deletion genotypes affect clinical sensitivity of HRP2-based RDTs. Methods Cross-reactivity between HRP2 and HRP3 was tested on malaria RDTs using culture-adapted P. falciparum parasites with both hrp2 and hrp3 intact or with one or both genes deleted. Ten-fold serial dilutions of four culture-adapted P. falciparum parasites [3D7 (hrp2+/hrp3+), Dd2 (hrp2−/hrp3+), HB3 (hrp2+/hrp3−) and 3BD5 (hrp2−/hrp3−)] ranging from 100,000 to 0.01 parasites/µL were prepared. HRP2, Plasmodium lactate dehydrogenase (pLDH) and aldolase concentrations were determined for the diluted samples using a multiplex bead assay. The samples were subsequently tested on three RDT products designed to detect P. falciparum by HRP2 alone or in combination with pLDH. Results At parasite densities of approximately 1000 parasites/µL, parasites that expressed either hrp2 or hrp3 were detected by all three RDTs. Multiplex based antigen measurement using HRP2- conjugated beads demonstrated higher antigen concentration when both hrp2 and hrp3 genes were intact (3D7 parasites, 47.9 ng/ml) compared to HB3 (3.02 ng/mL) and Dd2 (0.20 ng/mL) strains that had one gene deleted. 3D7 at 10 parasites/µL (0.45 ng/mL) was reactive on all three RDT products whereas none of the other parasites were reactive at that density. Conclusions Above a certain antigen threshold, HRP3 cross-reactivity on HRP2-based RDTs is sufficient to mask the effects of deletions of hrp2 only. Studies of hrp2 deletion and its effects on HRP2-based RDTs must be studied alongside hrp3 deletions and include clinical sample reactivity on HRP2-based tests.
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Affiliation(s)
- Amy Kong
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Scott A Wilson
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.,The CDC Foundation, 600 Peachtree Street NE, Suite 1000, Atlanta, GA, 30308, USA
| | - Yong Ah
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.,The CDC Foundation, 600 Peachtree Street NE, Suite 1000, Atlanta, GA, 30308, USA
| | - Douglas Nace
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Eric Rogier
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Michael Aidoo
- Malaria Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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Gibbons J, Qin J, Malla P, Wang Z, Brashear A, Wang C, Miao J, Adams JH, Kim K, Jiang R, Cui L. Lineage-Specific Expansion of Plasmodium falciparum Parasites With pfhrp2 Deletion in the Greater Mekong Subregion. J Infect Dis 2021; 222:1561-1569. [PMID: 32386321 DOI: 10.1093/infdis/jiaa250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Deletion of the pfhrp2 gene in Plasmodium falciparum can lead to false-negative rapid diagnostic test (RDT) results, constituting a major challenge for evidence-based malaria treatment. Here we analyzed the whole genome sequences of 138 P. falciparum clinical samples collected from the China-Myanmar boarder for pfhrp2 and pfhrp3 gene deletions. We found pfhrp2 and pfhrp3 deletions in 9.4% and 3.6% of samples, respectively, with no samples harboring deletions of both genes. The pfhrp2 deletions showed 2 distinct breakpoints, representing 2 different chromosomal deletion events. A phylogenetic analysis performed using genome-wide single-nucleotide polymorphisms revealed that the 2 pfhrp2 breakpoint groups as well as all the pfhrp3-negative parasites formed separate clades, suggesting they might have resulted from clonal expansion of pfhrp2- and pfhrp3-negative parasites. These findings highlight the need for urgent surveys to determine the prevalence of pfhrp2-negative parasites causing false-negative RDT results and a plan for switching of RDTs pending the survey results.
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Affiliation(s)
- Justin Gibbons
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Junling Qin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Pallavi Malla
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Zenglei Wang
- The National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing, China
| | - Awtum Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Kami Kim
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Rays Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Liwang Cui
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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35
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Alemayehu GS, Blackburn K, Lopez K, Cambel Dieng C, Lo E, Janies D, Golassa L. Detection of high prevalence of Plasmodium falciparum histidine-rich protein 2/3 gene deletions in Assosa zone, Ethiopia: implication for malaria diagnosis. Malar J 2021; 20:109. [PMID: 33622309 PMCID: PMC8095343 DOI: 10.1186/s12936-021-03629-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) targeting histidine rich protein 2(HRP2) are widely used for diagnosis of Plasmodium falciparum infections. Besides PfHRP2, the PfHRP3 antigen contributes to the detection of P. falciparum infections in PfHRP2 RDTs. However, the performance HRP2-based RDT is affected by pfhrp2/3 gene deletions resulting in false-negative test results. The objective of this study was to determine the presence and prevalence of pfhrp2/3 gene deletions including the respective flanking regions among symptomatic patients in Assosa zone, Northwest Ethiopia. Methods A health-facility based cross-sectional study was conducted in febrile patients seeking a malaria diagnosis in 2018. Blood samples were collected by finger-prick for microscopic examination of blood smears, malaria RDT, and molecular analysis using dried blood spots (DBS) prepared on Whatman filter paper. A total of 218 P. falciparum positive samples confirmed by quantitative PCR were included for molecular assay of pfhrp2/3 target gene. Results Of 218 P. falciparum positive samples, exon 2 deletions were observed in 17.9% of pfhrp2 gene and in 9.2% of pfhrp3 gene. A high proportion of deletions in short segments of pfhrp2 exon1-2 (50%) was also detected while the deletions of the pfhrp3 exon1-2 gene were 4.1%. The deletions were extended to the downstream and upstream of the flanking regions in pfhrp2/3 gene (above 30%). Of eighty-six PfHRP2 RDT negative samples, thirty-six lacked pfhrp2 exon 2. Five PfHRP2 RDT negative samples had double deletions in pfhrp2 exon 2 and pfhrp3 exon2. Of these double deletions, only two of the samples with a parasite density above 2000 parasite/µl were positive by the microscopy. Three samples with intact pfhrp3 exon2 in the pfhrp2 exon2 deleted parasite isolates were found to be positive by PfHRP2 RDT and microscopy with a parasite density above 10,000/µl. Conclusion This study confirms the presence of deletions of pfhrp2/3 gene including the flanking regions. Pfhrp2/3 gene deletions results in false-negative results undoubtedly affect the current malaria control and elimination effort in the country. However, further countrywide investigations are required to determine the magnitude of pfhrp2/3 gene deletions and its consequences on routine malaria diagnosis.
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Affiliation(s)
| | - Kayla Blackburn
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Karen Lopez
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Cheikh Cambel Dieng
- Department of Biological Sciences, Charlotte, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Eugenia Lo
- Department of Biological Sciences, Charlotte, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Lemu Golassa
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. Nat Microbiol 2021; 6:1289-1299. [PMID: 34580442 PMCID: PMC8478644 DOI: 10.1038/s41564-021-00962-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023]
Abstract
In Africa, most rapid diagnostic tests (RDTs) for falciparum malaria recognize histidine-rich protein 2 antigen. Plasmodium falciparum parasites lacking histidine-rich protein 2 (pfhrp2) and 3 (pfhrp3) genes escape detection by these RDTs, but it is not known whether these deletions confer sufficient selective advantage to drive rapid population expansion. By studying blood samples from a cohort of 12,572 participants enroled in a prospective, cross-sectional survey along Ethiopia's borders with Eritrea, Sudan and South Sudan using RDTs, PCR, an ultrasensitive bead-based immunoassay for antigen detection and next-generation sequencing, we estimate that histidine-rich protein 2-based RDTs would miss 9.7% (95% confidence interval 8.5-11.1) of P. falciparum malaria cases owing to pfhrp2 deletion. We applied a molecular inversion probe-targeted deep sequencing approach to identify distinct subtelomeric deletion patterns and well-established pfhrp3 deletions and to uncover recent expansion of a singular pfhrp2 deletion in all regions sampled. We propose a model in which pfhrp3 deletions have arisen independently multiple times, followed by strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment. Existing diagnostic strategies need to be urgently reconsidered in Ethiopia, and improved surveillance for pfhrp2 deletion is needed throughout the Horn of Africa.
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Góes L, Chamma-Siqueira N, Peres JM, Nascimento JM, Valle S, Arcanjo AR, Lacerda M, Blume L, Póvoa M, Viana G. Evaluation of Histidine-Rich Proteins 2 and 3 Gene Deletions in Plasmodium falciparum in Endemic Areas of the Brazilian Amazon. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 18:ijerph18010123. [PMID: 33375379 PMCID: PMC7795390 DOI: 10.3390/ijerph18010123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/30/2022]
Abstract
Histidine-rich proteins 2 and 3 gene (pfhrp2 and pfhrp3) deletions affect the efficacy of rapid diagnostic tests (RDTs) based on the histidine-rich protein 2 (HRP2), compromising the correct identification of the Plasmodium falciparum species. Therefore, molecular surveillance is necessary for the investigation of the actual prevalence of this phenomenon and the extent of the disappearance of these genes in these areas and other South American countries, thus guiding national malaria control programs on the appropriate use of RDTs. This study aimed to evaluate the pfhrp2 and pfhrp3 gene deletion in P. falciparum in endemic areas of the Brazilian Amazon. Aliquots of DNA from the biorepository of the Laboratory of Basic Research in Malaria, Evandro Chagas Institute, with a positive diagnosis for P. falciparum infection as determined by microscopy and molecular assays, were included. Monoinfection was confirmed by nested-polymerase chain reaction assay, and DNA quality was assessed by amplification of the merozoite surface protein-2 gene (msp2). The pfhrp2 and pfhrp3 genes were amplified using primers for the region between exons 1 and 2 and for all extension of exon 2. Aliquots of DNA from 192 P. falciparum isolates were included in the study, with 68.7% (132/192) from the municipality of Cruzeiro do Sul (Acre) and 31.3% (60/192) from Manaus (Amazonas). Of this total, 82.8% (159/192) of the samples were considered of good quality. In the state of Acre, 71.7% (71/99) showed pfhrp2 gene deletion and 94.9% (94/99) showed pfhrp3 gene deletion, while in the state of Amazonas, 100.0% (60/60) of the samples showed pfhrp2 gene deletion and 98.3% (59/60) showed pfhrp3 gene deletion. Moreover, 79.8% (127/159) of isolates displayed gene deletion. Our findings confirm the presence of a parasite population with high frequencies of pfhrp2 and pfhrp3 gene deletions in the Brazilian Amazon region. This suggests reconsidering the use of HRP2-based RDTs in the Acre and Amazonas states and calls attention to the importance of molecular surveillance and mapping of pfhrp2/pfhrp3 deletions in this area and in other locations in the Amazon region to guarantee appropriate patient care, control and ultimately contribute to achieving P. falciparum malaria elimination.
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Affiliation(s)
- Leandro Góes
- Graduate Program in Epidemiology and Health Surveillance (PPGEVS), Centre for Education and Graduate Programs (NEP), Evandro Chagas Institute (IEC/SVS/MS), 67.030-000 Ananindeua, Pará, Brazil;
| | - Nathália Chamma-Siqueira
- Parasitology Section, Evandro Chagas Institute-IEC/SVS/MS, 67.030-000 Ananindeua, Pará, Brazil; (J.M.P.); (J.M.N.); (M.P.)
- Correspondence: (N.C.-S.); (G.V.)
| | - José Mário Peres
- Parasitology Section, Evandro Chagas Institute-IEC/SVS/MS, 67.030-000 Ananindeua, Pará, Brazil; (J.M.P.); (J.M.N.); (M.P.)
| | - José Maria Nascimento
- Parasitology Section, Evandro Chagas Institute-IEC/SVS/MS, 67.030-000 Ananindeua, Pará, Brazil; (J.M.P.); (J.M.N.); (M.P.)
| | - Suiane Valle
- Hemonúcleo Cruzeiro do Sul, State Health Department of Acre, 69.980-000 Cruzeiro do Sul, Acre, Brazil;
| | - Ana Ruth Arcanjo
- Central Public Health Laboratory of Amazonas (LACEN/Amazonas), 69.020-245 Manaus, Amazonas, Brazil;
| | - Marcus Lacerda
- Heitor Vieira Dourado Tropical Medicine Foundation, 69.040-000 Manaus, Brazil;
- Leônidas and Maria Deane Institute-Fiocruz Amazônia, 69.027-070 Manaus, Amazonas, Brazil
| | - Liana Blume
- Malaria Technical Group, General Coordination for the Monitoring of Zoonoses and Malaria Vector Transmission Diseases, CGZV Department of Immunization and Communicable Diseases, DEIDT, Health Surveillance Secretariat, SVS, Ministry of Health, 70.070-942 Brasília, Brazil;
| | - Marinete Póvoa
- Parasitology Section, Evandro Chagas Institute-IEC/SVS/MS, 67.030-000 Ananindeua, Pará, Brazil; (J.M.P.); (J.M.N.); (M.P.)
- National Council for Scientific and Technological Development, CNPq, 71.605-001 Brasília, Brazil
| | - Giselle Viana
- Parasitology Section, Evandro Chagas Institute-IEC/SVS/MS, 67.030-000 Ananindeua, Pará, Brazil; (J.M.P.); (J.M.N.); (M.P.)
- Correspondence: (N.C.-S.); (G.V.)
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Golassa L, Messele A, Amambua-Ngwa A, Swedberg G. High prevalence and extended deletions in Plasmodium falciparum hrp2/3 genomic loci in Ethiopia. PLoS One 2020; 15:e0241807. [PMID: 33152025 PMCID: PMC7644029 DOI: 10.1371/journal.pone.0241807] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/20/2020] [Indexed: 11/30/2022] Open
Abstract
Deletions in Plasmodium falciparum histidine rich protein 2(pfhrp2) gene threaten the usefulness of the most widely used HRP2-based malaria rapid diagnostic tests (mRDTs) that cross react with its structural homologue, PfHRP3. Parasites with deleted pfhrp2/3 genes remain undetected and untreated due to 'false-negative' RDT results. As Ethiopia recently launched malaria elimination by 2030 in certain selected areas, the availability of RDTs and the scale of their use have rapidly increased in recent years. Thus, it is important to explore the presence and prevalence of deletion in the target genes, pfhrp2 and pfhrp3. From a total of 189 febrile patients visited Adama Malaria Diagnostic centre, sixty-four microscopically-and polymerase chain reaction (PCR)-confirmed P. falciparum clinical isolates were used to determine the frequency of pfhrp2/3 gene deletions. Established PCR assays were applied to DNA extracted from blood spotted onto filter papers to amplify across pfhrp2/3 exons and flanking regions. However, analysis of deletions in pfhrp2, pfhrp3 and flanking genomic regions was successful for 50 of the samples. The pfhrp2 gene deletion was fixed in the population with all 50(100%) isolates presenting a deletion variant. This deletion extended downstream towards the Pf3D7 0831900 (MAL7PI.230) gene in 11/50 (22%) cases. In contrast, only 2/50 (4%) of samples had deletions for the Pf3D7 0831700 (MALPI.228) gene, upstream of pfhrp2. Similarly, the pfhrp3 gene was deleted in all isolates (100%), while 40% of the isolates had an extension of the deletion to the downstream flanking region that codes for Pf3D7 13272400 (MAL13PI.485).The pfhrp3 deletion also extended upstream to Pf3D7 081372100 (MAL13PI.475) region in 49/50 (95%) of the isolates, exhibiting complete absence of the locus. Although all samples showed deletions of pfhrp2 exon regions, amplification of an intron region was successful in five cases. Two different repeat motifs in the intron regions were observed in the samples tested. Pfhrp2/3 gene deletions are fixed in Ethiopia and this will likely reduce the effectiveness of PfHRP2-based mRDTs. It will be important to determine the sensitivity PfHRP 2/3-based RDTs in these populations and conduct a countrywide survey to determine the extent of these deletions and its effect on routine RDT-based malaria diagnosis.
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Affiliation(s)
- Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred Amambua-Ngwa
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Gote Swedberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Gatton ML, Chaudhry A, Glenn J, Wilson S, Ah Y, Kong A, Ord RL, Rees-Channer RR, Chiodini P, Incardona S, Cheng Q, Aidoo M, Cunningham J. Impact of Plasmodium falciparum gene deletions on malaria rapid diagnostic test performance. Malar J 2020; 19:392. [PMID: 33148265 PMCID: PMC7640408 DOI: 10.1186/s12936-020-03460-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022] Open
Abstract
Background Malaria rapid diagnostic tests (RDTs) have greatly improved access to diagnosis in endemic countries. Most RDTs detect Plasmodium falciparum histidine-rich protein 2 (HRP2), but their sensitivity is seriously threatened by the emergence of pfhrp2-deleted parasites. RDTs detecting P. falciparum or pan-lactate dehydrogenase (Pf- or pan-LDH) provide alternatives. The objective of this study was to systematically assess the performance of malaria RDTs against well-characterized pfhrp2-deleted P. falciparum parasites. Methods Thirty-two RDTs were tested against 100 wild-type clinical isolates (200 parasites/µL), and 40 samples from 10 culture-adapted and clinical isolates of pfhrp2-deleted parasites. Wild-type and pfhrp2-deleted parasites had comparable Pf-LDH concentrations. Pf-LDH-detecting RDTs were also tested against 18 clinical isolates at higher density (2,000 parasites/µL) lacking both pfhrp2 and pfhrp3. Results RDT positivity against pfhrp2-deleted parasites was highest (> 94%) for the two pan-LDH-only RDTs. The positivity rate for the nine Pf-LDH-detecting RDTs varied widely, with similar median positivity between double-deleted (pfhrp2/3 negative; 63.9%) and single-deleted (pfhrp2-negative/pfhrp3-positive; 59.1%) parasites, both lower than against wild-type P. falciparum (93.8%). Median positivity for HRP2-detecting RDTs against 22 single-deleted parasites was 69.9 and 35.2% for HRP2-only and HRP2-combination RDTs, respectively, compared to 96.0 and 92.5% for wild-type parasites. Eight of nine Pf-LDH RDTs detected all clinical, double-deleted samples at 2,000 parasites/µL. Conclusions The pan-LDH-only RDTs evaluated performed well. Performance of Pf-LDH-detecting RDTs against wild-type P. falciparum does not necessarily predict performance against pfhrp2-deleted parasites. Furthermore, many, but not all HRP2-based RDTs, detect pfhrp2-negative/pfhrp3-positive samples, with implications for the HRP2-based RDT screening approach for detection and surveillance of HRP2-negative parasites.
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Affiliation(s)
| | - Alisha Chaudhry
- Queensland University of Technology, Brisbane, QLD, Australia
| | | | | | - Yong Ah
- The CDC Foundation, Atlanta, GA, USA
| | - Amy Kong
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | | | - Peter Chiodini
- Hospital for Tropical Diseases, London, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | - Sandra Incardona
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Qin Cheng
- Australian Defence Force Malaria and Infectious Diseases Institute (FORMERLY Australian Army Malaria Institute), Brisbane, QLD, Australia
| | - Michael Aidoo
- Centers for Disease Control and Prevention, Atlanta, USA
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40
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Bakari C, Jones S, Subramaniam G, Mandara CI, Chiduo MG, Rumisha S, Chacky F, Molteni F, Mandike R, Mkude S, Njau R, Herman C, Nace DP, Mohamed A, Udhayakumar V, Kibet CK, Nyanjom SG, Rogier E, Ishengoma DS. Community-based surveys for Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions in selected regions of mainland Tanzania. Malar J 2020; 19:391. [PMID: 33148255 PMCID: PMC7640459 DOI: 10.1186/s12936-020-03459-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histidine-rich protein 2 (HRP2)-based malaria rapid diagnostic tests (RDTs) are effective and widely used for the detection of wild-type Plasmodium falciparum infections. Although recent studies have reported false negative HRP2 RDT results due to pfhrp2 and pfhrp3 gene deletions in different countries, there is a paucity of data on the deletions of these genes in Tanzania. METHODS A community-based cross-sectional survey was conducted between July and November 2017 in four regions: Geita, Kigoma, Mtwara and Ruvuma. All participants had microscopy and RDT performed in the field and provided a blood sample for laboratory multiplex antigen detection (for Plasmodium lactate dehydrogenase, aldolase, and P. falciparum HRP2). Samples showing RDT false negativity or aberrant relationship of HRP2 to pan-Plasmodium antigens were genotyped to detect the presence/absence of pfhrp2/3 genes. RESULTS Of all samples screened by the multiplex antigen assay (n = 7543), 2417 (32.0%) were positive for any Plasmodium antigens while 5126 (68.0%) were negative for all antigens. The vast majority of the antigen positive samples contained HRP2 (2411, 99.8%), but 6 (0.2%) had only pLDH and/or aldolase without HRP2. Overall, 13 samples had an atypical relationship between a pan-Plasmodium antigen and HRP2, but were positive by PCR. An additional 16 samples with negative HRP2 RDT results but P. falciparum positive by microscopy were also chosen for pfhrp2/3 genotyping. The summation of false negative RDT results and laboratory antigen results provided 35 total samples with confirmed P. falciparum DNA for pfhrp2/3 genotyping. Of the 35 samples, 4 (11.4%) failed to consistently amplify positive control genes; pfmsp1 and pfmsp2 and were excluded from the analysis. The pfhrp2 and pfhrp3 genes were successfully amplified in the remaining 31 (88.6%) samples, confirming an absence of deletions in these genes. CONCLUSIONS This study provides evidence that P. falciparum parasites in the study area have no deletions of both pfhrp2 and pfhrp3 genes. Although single gene deletions could have been missed by the multiplex antigen assay, the findings support the continued use of HRP2-based RDTs in Tanzania for routine malaria diagnosis. There is a need for the surveillance to monitor the status of pfhrp2 and/or pfhrp3 deletions in the future.
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Affiliation(s)
- Catherine Bakari
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Sophie Jones
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Williams Consulting, Baltimore, MD, USA
| | - Gireesh Subramaniam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Atlanta, GA, USA
| | - Celine I Mandara
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Mercy G Chiduo
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Susan Rumisha
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Frank Chacky
- National Malaria Control Programme (NMCP), Dodoma, Tanzania
| | | | - Renata Mandike
- National Malaria Control Programme (NMCP), Dodoma, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Programme (NMCP), Dodoma, Tanzania
| | - Ritha Njau
- World Health Organization (WHO) Country Office, Dar es Salaam, Tanzania
| | - Camelia Herman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
- CDC Foundation (CDCF), Atlanta, GA, USA
| | - Douglas P Nace
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ally Mohamed
- National Malaria Control Programme (NMCP), Dodoma, Tanzania
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Caleb K Kibet
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Steven G Nyanjom
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H Chan School of Public Health, Boston, MA, USA.
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Bosco AB, Anderson K, Gresty K, Prosser C, Smith D, Nankabirwa JI, Nsobya S, Yeka A, Opigo J, Gonahasa S, Namubiru R, Arinaitwe E, Mbaka P, Kissa J, Won S, Lee B, Lim CS, Karamagi C, Cunningham J, Nakayaga JK, Kamya MR, Cheng Q. Molecular surveillance reveals the presence of pfhrp2 and pfhrp3 gene deletions in Plasmodium falciparum parasite populations in Uganda, 2017-2019. Malar J 2020; 19:300. [PMID: 32843041 PMCID: PMC7449024 DOI: 10.1186/s12936-020-03362-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/05/2020] [Indexed: 01/22/2023] Open
Abstract
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.
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Affiliation(s)
- Agaba B Bosco
- College of Health Sciences, Makerere University, Kampala, Uganda. .,National Malaria Control Division, Kampala, Uganda.
| | - Karen Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Defence Force Malaria and Infectious Disease Institute, Enoggera, Australia
| | - Karryn Gresty
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Defence Force Malaria and Infectious Disease Institute, Enoggera, Australia
| | - Christiane Prosser
- Australian Defence Force Malaria and Infectious Disease Institute, Enoggera, Australia
| | - David Smith
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Defence Force Malaria and Infectious Disease Institute, Enoggera, Australia
| | - Joaniter I Nankabirwa
- College of Health Sciences, Makerere University, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Sam Nsobya
- College of Health Sciences, Makerere University, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Adoke Yeka
- College of Health Sciences, Makerere University, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Jimmy Opigo
- National Malaria Control Division, Kampala, Uganda
| | | | - Rhoda Namubiru
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Paul Mbaka
- World Health Organization Country Office, Kampala, Uganda
| | - John Kissa
- National Health Information Division, Ministry of Health, Kampala, Uganda
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Bora Lee
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Health Sciences, Korea University, Seoul, South Korea
| | - Charles Karamagi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Joan K Nakayaga
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses R Kamya
- College of Health Sciences, Makerere University, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Qin Cheng
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Defence Force Malaria and Infectious Disease Institute, Enoggera, Australia
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Jones S, Subramaniam G, Plucinski MM, Patel D, Padilla J, Aidoo M, Talundzic E. One-step PCR: A novel protocol for determination of pfhrp2 deletion status in Plasmodium falciparum. PLoS One 2020; 15:e0236369. [PMID: 32702040 PMCID: PMC7377462 DOI: 10.1371/journal.pone.0236369] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/03/2020] [Indexed: 01/08/2023] Open
Abstract
Histidine-rich protein 2 (HRP2) detecting rapid diagnostic tests (RDTs) have played an important role in enabling prompt malaria diagnosis in remote locations. However, emergence of pfhrp2 deleted parasites is threatening the efficacy of RDTs, and the World Health Organization (WHO) has highlighted surveillance of these deletions as a priority. Nested PCR is used to confirm pfhrp2 deletion but is costly and laborious. Due to spurious amplification of paralogue pfhrp3, the identity of nested exon 1 PCR product must be confirmed by sequencing. Here we describe a new one-step PCR method for detection of pfhrp2. To determine sensitivity and specificity, all PCRs were performed in triplicate. Using photo-induced electron transfer (PET) PCR detecting 18srRNA as true positive, one-step had comparable sensitivity of 95.0% (88.7–98.4%) to nested exon 1, 99.0% (94.6–99.9%) and nested exon 2, 98.0% (93.0–99.8%), and comparable specificity 93.8% (69.8–99.8%) to nested exon 1 100.0% (79.4–100.0%) and nested exon 2, 100.0% (74.4–100.0%). Sequencing revealed that one step PCR does not amplify pfhrp3. Logistic regression models applied to measure the 95% level of detection of the one-step PCR in clinical isolates provided estimates of 133p/μL (95% confidence interval (CI): 3-793p/μL) for whole blood (WB) samples and 385p/μL (95% CI: 31–2133 p/μL) for dried blood spots (DBSs). When considering protocol attributes, the one-step PCR is less expensive, faster and more suitable for high throughput. In summary, we have developed a more accurate PCR method that may be ideal for the application of the WHO protocol for investigating pfhrp2 deletions in symptomatic individuals presenting to health care facilities.
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Affiliation(s)
- Sophie Jones
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Williams Consulting, Baltimore, Maryland, United States of America
- * E-mail:
| | - Gireesh Subramaniam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Atlanta, Georgia, United States of America
| | - Mateusz M. Plucinski
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- President’s Malaria Initiative, Atlanta, Georgia, United States of America
| | - Dhruviben Patel
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Williams Consulting, Baltimore, Maryland, United States of America
| | - Jasmine Padilla
- Oak Ridge Institute for Science and Education, Atlanta, Georgia, United States of America
- Biotechnology Core Facilities Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael Aidoo
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Thomson R, Parr JB, Cheng Q, Chenet S, Perkins M, Cunningham J. Prevalence of Plasmodium falciparum lacking histidine-rich proteins 2 and 3: a systematic review. Bull World Health Organ 2020; 98:558-568F. [PMID: 32773901 PMCID: PMC7411324 DOI: 10.2471/blt.20.250621] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
Objective To calculate prevalence estimates and evaluate the quality of studies reporting Plasmodium falciparum lacking histidine-rich proteins 2 and 3, to inform an international response plan. Methods We searched five online databases, without language restriction, for articles reporting original data on Plasmodium falciparum-infected patients with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3). We calculated prevalence estimates of pfhrp2/3 deletions and mapped the data by country. The denominator was all P. falciparum-positive samples testing positive by microscopy and confirmed positive by species-specific polymerase chain reaction testing (PCR). If microscopy was not performed, we used the number of samples based on a different diagnostic method or PCR alone. We scored studies for risk of bias and the quality of laboratory methods using a standardized scoring system. Findings A total of 38 articles reporting 55 studies from 32 countries and one territory worldwide were included in the review. We found considerable heterogeneity in the populations studied, methods used and estimated prevalence of P. falciparum parasites with pfhrp2/3 deletions. The derived prevalence of pfhrp2 deletions ranged from 0% to 100%, including focal areas in South America and Africa. Only three studies (5%) fulfilled all seven criteria for study quality. Conclusion The lack of representative surveys or consistency in study design impairs evaluations of the risk of false-negative results in malaria diagnosis due to pfhrp2/3 deletions. Accurate mapping and strengthened monitoring of the prevalence of pfhrp2/3 deletions is needed, along with harmonized methods that facilitate comparisons across studies.
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Affiliation(s)
| | - Jonathan B Parr
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, United States of America
| | - Qin Cheng
- Australian Defence Force Malaria and Infectious Disease Institute, Queensland, Australia
| | - Stella Chenet
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru
| | - Mark Perkins
- Department of Emergency Preparedness, World Health Organization, Geneva, Switzerland
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, avenue Appia 20, 1211 Geneva 27, Switzerland
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Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions and Their Implications in Malaria Control. Diseases 2020; 8:diseases8020015. [PMID: 32443811 PMCID: PMC7349124 DOI: 10.3390/diseases8020015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/25/2020] [Accepted: 05/05/2020] [Indexed: 01/15/2023] Open
Abstract
Malaria remains the biggest threat to public health, especially among pregnant women and young children in sub-Saharan Africa. Prompt and accurate diagnosis is critical for effective case management and detection of drug resistance. Conventionally, microscopy and rapid diagnostic tests (RDTs) are the tools of choice for malaria diagnosis. RDTs are simple to use and have been extensively used in the diagnosis of malaria among travelers to malaria-endemic regions, routine case management, and surveillance studies. Most RDTs target the histidine-rich protein (PfHRP) which is exclusively found in Plasmodium falciparum and a metabolic enzyme Plasmodium lactate dehydrogenase (pLDH) which is common among all Plasmodium species. Other RDTs incorporate the enzyme aldolase that is produced by all Plasmodium species. Recently, studies have reported false-negative RDTs primarily due to the deletion of the histidine-rich protein (pfhrp2 and pfhrp3) genes in field isolates of P. falciparum. Herein, we review published literature to establish pfhrp2/pfhrp3 deletions, the extent of these deletions in different geographical regions, and the implication in malaria control. We searched for publications on pfhrp2/pfhrp3 deletions and retrieved all publications that reported on this subject. Overall, 20 publications reported on pfhrp2/pfhrp3 deletions, and most of these studies were done in Central and South America, with very few in Asia and Africa. The few studies in Africa that reported on the occurrence of pfhrp2/pfhrp3 deletions rarely evaluated deletions on the flanking genes. More studies are required to evaluate the existence and extent of these gene deletions, whose presence may lead to delayed or missed treatment. This information will guide appropriate diagnostic approaches in the respective areas.
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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Dong Y, Liu S, Deng Y, Xu Y, Chen M, Liu Y, Xue J. Genetic polymorphism of histidine rich protein 2 in Plasmodium falciparum isolates from different infection sources in Yunnan Province, China. Malar J 2019; 18:446. [PMID: 31888663 PMCID: PMC6937805 DOI: 10.1186/s12936-019-3084-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/21/2019] [Indexed: 11/22/2022] Open
Abstract
Background Failed diagnoses of some falciparum malaria cases by RDTs are constantly reported in recent years. Plasmodium falciparum histidine-rich protein 2 (pfhpr2) gene deficiency has been found to be the major reason of RDTs failure in many countries. This article analysed the deletion of pfhpr2 gene of falciparum malaria cases isolated in Yunnan Province, China. Methods Blood samples from falciparum malaria cases diagnosed in Yunnan Province were collected. Plasmodium genomic DNA was extracted and the pfhrp2 gene exon2 region was amplified via nested PCR. The haplotype of the DNA sequence, the nucleic acid diversity index (PI) and expected heterozygosity (He) were analyzed. Count PfHRP2 amino acid peptide sequence repeat and its times, and predict the properties of PfHRP2 peptide chain reaction to RDTs testing. Results A total of 306 blood samples were collected, 84.9% (259/306) from which pfhrp2 PCR amplification products (gene exon2) were obtained, while the remaining 47 samples were false amplification. The length of the 250 DNA sequences ranged from 345 - 927 bp, with 151 haplotypes, with PI and He values of 0.169 and 0.983, respectively. The length of the PfHRP2 peptide chain translated from 250 DNA sequences ranged from 115 to 309 aa. All peptide chains had more than an amino acid codon deletion. All 250 PfHRP2 strands ended with a type 12 amino acid repeat, 98.0% (245/250) started with a type 1 repetition and 2.0% (5/250) with a type 2 repetition. The detection rate for type 2 duplicates was 100% (250/250). Prediction of RDT sensitivity of PfHRP2 peptide chains based on type 2 and type 7 repeats showed that 9.60% (24/250), 50.0% (125/250), 13.20% (33/250) and 27.20.5% (68/250) of the 250 peptide chains were very sensitive, sensitive, borderline and non-sensitive, respectively. Conclusion The diversified polymorphism of the pfhrp2 gene deletion from different infection sources in the Yunnan province are extremely complex. The cause of the failure of pfhrp2 exon2 amplification is still to be investigated. The results of this study appeal to Yunnan Province for a timely evaluation of the effectiveness and applicability of RDTs in the diagnosis of malaria.
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Affiliation(s)
- Ying Dong
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China.
| | - Shuping Liu
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China.,School of Basic Medical Sciences, Dali University, Dali, 667000, China
| | - Yan Deng
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China
| | - Yanchun Xu
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China
| | - Mengni Chen
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China
| | - Yan Liu
- Yunnan Institute of Parasitic Diseases Control, Yunnan Provincial Key Laboratory, Yunnan Centre of Malaria Research, Academician Workstation of Professor Jin Ningyi, Pu'er, 665000, China
| | - Jingpo Xue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, China
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Herman C, Huber CS, Jones S, Steinhardt L, Plucinski MM, Lemoine JF, Chang M, Barnwell JW, Udhayakumar V, Rogier E. Multiplex malaria antigen detection by bead-based assay and molecular confirmation by PCR shows no evidence of Pfhrp2 and Pfhrp3 deletion in Haiti. Malar J 2019; 18:380. [PMID: 31775743 PMCID: PMC6882344 DOI: 10.1186/s12936-019-3010-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/16/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Plasmodium falciparum parasite is the only human malaria that produces the histidine-rich protein 2 and 3 (HRP2/3) antigens. Currently, HRP2/3 are widely used in malaria rapid diagnostic tests (RDTs), but several global reports have recently emerged showing genetic deletion of one or both of these antigens in parasites. Deletion of these antigens could pose a major concern for P. falciparum diagnosis in Haiti which currently uses RDTs based solely on the detection of the HRP2/3 antigens. METHODS From September 2012 through February 2014, dried blood spots (DBS) were collected in Haiti from 9317 febrile patients presenting to 17 health facilities in 5 departments throughout the country as part of a bed net intervention study. All DBS from RDT positive persons and a random sampling of DBS from RDT negative persons were assayed for P. falciparum DNA by nested and PET-PCR (n = 2695 total). All PCR positive samples (n = 331) and a subset of PCR negative samples (n = 95) were assayed for three malaria antigens by a multiplex bead assay: pan-Plasmodium aldolase (pAldo), pan-Plasmodium lactate dehydrogenase (pLDH), and HRP2/3. Any samples positive for P. falciparum DNA, but negative for HRP2/3 antigens were tested by nested PCR for Pfhrp2 and Pfhrp3 gene deletions. RESULTS Of 2695 DBS tested for Plasmodium DNA, 345 (12.8%) were originally found to be positive for P. falciparum DNA; 331 of these had DBS available for antigen detection. Of these, 266 (80.4%) were positive for pAldo, 221 (66.8%) positive for pLDH, and 324 (97.9%) were positive for HRP2/3 antigens. Seven samples (2.1%) positive for P. falciparum DNA were not positive for any of the three antigens by the bead assay, and were investigated for potential Pfhrp2/3 gene deletion by PCR. These samples either successfully amplified Pfhrp2/3 genes or were at an estimated parasite density too low for sufficient DNA to perform successful genotyping. CONCLUSIONS Malaria positive samples in multiple Haitian sites were found to contain the HRP2/3 antigens, and no evidence was found of Pfhrp2/3 deletions. Malaria RDTs based on the detection of the HRP2/3 antigens remain a reliable P. falciparum diagnostic tool as Haiti works towards malaria elimination.
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Affiliation(s)
- Camelia Herman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA.,CDC Foundation (CDCF), Atlanta, GA, USA
| | - Curtis S Huber
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sophie Jones
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Atlanta Research and Education Foundation (AREF), Atlanta, GA, USA
| | - Laura Steinhardt
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mateusz M Plucinski
- U.S. President's Malaria Initiative, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jean F Lemoine
- Programme National de Contrôle de la Malaria/MSPP, Port-au-Prince, Haiti
| | - Michelle Chang
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John W Barnwell
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Agaba BB, Yeka A, Nsobya S, Arinaitwe E, Nankabirwa J, Opigo J, Mbaka P, Lim CS, Kalyango JN, Karamagi C, Kamya MR. Systematic review of the status of pfhrp2 and pfhrp3 gene deletion, approaches and methods used for its estimation and reporting in Plasmodium falciparum populations in Africa: review of published studies 2010-2019. Malar J 2019; 18:355. [PMID: 31694718 PMCID: PMC6836395 DOI: 10.1186/s12936-019-2987-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Malaria rapid diagnostic tests based on histidine-rich protein-2 have played a vital role in improving malaria case management and surveillance particularly in Africa, where Plasmodium falciparum is predominant. However, their usefulness has been threatened by the emergence of gene deletion on P. falciparum histidine rich protein 2 (pfhrp2) and P. falciparum histidine rich protein 3 (pfhrp3). Use of standard and recommended methods is key for accurate investigation, confirmation and reporting of pfhrp2 and pfhrp3 gene deletion. Methods A systematic review was conducted to assess the status, methods and approaches that have been used for investigation, confirmation and reporting of pfhrp2 and pfhrp3 gene deletion in Africa. An online search was done using PubMed and MEDLINE Google Scholar for all articles published in English on pfhrp2/3 gene deletion in Africa. Relevant articles that met the inclusion criteria were summarized and assessed based on the protocol recommended by the World Health Organization for confirmation and reporting of pfhrp2/3 gene deletion. Results The search identified a total of 18 articles out of which 14 (77.7%) fulfilled the criteria for inclusion and were retained for review. The articles were distributed across 12 countries where the pfhrp2 and pfhrp3 gene deletion studies were conducted and reported. The level of pfhrp2/3 gene deletion across selected studies in Africa ranged from the highest 62% to the lowest 0.4%. There was wide variation in methods and approaches including study designs, size and sampling and whether both pfhrp2 and pfhrp3 double deletions or pfhrp2 single deletion were investigated, with a wide variation in laboratory methods. Conclusion Based on the review, there is evidence of the presence of pfhrp2/3 gene-deleted P. falciparum parasites in Africa. The approaches and methods used for investigation, confirmation and reporting of pfhrp2/3 deleted parasites have varied between studies and across countries. Countries that are considering plans to investigate, confirm and report pfhrp2/3 deletion should use recommended standard and harmonized methods to prevent unnecessary recommendations for costly switch of RDTs in Africa.
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Affiliation(s)
- Bosco B Agaba
- School of Medicine, College of Health Sciences Makerere University, Kampala, Uganda. .,Clinical Epidemiology Unit, Makerere University Kampala, Kampala, Uganda. .,National Malaria Control Programme, Kampala, Uganda.
| | - Adoke Yeka
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Sam Nsobya
- School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Joaniter Nankabirwa
- School of Medicine, College of Health Sciences Makerere University, Kampala, Uganda.,Clinical Epidemiology Unit, Makerere University Kampala, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Jimmy Opigo
- National Malaria Control Programme, Kampala, Uganda
| | - Paul Mbaka
- World Health Organization Country Office, Kampala, Uganda
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Health Sciences, Korea University, Seoul, South Korea
| | - Joan N Kalyango
- Clinical Epidemiology Unit, Makerere University Kampala, Kampala, Uganda
| | - Charles Karamagi
- Clinical Epidemiology Unit, Makerere University Kampala, Kampala, Uganda
| | - Moses R Kamya
- School of Medicine, College of Health Sciences Makerere University, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
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Funwei R, Nderu D, Nguetse CN, Thomas BN, Falade CO, Velavan TP, Ojurongbe O. Molecular surveillance of pfhrp2 and pfhrp3 genes deletion in Plasmodium falciparum isolates and the implications for rapid diagnostic tests in Nigeria. Acta Trop 2019; 196:121-125. [PMID: 31103699 DOI: 10.1016/j.actatropica.2019.05.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 04/05/2019] [Accepted: 05/15/2019] [Indexed: 11/28/2022]
Abstract
Prompt diagnosis and appropriate treatment of malaria remain the hallmark for reducing malaria-related mortality in high transmission areas. Plasmodium falciparum histidine-rich protein2 (PfHRP2) based rapid diagnostic tests (RDT) play a vital role in prompt and accurate malaria diagnosis. However, pfhrp2 gene deletion threatens the RDT test sensitivity. This study reports the presence of pfhrp2 and pfhrp3 genes deletion among parasite isolates in Nigeria. Febrile children were screened using histidine-rich protein (HRP2) specific RDT (SD-Bioline RDT) and microscopy for P. falciparum infections. All RDT negative samples were re-evaluated by polymerase chain reaction (PCR). The presence of parasite in RDT false negative cases and randomly selected RDT positive cases were validated using PCRs targeting glutamate-rich protein (glurp) and merozoite surface proteins (msp-1 and msp-2). Thereafter, exon 2 of pfhrp2 and pfhrp3 were amplified, and Sanger sequenced. A total of 511 febrile children were enrolled out of which 309 (61%) were positive by RDT. The presence of pfhrp2 and pfhrp3 genes were analyzed in 66 PCR positive samples comprising of 31 RDT false negative and 35 RDT true positive randomly selected samples. The pfhrp2 and pfhrp3 genes failed to amplify in 17% (11/66) and 6% (4/66) samples, respectively. Seven of the eleven samples had only pfhrp2 deletion while four had both pfhrp2 and pfhrp3 deletions. The absence of the pfhrp2 gene may be responsible for the seven RDT false negative cases observed. Three RDT positive cases lacked pfhrp2 whereas pfhrp3 was absent in only four RDT false negative cases. The pfhrp2 and pfhrp3 amino acid repeat sequences were highly diverse. The P. falciparum isolates lacking pfhrp2 and pfhrp3 genes may be circulating and contributing to RDT false negativity in Nigeria. More studies in larger population and seasonally defined cases will be needed to determine the extent of pfhrp2/3 genes deletion in different geographical areas of Nigeria.
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Affiliation(s)
- Roland Funwei
- Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria; Department of Pharmacy Technician Studies, Bayelsa State College of Health Technology, Nigeria
| | - David Nderu
- Institute of Tropical Medicine, University of Tübingen, Germany
| | - Christian N Nguetse
- Department of Pediatrics, Stanford University School of Medicine, Stanford, USA
| | - Bolaji N Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY, USA
| | - Catherine O Falade
- Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria; Institute for Advanced Medical Research and Training, University College Hospital Ibadan, Nigeria
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, Germany; Faculty of Medicine. Duy Tan University, Da Nang, Vietnam
| | - Olusola Ojurongbe
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo, Nigeria.
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Vera-Arias CA, Castro LE, Gómez-Obando J, Sáenz FE. Diverse origin of Plasmodium falciparum in northwest Ecuador. Malar J 2019; 18:251. [PMID: 31349843 PMCID: PMC6660669 DOI: 10.1186/s12936-019-2891-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ecuador plans to eliminate malaria by 2020, and the country has already seen a decrease in the number of cases from more than 100,000 in 2000 to only 618 in 2015. Around 30% of malaria infections in Ecuador are caused by Plasmodium falciparum. Most malaria population genetics studies performed in Latin America, especially in the Pacific Coast, indicate a high clonality and a clear structure of P. falciparum populations. It was shown that an outbreak of P. falciparum in northwest Ecuador was the result of a clonal expansion of parasites circulating at low levels in the country or re-invading Ecuador from neighbouring territories. However, general characteristics of P. falciparum circulating in the northwest coast of Ecuador have not been determined. The main goal of this study was to genetically characterize the population structure of P. falciparum in coastal Ecuadorian localities bordering with Colombia. METHODS Molecular investigation of 41 samples collected from 2013 to 2016 in San Lorenzo County, northwest Ecuador was performed using seven neutral microsatellite markers. RESULTS The genetic population structure of P. falciparum in northwest Ecuador is clearly defined as three different genetic groups previously reported in Ecuador, Peru and Colombia. CONCLUSIONS The limited number of P. falciparum clonal types that are circulating in northwest Ecuador, are related to ancestral parasite clonal lineages reported in the Pacific Coast. These parasites could be a product of migration from neighbouring regions or residual clonal types circulating in the country in low proportions. Studies of the genetic characterization of P. falciparum in eliminating areas help determine the possible origin of parasites in order to create strategies to prevent the entrance of new lineages and achieve local elimination of malaria.
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Affiliation(s)
- Claudia A Vera-Arias
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076, Apartado: 17-01-2184, Quito, Ecuador
| | | | - Javier Gómez-Obando
- Ministerio de Salud Pública, Distrito de Salud de San Lorenzo, San Lorenzo, Ecuador
| | - Fabián E Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076, Apartado: 17-01-2184, Quito, Ecuador.
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