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Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Arévalo de Los Rios S, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Van Geertruyden JP, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Sci Rep 2024; 14:16291. [PMID: 39009685 PMCID: PMC11250820 DOI: 10.1038/s41598-024-66925-x] [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: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024] Open
Abstract
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = 0.07-0.52 and Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru.
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Oscar Nolasco
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Johanna H Kattenberg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Carlos Fernandez-Miñope
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Keare Barazorda
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | | | - Hugo Rodriguez-Ferrucci
- Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana, Iquitos, Loreto, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Pierre Van Geertruyden
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium.
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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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Ikegbunam M, Maurer M, Abone H, Ezeagwuna D, Sandri TL, Esimone C, Ojurongbe O, Woldearegai TG, Kreidenweiss A, Held J, Fendel R. Evaluating Malaria Rapid Diagnostic Tests and Microscopy for Detecting Plasmodium Infection and Status of Plasmodium falciparum Histidine-Rich Protein 2/3 Gene Deletions in Southeastern Nigeria. Am J Trop Med Hyg 2024; 110:902-909. [PMID: 38531105 PMCID: PMC11066366 DOI: 10.4269/ajtmh.23-0690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
Delays in malaria diagnosis increase treatment failures and deaths. In endemic regions, standard diagnostic methods are microscopy and malaria rapid diagnostic tests (mRDTs) detecting Plasmodium falciparum histidine-rich protein 2/3 (PFHRP2/PFHRP3), but gene deletions can allow certain parasites to remain undetected. We enlisted a cohort comprising 207 symptomatic individuals, encompassing both children and adults, at a hospital in Nnewi, Nigeria. The prevalence of parasites was determined using a highly sensitive, species-specific quantitative polymerase chain reaction (SS-qPCR). Within a subset of 132 participants, we assessed the sensitivity and specificity of microscopy and HRP2-mRDTs in comparison to SS-qPCR for the detection of P. falciparum. We also investigated the prevalence of pfhrp2/pfhrp3 gene deletions. Greater sensitivity was achieved with mRDTs (95%) compared with microscopy (77%). Also, mRDTs exhibited greater specificity (68%) than microscopy (44%). The positive predictive value of mRDTs (89%) surpassed that of microscopy (80%), suggesting a greater probability of accurately indicating the presence of infection. The negative predictive value of mRDTs (82%) was far greater than microscopy (39%). Of the 165 P. falciparum-positive samples screened for pfhrp2/pfhrp3 gene deletions, one gene deletion was detected in one sample. Regarding infection prevalence, 84% were positive for Plasmodium spp. (by reverse transcription [RT]-qPCR), with P. falciparum responsible for the majority (97%) of positive cases. Thus, exclusive reliance on microscopy in endemic areas may impede control efforts resulting from false negatives, underscoring the necessity for enhanced training and advocating for high-throughput molecular testing such as RT-qPCR or qPCR at referral centers to address limitations.
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Affiliation(s)
- Moses Ikegbunam
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka, Nigeria
- Molecular Research Foundation for Students and Scientist, Nnamdi Azikiwe University, Awka, Nigeria
| | - Maike Maurer
- Institute of Tropical Medicine, University of Tübingen, Germany
| | - Harrison Abone
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Dorothy Ezeagwuna
- Departement of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Thaisa Lucas Sandri
- Institute of Tropical Medicine, University of Tübingen, Germany
- Synovo GmbH, Tübingen, Germany
| | - Charles Esimone
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka, Nigeria
- Molecular Research Foundation for Students and Scientist, Nnamdi Azikiwe University, Awka, Nigeria
| | - Olusola Ojurongbe
- Department of Medical Microbiology & Parasitology, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Tamirat Gebru Woldearegai
- Institute of Tropical Medicine, University of Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
- Center de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
- Center de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
- Center de Recherches Médicales de Lambaréné (CERMEL), Gabon
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Okanda D, Ndwiga L, Osoti V, Achieng N, Wambua J, Ngetsa C, Lubell-Doughtie P, Shankar A, Bejon P, Ochola-Oyier LI. Low frequency of Plasmodium falciparum hrp2/3 deletions from symptomatic infections at a primary healthcare facility in Kilifi, Kenya. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1083114. [PMID: 38455911 PMCID: PMC10910971 DOI: 10.3389/fepid.2023.1083114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/23/2023] [Indexed: 03/09/2024]
Abstract
There is a growing concern for malaria control in the Horn of Africa region due to the spread and rise in the frequency of Plasmodium falciparum Histidine-rich Protein (hrp) 2 and 3 deletions. Parasites containing these gene deletions escape detection by the major PfHRP2-based rapid diagnostic test. In this study, the presence of Pfhrp2/3 deletions was examined in uncomplicated malaria patients in Kilifi County, from a region of moderate-high malaria transmission. 345 samples were collected from the Pingilikani dispensary in 2019/2020 during routine malaria care for patients attending this primary health care facility. The Carestart™ RDT and microscopy were used to test for malaria. In addition, qPCR was used to confirm the presence of parasites. In total, 249 individuals tested positive for malaria by RDT, 242 by qPCR, and 170 by microscopy. 11 samples that were RDT-negative and microscopy positive and 25 samples that were qPCR-positive and RDT-negative were considered false negative tests and were examined further for Pfhrp2/3 deletions. Pfhrp2/3-negative PCR samples were further genotyped at the dihydrofolate reductase (Pfdhfr) gene which served to further confirm that parasite DNA was present in the samples. The 242 qPCR-positive samples (confirmed the presence of DNA) were also selected for Pfhrp2/3 genotyping. To determine the frequency of false negative results in low parasitemia samples, the RDT- and qPCR-negative samples were genotyped for Pfdhfr before testing for Pfhrp2/3. There were no Pfhrp2 and Pfhrp3 negative but positive for dhfr parasites in the 11 (RDT negative and microscopy positive) and 25 samples (qPCR-positive and RDT-negative). In the larger qPCR-positive sample set, only 5 samples (2.1%) were negative for both hrp2 and hrp3, but positive for dhfr. Of the 5 samples, there were 4 with more than 100 parasites/µl, suggesting true hrp2/3 deletions. These findings revealed that there is currently a low prevalence of Pfhrp2 and Pfhrp3 deletions in the health facility in Kilifi. However, routine monitoring in other primary health care facilities across the different malaria endemicities in Kenya is urgently required to ensure appropriate use of malaria RDTs.
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Affiliation(s)
- Dorcas Okanda
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Leonard Ndwiga
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Victor Osoti
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nicole Achieng
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Juliana Wambua
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Caroline Ngetsa
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Anuraj Shankar
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Philip Bejon
- Biosciences Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
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Stabler TC, Dwivedi A, Shrestha B, Joshi S, Schindler T, Ouattara A, García GA, Daubenberger C, Silva JC. Gene Coverage Count and Classification (GC 3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum. Malar J 2022; 21:357. [PMID: 36447234 PMCID: PMC9706933 DOI: 10.1186/s12936-022-04376-3] [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: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The ability of malaria rapid diagnostic tests (RDTs) to effectively detect active infections is being compromised by the presence of malaria strains with genomic deletions at the hrp2 and hrp3 loci, encoding the antigens most commonly targeted in diagnostics for Plasmodium falciparum detection. The presence of such deletions can be determined in publically available P. falciparum whole genome sequencing (WGS) datasets. A computational approach was developed and validated, termed Gene Coverage Count and Classification (GC3), to analyse genome-wide sequence coverage data and provide informative outputs to assess presence and coverage profile of a target locus in WGS data. GC3 was applied to detect deletions at hrp2 and hrp3 (hrp2/3) and flanking genes in different geographic regions and across time points. METHODS GC3 uses Python and R scripts to extract locus read coverage metrics from mapped WGS data according to user-defined parameters and generates relevant tables and figures. GC3 was tested using WGS data for laboratory reference strains with known hrp2/3 genotypes, and its results compared to those of a hrp2/3-specific qPCR assay. Samples with at least 25% of coding region positions with zero coverage were classified as having a deletion. Publicly available sequence data was analysed and compared with published deletion frequency estimates. RESULTS GC3 results matched the expected coverage of known laboratory reference strains. Agreement between GC3 and a hrp2/3-specific qPCR assay reported for 19/19 (100%) hrp2 deletions and 18/19 (94.7%) hrp3 deletions. Among Cambodian (n = 127) and Brazilian (n = 20) WGS datasets, which had not been previously analysed for hrp2/3 deletions, GC3 identified hrp2 deletions in three and four samples, and hrp3 deletions in 10 and 15 samples, respectively. Plots of hrp2/3 coding regions, grouped by year of sample collection, showed a decrease in median standardized coverage among Malawian samples (n = 150) suggesting the importance of a careful, properly controlled follow up to determine if an increase in frequency of deletions has occurred between 2007-2008 and 2014-2015. Among Malian (n = 90) samples, median standardized coverage was lower in 2002 than 2010, indicating widespread deletions present at the gene locus in 2002. CONCLUSIONS The GC3 tool accurately classified hrp2/3 deletions and provided informative tables and figures to analyse targeted gene coverage. GC3 is an appropriate tool when performing preliminary and exploratory assessment of locus coverage data.
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Affiliation(s)
- Thomas C Stabler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Biraj Shrestha
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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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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7
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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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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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9
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Douglas NM, Burkot TR, Price RN. Malaria eradication revisited. Int J Epidemiol 2022; 51:382-392. [PMID: 34918106 DOI: 10.1093/ije/dyab259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/06/2021] [Indexed: 01/13/2023] Open
Affiliation(s)
- Nicholas M Douglas
- Department of Medicine, University of Otago, Christchurch, New Zealand.,Division of Global and Tropical Health, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Department of Infectious Diseases, Christchurch Hospital, Christchurch, New Zealand
| | - Thomas R Burkot
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Ric N Price
- Division of Global and Tropical Health, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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10
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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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11
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Costa GL, Mascarenhas MEP, Martin TOG, Fortini LG, Louzada J, Pereira DB, Aguiar ACC, Carvalho LH, de Brito CFA, Fontes CJF, de Sousa TN. A Comprehensive Analysis of the Genetic Diversity of Plasmodium falciparum Histidine-Rich Protein 2 (PfHRP2) in the Brazilian Amazon. Front Cell Infect Microbiol 2021; 11:742681. [PMID: 34621693 PMCID: PMC8491578 DOI: 10.3389/fcimb.2021.742681] [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: 07/16/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Early diagnosis and treatment are fundamental to the control and elimination of malaria. In many endemic areas, routine diagnosis is primarily performed microscopically, although rapid diagnostic tests (RDTs) provide a useful point-of-care tool. Most of the commercially available RDTs detect histidine-rich protein 2 (HRP2) of Plasmodium falciparum in the blood of infected individuals. Nonetheless, parasite isolates lacking the pfhrp2 gene are relatively frequent in some endemic regions, thereby hampering the diagnosis of malaria using HRP2-based RDTs. To track the efficacy of RDTs in areas of the Brazilian Amazon, we assessed pfhrp2 deletions in 132 P. falciparum samples collected from four malaria-endemic states in Brazil. Our findings show low to moderate levels of pfhrp2 deletion in different regions of the Brazilian Amazon. Overall, during the period covered by this study (2002-2020), we found that 10% of the P. falciparum isolates were characterized by a pfhrp2 deletion. Notably, however, the presence of pfhrp2-negative isolates has not been translated into a reduction in RDT efficacy, which in part may be explained by the presence of polyclonal infections. A further important finding was the discrepancy in the proportion of pfhrp2 deletions detected using two assessed protocols (conventional PCR versus nested PCR), which reinforces the need to perform a carefully planned laboratory workflow to assess gene deletion. This is the first study to perform a comprehensive analysis of PfHRP2 sequence diversity in Brazilian isolates of P. falciparum. We identified 10 PfHRP2 sequence patterns, which were found to be exclusive of each of the assessed regions. Despite the small number of PfHRP2 sequences available from South America, we found that the PfHRP2 sequences identified in Brazil and neighboring French Guiana show similar sequence patterns. Our findings highlight the importance of continuously monitoring the occurrence and spread of parasites with pfrhp2 deletions, while also taking into account the limitations of PCR-based testing methods associated with accuracy and the complexity of infections.
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Affiliation(s)
- Gabriel Luíz Costa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Maria Eduarda Pereira Mascarenhas
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | | | - Laura Guimarães Fortini
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | | | | | | | - Luzia Helena Carvalho
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | | | - Tais Nóbrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
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