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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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Bechtold P, Wagner P, Hosch S, Gregorini M, Stark WJ, Gody JC, Kodia-Lenguetama ER, Pagonendji MS, Donfack OT, Phiri WP, García GA, Nsanzanbana C, Daubenberger CA, Schindler T, Vickos U. Development and evaluation of PlasmoPod: A cartridge-based nucleic acid amplification test for rapid malaria diagnosis and surveillance. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001516. [PMID: 37756280 PMCID: PMC10529553 DOI: 10.1371/journal.pgph.0001516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Malaria surveillance is hampered by the widespread use of diagnostic tests with low sensitivity. Adequate molecular malaria diagnostics are often only available in centralized laboratories. PlasmoPod is a novel cartridge-based nucleic acid amplification test for rapid, sensitive, and quantitative detection of malaria parasites. PlasmoPod is based on reverse-transcription quantitative polymerase chain reaction (RT-qPCR) of the highly abundant Plasmodium spp. 18S ribosomal RNA/DNA biomarker and is run on a portable qPCR instrument which allows diagnosis in less than 30 minutes. Our analytical performance evaluation indicates that a limit-of-detection as low as 0.02 parasites/μL can be achieved and no cross-reactivity with other pathogens common in malaria endemic regions was observed. In a cohort of 102 asymptomatic individuals from Bioko Island with low malaria parasite densities, PlasmoPod accurately detected 83 cases, resulting in an overall detection rate of 81.4%. Notably, there was a strong correlation between the Cq values obtained from the reference RT-qPCR assay and those obtained from PlasmoPod. In an independent cohort, using dried blood spots from malaria symptomatic children living in the Central African Republic, we demonstrated that PlasmoPod outperforms malaria rapid diagnostic tests based on the PfHRP2 and panLDH antigens as well as thick blood smear microscopy. Our data suggest that this 30-minute sample-to-result RT-qPCR procedure is likely to achieve a diagnostic performance comparable to a standard laboratory-based RT-qPCR setup. We believe that the PlasmoPod rapid NAAT could enable widespread accessibility of high-quality and cost-effective molecular malaria surveillance data through decentralization of testing and surveillance activities, especially in elimination settings.
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Affiliation(s)
- Philippe Bechtold
- Institute for Chemical and Bioengineering, ETH Zurich, Zuerich, Switzerland
- Diaxxo AG, Zuerich, Switzerland
| | - Philipp Wagner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Michele Gregorini
- Institute for Chemical and Bioengineering, ETH Zurich, Zuerich, Switzerland
- Diaxxo AG, Zuerich, Switzerland
| | - Wendelin J. Stark
- Institute for Chemical and Bioengineering, ETH Zurich, Zuerich, Switzerland
- Diaxxo AG, Zuerich, Switzerland
| | - Jean Chrysostome Gody
- Paediatric Hospital and University Complex of Bangui, Bangui, Central African Republic
| | | | | | | | | | | | - Christian Nsanzanbana
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Claudia A. Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ulrich Vickos
- Infectious and Tropical Diseases Unit, Department of Medicine, Amitié Hospital, Bangui, Central African Republic
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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3
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Haldar K, Alam MS, Koepfli C, Lobo NF, Phru CS, Islam MN, Faiz A, Khan WA, Haque R. Bangladesh in the era of malaria elimination. Trends Parasitol 2023; 39:760-773. [PMID: 37500334 DOI: 10.1016/j.pt.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Bangladesh has dramatically reduced malaria by 93% from 2008 to 2020. The strategy has been district-wise, phased elimination; however, the last districts targeted for elimination include remote, forested regions which present several challenges for prevention, detection, and treatment of malaria. These districts border Myanmar which harbors Plasmodium falciparum malaria parasites resistant to artemisinins, key drugs used in artemisinin-based combination therapies (ACTs) that have been vital for control programs. Challenges in monitoring emergence of artemisinin resistance (AR), tracking parasite reservoirs, changes in vector behavior and responses to insecticides, as well as other environmental and host factors (including the migration of Forcibly Displaced Myanmar Nationals; FDMNs) may pose added hazards in the final phase of eliminating malaria in Bangladesh.
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Affiliation(s)
- Kasturi Haldar
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA.
| | - Mohammed Shafiul Alam
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA
| | - Neil F Lobo
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA
| | - Ching Shwe Phru
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | | | - Abul Faiz
- Dev Care Foundation, Dhaka, Bangladesh
| | - Wasif Ali Khan
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
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Low Prevalence of Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions—A Multiregional Study in Central and West Africa. Pathogens 2023; 12:pathogens12030455. [PMID: 36986377 PMCID: PMC10054520 DOI: 10.3390/pathogens12030455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/15/2023] Open
Abstract
Plasmodium falciparum parasites carrying deletions of histidine-rich protein 2 and 3 genes, pfhrp2 and pfhrp3, respectively, are likely to escape detection via HRP2-based rapid diagnostic tests (RDTs) and, consequently, treatment, posing a major risk to both the health of the infected individual and malaria control efforts. This study assessed the frequency of pfhrp2- and pfhrp3-deleted strains at four different study sites in Central Africa (number of samples analyzed: Gabon N = 534 and the Republic of Congo N = 917) and West Africa (number of samples analyzed: Nigeria N = 466 and Benin N = 120) using a highly sensitive multiplex qPCR. We found low prevalences for pfhrp2 (1%, 0%, 0.03% and 0) and pfhrp3 single deletions (0%, 0%, 0.03% and 0%) at all study sites (Gabon, the Republic of Congo, Nigeria and Benin, respectively). Double-deleted P. falciparum were only found in Nigeria in 1.6% of all internally controlled samples. The results of this pilot investigation do not point towards a high risk for false-negative RDT results due to pfhrp2/pfhrp3 deletions in Central and West African regions. However, as this scenario can change rapidly, continuous monitoring is essential to ensure that RDTs remain a suitable tool for the malaria diagnostic strategy.
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Mwangonela ZE, Ye Y, Rachel Q, Msuya HM, Mwamlima TG, Mswata SS, Chaki PP, Kimaro EG, Mweya CN, Mpina MG, Mwangoka GW. Field evaluation of the novel One Step Malaria Pf and Pf/Pv rapid diagnostic tests and the proportion of HRP-2 gene deletion identified on samples collected in the Pwani region, Tanzania. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2023; 47:17. [PMID: 36776799 PMCID: PMC9904258 DOI: 10.1186/s42269-023-00992-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Background Malaria rapid diagnostic tests (mRDTs) have played an important role in the early detection of clinical malaria in an endemic area. While several mRDTs are currently on the market, the availability of mRDTs with high sensitivity and specificity will merit the fight against malaria. We evaluated the field performance of a novel One Step Malaria (P.f/P.v) Tri-line and One Step Malaria (P.f) rapid test kits in Pwani, Tanzania. Methods In a cross-sectional study conducted in Bagamoyo and Kibiti districts in Tanzania, symptomatic patients were tested using the SD BIOLINE, One Step Malaria (P.f/P.v) Tri-line and One Step Malaria (P.f) rapid test kits, microscope, and quantitative Polymerase Chain Reaction (qPCR). An additional qPCR assay was carried out to detect Histidine-Rich Protein 2 (HRP-2) gene deletion on mRDT negative but microscope and qPCR positive samples. Microscope results confirmed by qPCR were used for analysis, where qPCR was used as a reference method. Results The sensitivity and specificity of One Step P.f/P.v Tri-line mRDTs were 96.0% (CI 93.5-97.7%) and 98.3% (CI 96.8-99.2%), respectively. One Step P.f mRDT had sensitivity and specificity of 95.2% (CI 92.5-97.1%) and 97.9% (CI 96.3-99.0%) respectively. Positive predictive value (PPV) was 97.6% (CI 95.4-98.7%) and negative predictive value (NPV) was 96.2% (CI 95.5-98.3%) for the One Step P.f/P.v Tri-line mRDTs respectively, while One Step P.f mRDT had positive predictive value (PPV) and negative predictive value (NPV) of 97.0% (CI 94.8-98.3%) and 96.7 (CI 94.9-97.9%) respectively. 9.8% (CI 7.84-11.76) of all samples tested and reported to be malaria-negative by mRDT had HRP-2 gene deletion. Conclusion One Step Malaria P.f/P.v Tri-line and One Step Malaria P.f rapid test kits have similar sensitivity and specificity as the standard mRDT that is currently in the market, demonstrating the potential to contribute in the fight against malaria in endemic settings. However, the identified malaria parasites population with HRP-2 gene deletion pose a threat to the current mRDT usability in the field and warrants further investigations.
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Affiliation(s)
- Zena E. Mwangonela
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
- The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Young Ye
- InTec Products, Inc., 332 Xinguang Road Xinyang Industrial Area, Haicang, Xiamen City, 361022 China
| | - Qin Rachel
- InTec Products, Inc., 332 Xinguang Road Xinyang Industrial Area, Haicang, Xiamen City, 361022 China
| | - Hajirani M. Msuya
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
| | - Tunu G. Mwamlima
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
- The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Sarah S. Mswata
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
| | - Prosper P. Chaki
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
| | - Ester G. Kimaro
- The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Clement N. Mweya
- Univesity of Dar Es Salaam, Mbeya College of Health and Allied Science, P.O.Box 608, Mbeya, Tanzania
| | | | - Grace W. Mwangoka
- Ifakara Health Institute Bagamoyo Branch, P.O.Box 74, Bagamoyo, Tanzania
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6
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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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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:tropicalmed7100265. [PMID: 36288006 PMCID: PMC9611031 DOI: 10.3390/tropicalmed7100265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [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
- Correspondence: or
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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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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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10
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Hosch S, Yoboue CA, Donfack OT, Guirou EA, Dangy JP, Mpina M, Nyakurungu E, Blöchliger K, Guerra CA, Phiri WP, Ayekaba MO, García GA, Tanner M, Daubenberger C, Schindler T. Analysis of nucleic acids extracted from rapid diagnostic tests reveals a significant proportion of false positive test results associated with recent malaria treatment. Malar J 2022; 21:23. [PMID: 35073934 PMCID: PMC8785039 DOI: 10.1186/s12936-022-04043-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Surveillance programmes often use malaria rapid diagnostic tests (RDTs) to determine the proportion of the population carrying parasites in their peripheral blood to assess the malaria transmission intensity. Despite an increasing number of reports on false-negative and false-positive RDT results, there is a lack of systematic quality control activities for RDTs deployed in malaria surveillance programmes. METHODS The diagnostic performance of field-deployed RDTs used for malaria surveys was assessed by retrospective molecular analysis of the blood retained on the tests. RESULTS Of the 2865 RDTs that were collected in 2018 on Bioko Island and analysed in this study, 4.7% had a false-negative result. These false-negative RDTs were associated with low parasite density infections. In 16.6% of analysed samples, masked pfhrp2 and pfhrp3 gene deletions were identified, in which at least one Plasmodium falciparum strain carried a gene deletion. Among all positive RDTs analysed, 28.4% were tested negative by qPCR and therefore considered to be false-positive. Analysing the questionnaire data collected from the participants, this high proportion of false-positive RDTs could be explained by P. falciparum histidine rich protein 2 (PfHRP2) antigen persistence after recent malaria treatment. CONCLUSION Malaria surveillance depending solely on RDTs needs well-integrated quality control procedures to assess the extent and impact of reduced sensitivity and specificity of RDTs on malaria control programmes.
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Affiliation(s)
- Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Charlene Aya Yoboue
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | | | - Etienne A Guirou
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jean-Pierre Dangy
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maxmillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, United Republic of Tanzania.,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Elizabeth Nyakurungu
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania.,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Koranan Blöchliger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Carlos A Guerra
- Medical Care Development International, Malabo, Equatorial Guinea
| | - Wonder P Phiri
- Medical Care Development International, Malabo, Equatorial Guinea
| | | | | | - Marcel Tanner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland. .,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea.
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11
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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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12
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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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13
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Schlabe S, Reiter-Owona I, Nordmann T, Dolscheid-Pommerich R, Tannich E, Hoerauf A, Rockstroh J. Rapid diagnostic test negative Plasmodium falciparum malaria in a traveller returning from Ethiopia. Malar J 2021; 20:145. [PMID: 33712017 PMCID: PMC7952815 DOI: 10.1186/s12936-021-03678-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Background Plasmodium falciparum strains with mutations/deletions of the genes encoding the histidine-rich proteins 2/3 (pfhrp2/3) have emerged during the last 10 years leading to false-negative results in HRP2-based rapid diagnostic tests (RDTs). This can lead to unrecognized infections in individuals and to setbacks in malaria control in endemic countries where RDTs are the backbone of malaria diagnostics and control. Case description Here the detection of a pfhrp2/3-negative P. falciparum infection acquired in Ethiopia by a 63-year old female traveller is presented. After onset of symptoms during travel, she was first tested negative for malaria, most probably by RDT, at a local hospital in Harar, Ethiopia. Falciparum malaria was finally diagnosed microscopically upon her return to Germany, over 4 weeks after infection. At a parasite density of approximately 5387 parasites/µl, two different high-quality RDTs: Palutop + 4 OPTIMA, NADALRMalaria PF/pan Ag 4 Species, did not respond at their respective P. falciparum test lines. pfhrp2/3 deletion was confirmed by multiplex-PCR. The patient recovered after a complete course of atovaquone and proguanil. According to the travel route, malaria was acquired most likely in the Awash region, Central Ethiopia. This is the first case of imported P. falciparum with confirmed pfhrp2/3 deletion from Ethiopia. Conclusion HRP2-negative P. falciparum strains may not be recognized by the presently available HRP2-based RDTs. When malaria is suspected, confirmation by microscopy and/or qPCR is necessary in order to detect falciparum malaria, which requires immediate treatment. This case of imported P. falciparum, non-reactive to HRP2-based RDT, possibly underlines the necessity for standardized, nationwide investigations in Ethiopia and should alert clinicians from non-endemic countries to the possibility of false-negative RDT results which may increase in returning travellers with potentially life-threatening infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03678-2.
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Affiliation(s)
- Stefan Schlabe
- Department of Internal Medicine I, University Hospital of Bonn, Venusberg Campus 1, Building 26, 53127, Bonn, Germany. .,German Centre of Infection Research, Partner Site Bonn-Cologne, Bonn, Germany.
| | - Ingrid Reiter-Owona
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital of Bonn, Bonn, Germany
| | - Tamara Nordmann
- Department of Internal Medicine I, University Hospital of Bonn, Venusberg Campus 1, Building 26, 53127, Bonn, Germany.,National Reference Centre for Tropical Pathogens, Bernhard Nocht-Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Egbert Tannich
- National Reference Centre for Tropical Pathogens, Bernhard Nocht-Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital of Bonn, Bonn, Germany.,German Centre of Infection Research, Partner Site Bonn-Cologne, Bonn, Germany
| | - Jürgen Rockstroh
- Department of Internal Medicine I, University Hospital of Bonn, Venusberg Campus 1, Building 26, 53127, Bonn, Germany.,German Centre of Infection Research, Partner Site Bonn-Cologne, Bonn, Germany
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14
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Varo R, Balanza N, Mayor A, Bassat Q. Diagnosis of clinical malaria in endemic settings. Expert Rev Anti Infect Ther 2020; 19:79-92. [PMID: 32772759 DOI: 10.1080/14787210.2020.1807940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Malaria continues to be a major global health problem, with over 228 million cases and 405,000 deaths estimated to occur annually. Rapid and accurate diagnosis of malaria is essential to decrease the burden and impact of this disease, particularly in children. We aimed to review the main available techniques for the diagnosis of clinical malaria in endemic settings and explore possible future options to improve its rapid recognition. AREAS COVERED literature relevant to malaria diagnosis was identified through electronic searches in Pubmed, with no language or date restrictions and limited to humans. EXPERT OPINION Light microscopy is still considered the gold standard method for malaria diagnosis and continues to be at the frontline of malaria diagnosis. However, technologies as rapid diagnostic tests, mainly those who detect histidine-rich protein-2, offer an accurate, rapid and affordable alternative for malaria diagnosis in endemic areas. They are now the technique most extended in endemic areas for parasitological confirmation. In these settings, PCR-based assays are usually restricted to research and they are not currently helpful in the management of clinical malaria. Other technologies, such as isothermal methods could be an interesting and alternative approach to PCR in the future.
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Affiliation(s)
- Rosauro Varo
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Núria Balanza
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique.,ICREA, Pg. Lluís Companys 23 , Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan De Deu (University of Barcelona) , Barcelona, Spain.,Consorcio De Investigación Biomédica En Red De Epidemiología Y Salud Publica (CIBERESP) , Madrid, Spain
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15
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Kobayashi T. Uncovering hidden pfhrp2/3 deletion Plasmodium falciparum. EBioMedicine 2020; 56:102781. [PMID: 32516741 PMCID: PMC7281805 DOI: 10.1016/j.ebiom.2020.102781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/27/2022] Open
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16
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Grignard L, Nolder D, Sepúlveda N, Berhane A, Mihreteab S, Kaaya R, Phelan J, Moser K, van Schalkwyk DA, Campino S, Parr JB, Juliano JJ, Chiodini P, Cunningham J, Sutherland CJ, Drakeley C, Beshir KB. A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections. EBioMedicine 2020; 55:102757. [PMID: 32403083 PMCID: PMC7218259 DOI: 10.1016/j.ebiom.2020.102757] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/13/2020] [Accepted: 03/30/2020] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Many health facilities in malaria endemic countries are dependent on Rapid diagnostic tests (RDTs) for diagnosis and some National Health Service (NHS) hospitals without expert microscopists rely on them for diagnosis out of hours. The emergence of P. falciparum lacking the gene encoding histidine-rich protein 2 and 3 (HRP2 and HRP3) and escaping RDT detection threatens progress in malaria control and elimination. Currently, confirmation of RDT negative due to the deletion of pfhrp2 and pfhrp3, which encodes a cross-reactive protein isoform, requires a series of PCR assays. These tests have different limits of detection and many laboratories have reported difficulty in confirming the absence of the deletions with certainty. METHODS We developed and validated a novel and rapid multiplex real time quantitative (qPCR) assay to detect pfhrp2, pfhrp3, confirmatory parasite and human reference genes simultaneously. We also applied the assay to detect pfhrp2 and pfhrp3 deletion in 462 field samples from different endemic countries and UK travellers. RESULTS The qPCR assay demonstrated diagnostic sensitivity of 100% (n = 19, 95% CI= (82.3%; 100%)) and diagnostic specificity of 100% (n = 31; 95% CI= (88.8%; 100%)) in detecting pfhrp2 and pfhrp3 deletions. In addition, the assay estimates P. falciparum parasite density and accurately detects pfhrp2 and pfhrp3 deletions masked in polyclonal infections. We report pfhrp2 and pfhrp3 deletions in parasite isolates from Kenya, Tanzania and in UK travellers. INTERPRETATION The new qPCR is easily scalable to routine surveillance studies in countries where P. falciparum parasites lacking pfhrp2 and pfhrp3 are a threat to malaria control.
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Affiliation(s)
- Lynn Grignard
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Debbie Nolder
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Nuno Sepúlveda
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; Centre of Statistics and Applications of University of Lisbon, Portugal
| | - Araia Berhane
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Selam Mihreteab
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Robert Kaaya
- Kilimanjaro Christian Medical University College, Tanzania
| | - Jody Phelan
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Kara Moser
- University of North Carolina at Chapel Hill, United States
| | - Donelly A van Schalkwyk
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Susana Campino
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | | | | | - Peter Chiodini
- PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom; UCL Hospital for Tropical Diseases, United Kingdom
| | | | - Colin J Sutherland
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Chris Drakeley
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom.
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17
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Mayor A, Bassat Q. "Resistance" to diagnostics: A serious biological challenge for malaria control and elimination. EBioMedicine 2019; 50:9-10. [PMID: 31812497 PMCID: PMC6921289 DOI: 10.1016/j.ebiom.2019.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/30/2022] Open
Affiliation(s)
- Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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18
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Kreidenweiss A, Trauner F, Rodi M, Koehne E, Held J, Wyndorps L, Manouana GP, McCall M, Adegnika AA, Lalremruata A, Kremsner PG, Fendel R, Sandri TL. Monitoring the threatened utility of malaria rapid diagnostic tests by novel high-throughput detection of Plasmodium falciparum hrp2 and hrp3 deletions: A cross-sectional, diagnostic accuracy study. EBioMedicine 2019; 50:14-22. [PMID: 31761619 PMCID: PMC6921222 DOI: 10.1016/j.ebiom.2019.10.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 11/03/2022] Open
Abstract
Background Plasmodium falciparum deficient for hrp2 and hrp3 genes are a threat to malaria management and elimination, since they escape widely used HRP2-based rapid diagnostic tests and treatment. Hrp2/hrp3 deletions are increasingly reported from all malaria endemic regions but are currently only identified by laborious methodologies. Methods We developed a novel hydrolysis probe-based, quantitative, real-time PCR (4plex qPCR) for detection and discrimination of P. falciparum infection (cytb) and hrp2 and hrp3 gene status, and to control assay validity (btub). A cross-sectional, diagnostic accuracy study was performed in Gabon for assay validation and deletion screening. Findings In parallel to identification of P. falciparum infection in samples down to 0.05 parasites/µl, the 4plex qPCR enabled specific and valid interrogation of the parasites´s hrp2 and hrp3 genes in one go - even in low parasitemic samples. The assay was precise and robust also when performed in a routine healthcare setting in Gabon. The risk of falsely identifying hrp2 or hrp3 deletion was reduced by 100-fold compared to conventional PCR. Evaluation against microscopy was performed on 200 blood samples collected in Gabon: sensitivity and specificity of 4plex qPCR (cytb) were 100% and 80%, respectively. Stringent testing revealed hrp2 deletion in 2 of 95 P. falciparum positive and validated samples. Interpretation The novel 4plex qPCR is sensitive, accurate and allows resource-efficient rapid screening. Monitoring and mapping of hrp2/hrp3 deletions is required to identify areas where control strategies may need to be adapted to ensure appropriate patient care and ultimately achieve malaria elimination. Funding BMBF (03VP00402).
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Affiliation(s)
- Andrea Kreidenweiss
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, B.P. 242, Lambaréné, Gabon.
| | - Franziska Trauner
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | - Miriam Rodi
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | - Erik Koehne
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, B.P. 242, Lambaréné, Gabon
| | - Lea Wyndorps
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | | | - Matthew McCall
- Centre de Recherches Médicales de Lambaréné, B.P. 242, Lambaréné, Gabon
| | - Ayola Akim Adegnika
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, B.P. 242, Lambaréné, Gabon; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Albert Lalremruata
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, B.P. 242, Lambaréné, Gabon; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany
| | - Thaisa Lucas Sandri
- Institute of Tropical Medicine, University Hospital Tübingen, Wilhelmstrasse 27, D-72074 Tübingen, Germany.
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