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Mshani IH, Jackson FM, Mwanga RY, Kweyamba PA, Mwanga EP, Tambwe MM, Hofer LM, Siria DJ, González-Jiménez M, Wynne K, Moore SJ, Okumu F, Babayan SA, Baldini F. Screening of malaria infections in human blood samples with varying parasite densities and anaemic conditions using AI-Powered mid-infrared spectroscopy. Malar J 2024; 23:188. [PMID: 38880870 PMCID: PMC11181574 DOI: 10.1186/s12936-024-05011-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND Effective testing for malaria, including the detection of infections at very low densities, is vital for the successful elimination of the disease. Unfortunately, existing methods are either inexpensive but poorly sensitive or sensitive but costly. Recent studies have shown that mid-infrared spectroscopy coupled with machine learning (MIRs-ML) has potential for rapidly detecting malaria infections but requires further evaluation on diverse samples representative of natural infections in endemic areas. The aim of this study was, therefore, to demonstrate a simple AI-powered, reagent-free, and user-friendly approach that uses mid-infrared spectra from dried blood spots to accurately detect malaria infections across varying parasite densities and anaemic conditions. METHODS Plasmodium falciparum strains NF54 and FCR3 were cultured and mixed with blood from 70 malaria-free individuals to create various malaria parasitaemia and anaemic conditions. Blood dilutions produced three haematocrit ratios (50%, 25%, 12.5%) and five parasitaemia levels (6%, 0.1%, 0.002%, 0.00003%, 0%). Dried blood spots were prepared on Whatman™ filter papers and scanned using attenuated total reflection-Fourier Transform Infrared (ATR-FTIR) for machine-learning analysis. Three classifiers were trained on an 80%/20% split of 4655 spectra: (I) high contrast (6% parasitaemia vs. negative), (II) low contrast (0.00003% vs. negative) and (III) all concentrations (all positive levels vs. negative). The classifiers were validated with unseen datasets to detect malaria at various parasitaemia levels and anaemic conditions. Additionally, these classifiers were tested on samples from a population survey in malaria-endemic villages of southeastern Tanzania. RESULTS The AI classifiers attained over 90% accuracy in detecting malaria infections as low as one parasite per microlitre of blood, a sensitivity unattainable by conventional RDTs and microscopy. These laboratory-developed classifiers seamlessly transitioned to field applicability, achieving over 80% accuracy in predicting natural P. falciparum infections in blood samples collected during the field survey. Crucially, the performance remained unaffected by various levels of anaemia, a common complication in malaria patients. CONCLUSION These findings suggest that the AI-driven mid-infrared spectroscopy approach holds promise as a simplified, sensitive and cost-effective method for malaria screening, consistently performing well despite variations in parasite densities and anaemic conditions. The technique simply involves scanning dried blood spots with a desktop mid-infrared scanner and analysing the spectra using pre-trained AI classifiers, making it readily adaptable to field conditions in low-resource settings. In this study, the approach was successfully adapted to field use, effectively predicting natural malaria infections in blood samples from a population-level survey in Tanzania. With additional field trials and validation, this technique could significantly enhance malaria surveillance and contribute to accelerating malaria elimination efforts.
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Affiliation(s)
- Issa H Mshani
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK.
| | - Frank M Jackson
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
| | - Rehema Y Mwanga
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
| | - Prisca A Kweyamba
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | - Emmanuel P Mwanga
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
| | - Mgeni M Tambwe
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
| | - Lorenz M Hofer
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | - Doreen J Siria
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
| | - Mario González-Jiménez
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
- School of Chemistry, The University of Glasgow, Glasgow, G128QQ, UK
| | - Klaas Wynne
- School of Chemistry, The University of Glasgow, Glasgow, G128QQ, UK
| | - Sarah J Moore
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- School of Life Sciences and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania
| | - Fredros Okumu
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
- School of Life Sciences and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania
- School of Public Health, The University of the Witwatersrand, Park Town, Johannesburg, South Africa
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
| | - Francesco Baldini
- Environmental Health, and Ecological Sciences Department, Ifakara Health Institute, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, The University of Glasgow, Glasgow, UK
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Ngasala B, Chacky F, Mohamed A, Molteni F, Nyinondi S, Kabula B, Mkali H, Thwai K, Popkin-Hall ZR, Mitchell C, Parr JB, Juliano JJ, Lin JT. Evaluation of Malaria Rapid Diagnostic Test Performance and pfhrp2 Deletion in Tanzania School Surveys, 2017. Am J Trop Med Hyg 2024; 110:887-891. [PMID: 38507797 PMCID: PMC11066367 DOI: 10.4269/ajtmh.23-0771] [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: 11/06/2023] [Accepted: 01/02/2024] [Indexed: 03/22/2024] Open
Abstract
As part of malaria nationwide monitoring and evaluation initiatives, there is an increasing trend of incorporating malaria rapid diagnostic tests (mRDTs) in surveys conducted within primary schools to detect malaria parasites. However, mRDTs based on the detection of histidine-rich protein 2 (HRP2) are known to yield false-positive results due to persistent antigenemia, and false-negative results may result from low parasitemia or Plasmodium falciparum hrp2/3 gene deletion. We evaluated diagnostic performance of an HRP2 and pan-parasite lactate dehydrogenase (HRP2/pLDH) mRDT against polymerase chain reaction (PCR) for detection of P. falciparum among 17,051 primary school-age children from eight regions of Tanzania in 2017. According to PCR, the prevalence of P. falciparum was 19.2% (95% CI: 18.6-19.8). Using PCR as reference, the sensitivity and specificity of mRDT was 76.2% (95% CI: 74.7-77.7) and 93.9% (95% CI: 93.5-94.3), respectively. Test agreement was lowest in low transmission areas, where true-positive mRDTs were outnumbered by false-negatives due to low parasitemia. Discordant samples (mRDT-negative but PCR-positive) were screened for pfhrp2/3 deletion by real-time PCR. Among those with a parasite density sufficient for analysis, pfhrp2 deletion was confirmed in 60 samples, whereas pfhrp3 deletion was confirmed in two samples; one sample had both pfhrp2 and pfhrp3 deletions. The majority of samples with gene deletions were detected in the high-transmission Kagera region. Compared with mRDTs, PCR and other molecular methods offer increased sensitivity and are not affected by pfhrp2/3 deletions, making them a useful supplement to mRDTs in schools and other epidemiological surveys.
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Affiliation(s)
- Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | | | - Kyaw Thwai
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Zachary R. Popkin-Hall
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Cedar Mitchell
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan B. Parr
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan J. Juliano
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Jessica T. Lin
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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3
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Rogier E, Battle N, Bakari C, Seth MD, Nace D, Herman C, Barakoti A, Madebe RA, Mandara CI, Lyimo BM, Giesbrecht DJ, Popkin-Hall ZR, Francis F, Mbwambo D, Garimo I, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey JA, Udhayakumar V, Ishengoma DS. Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021. Sci Rep 2024; 14:8158. [PMID: 38589477 PMCID: PMC11001933 DOI: 10.1038/s41598-024-58455-3] [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: 10/26/2023] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
Plasmodium falciparum with the histidine rich protein 2 gene (pfhrp2) deleted from its genome can escape diagnosis by HRP2-based rapid diagnostic tests (HRP2-RDTs). The World Health Organization (WHO) recommends switching to a non-HRP2 RDT for P. falciparum clinical case diagnosis when pfhrp2 deletion prevalence causes ≥ 5% of RDTs to return false negative results. Tanzania is a country of heterogenous P. falciparum transmission, with some regions approaching elimination and others at varying levels of control. In concordance with the current recommended WHO pfhrp2 deletion surveillance strategy, 100 health facilities encompassing 10 regions of Tanzania enrolled malaria-suspected patients between February and July 2021. Of 7863 persons of all ages enrolled and providing RDT result and blood sample, 3777 (48.0%) were positive by the national RDT testing for Plasmodium lactate dehydrogenase (pLDH) and/or HRP2. A second RDT testing specifically for the P. falciparum LDH (Pf-pLDH) antigen found 95 persons (2.5% of all RDT positives) were positive, though negative by the national RDT for HRP2, and were selected for pfhrp2 and pfhrp3 (pfhrp2/3) genotyping. Multiplex antigen detection by laboratory bead assay found 135/7847 (1.7%) of all blood samples positive for Plasmodium antigens but very low or no HRP2, and these were selected for genotyping as well. Of the samples selected for genotyping based on RDT or laboratory multiplex result, 158 were P. falciparum DNA positive, and 140 had sufficient DNA to be genotyped for pfhrp2/3. Most of these (125/140) were found to be pfhrp2+/pfhrp3+, with smaller numbers deleted for only pfhrp2 (n = 9) or only pfhrp3 (n = 6). No dual pfhrp2/3 deleted parasites were observed. This survey found that parasites with these gene deletions are rare in Tanzania, and estimated that 0.24% (95% confidence interval: 0.08% to 0.39%) of false-negative HRP2-RDTs for symptomatic persons were due to pfhrp2 deletions in this 2021 Tanzania survey. These data provide evidence for HRP2-based diagnostics as currently accurate for P. falciparum diagnosis in Tanzania.
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Affiliation(s)
- Eric Rogier
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Catherine Bakari
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Misago D Seth
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Douglas Nace
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Camelia Herman
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Achut Barakoti
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
- CDC Foundation, Atlanta, GA, USA
| | - Rashid A Madebe
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Beatus M Lyimo
- National Institute for Medical Research, Dar Es Salaam, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | | | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar Es Salaam, Tanzania
| | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Deus S Ishengoma
- National Institute for Medical Research, Dar Es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H Chan School of Public Health, Boston, MA, USA.
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Nana RRD, Ngum NL, Makoge V, Amvongo-Adja N, Hawadak J, Singh V. Rapid diagnostic tests for malaria diagnosis in Cameroon: impact of histidine rich protein 2/3 deletions and lactate dehydrogenase gene polymorphism. Diagn Microbiol Infect Dis 2024; 108:116103. [PMID: 37944271 DOI: 10.1016/j.diagmicrobio.2023.116103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
Malaria rapid diagnostic tests (mRDT) play a vital role in malaria control in endemic areas. In this study, histidine-rich protein (hrp) and lactate dehydrogenase (ldh) genes were genotyped in Plasmodium falciparum (Pf) and Plasmodium ovale (Po) spp. isolates. Deletions in P. falciparum hrp2/3 (pfhrp2/3) proteins and single nucleotide polymorphisms (SNPs) were analyzed. Twenty-four samples were analyzed for pfhrp2/3 gene deletions and 25 for SNPs in ldh gene (18 Pf and 7 Po spp.). Deletions in pfhrp2/3 genes were observed in 1.9% malaria positive isolates. The pfldh gene sequences showed one SNP at codon 272 (D272N) in 22.2% of samples while in Po spp., sequences were 100% similar to P. ovale curtisi but when compared to P. ovale wallikeri reference sequence, SNPs at positions 143 (P143S), 168 (K168N), 204 (V204I) were found. Findings suggest low prevalence in pfhrp2/3 genes and highlight the circulation of P. ovale curtisi in the studies areas.
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Affiliation(s)
- Rodrigue Roman Dongang Nana
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon; Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India..
| | - Ngum Lesly Ngum
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Valerie Makoge
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Nathalie Amvongo-Adja
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Joseph Hawadak
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India
| | - Vineeta Singh
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India..
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5
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Febrer-Sendra B, Crego-Vicente B, Nindia A, Martínez-Campreciós J, Aixut S, Mediavilla A, Silgado A, Oliveira-Souto I, Salvador F, Molina I, Muro A, Sulleiro E, Fernández-Soto P. First field and laboratory evaluation of LAMP assay for malaria diagnosis in Cubal, Angola. Parasit Vectors 2023; 16:343. [PMID: 37789462 PMCID: PMC10548721 DOI: 10.1186/s13071-023-05942-7] [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: 05/31/2023] [Accepted: 08/22/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Malaria is a globally distributed infectious disease. According to the World Health Organization, Angola is one of the six countries that account for over half the global malaria burden in terms of both malaria cases and deaths. Diagnosis of malaria still depends on microscopic examination of thin and thick blood smears and rapid diagnostic tests (RDTs), which often lack analytical and clinical sensitivity. Molecular methods could overcome these disadvantages. The aim of this study was to evaluate, for the first time to our knowledge, the performance of a loop-mediated isothermal amplification (LAMP) for the diagnosis of malaria in an endemic area in Cubal, Angola, and to assess the reproducibility at a reference laboratory. METHODS A total of 200 blood samples from patients attended at Hospital Nossa Senhora da Paz, Cubal, Angola, were analysed for Plasmodium spp. detection by microscopy, RDTs, and LAMP. LAMP assay was easily performed in a portable heating block, and the results were visualized by a simple colour change. Subsequently, the samples were sent to a reference laboratory in Spain to be reanalysed by the same colorimetric LAMP assay and also in real-time LAMP format. RESULTS In field tests, a total of 67/200 (33.5%) blood samples were microscopy-positive for Plasmodium spp., 98/200 RDT positive, and 112/200 (56%) LAMP positive. Using microscopy as reference standard, field LAMP detected more microscopy-positive samples than RDTs (66/67; 98% vs. 62/67; 92.5%). When samples were reanalysed at a reference laboratory in Spain using both colorimetric and real-time assays, the overall reproducibility achieved 84.5%. CONCLUSIONS This is the first study to our knowledge in which LAMP has been clinically evaluated on blood samples in a resource-poor malaria-endemic area. The colorimetric LAMP proved to be more sensitive than microscopy and RDTs for malaria diagnosis in field conditions. Furthermore, LAMP showed an acceptable level of reproducibility in a reference laboratory. The possibility to use LAMP in a real-time format in a portable device reinforces the reliability of the assay for molecular diagnosis of malaria in resource-poor laboratories in endemic areas.
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Affiliation(s)
- Begoña Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Beatriz Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | | | - Joan Martínez-Campreciós
- Hospital Nossa Senhora da Paz, Cubal, Angola
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Alejandro Mediavilla
- Microbiology Department Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Aroa Silgado
- Microbiology Department Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Inés Oliveira-Souto
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- International Health Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Fernando Salvador
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- International Health Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Israel Molina
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- International Health Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Elena Sulleiro
- Microbiology Department Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain.
- International Health Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain.
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain.
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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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7
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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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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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Genetic Sequence Variation in the Plasmodium falciparum Histidine-Rich Protein 2 Gene from Field Isolates in Tanzania: Impact on Malaria Rapid Diagnosis. Genes (Basel) 2022; 13:genes13091642. [PMID: 36140809 PMCID: PMC9498557 DOI: 10.3390/genes13091642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
Malaria rapid diagnosis test (RDT) is crucial for managing the disease, and the effectiveness of detection depends on parameters such as sensitivity and specificity of the RDT. Several factors can affect the performance of RDT. In this study, we focused on the pfhrp2 sequence variation and its impact on RDTs targeted by antigens encoded by Plasmodium falciparum histidine-rich protein 2 (pfhrp2). Field samples collected during cross-sectional surveys in Tanzania were sequenced to investigate the pfhrp2 sequence diversity and evaluate the impact on HRP2-based RDT performance. We observed significant mean differences in amino acid repeats between current and previous studies. Several new amino acid repeats were found to occur at different frequencies, including types AAY, AHHAHHAAN, and AHHAA. Based on the abundance of types 2 and 7 amino acid repeats, the binary predictive model was able to predict RDT insensitivity by about 69% in the study area. About 85% of the major epitopes targeted by monoclonal antibodies (MAbs) in RDT were identified. Our study suggested that the extensive sequence variation in pfhrp2 can contribute to reduced RDT sensitivity. The correlation between the different combinations of amino acid repeats and the performance of RDT in different malaria transmission settings should be investigated further.
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