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Molina-de la Fuente I, Pacheco MA, García L, González V, Riloha M, Oki C, Benito A, Escalante AA, Berzosa P. Evolution of pfhrp2 and pfhrp3 deletions in Equatorial Guinea between the pre- and post-RDT introduction. Malar J 2024; 23:215. [PMID: 39026276 PMCID: PMC11264669 DOI: 10.1186/s12936-024-05036-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Pfhrp2 and pfhrp3 deletions are threatening Plasmodium falciparum malaria diagnosis by rapid diagnostic tests (RDT) due to false negatives. This study assesses the changes in the frequencies of pfhrp2 and pfhrp3 deletions (pfhrp2Del and pfhrp3Del, respectively) and the genes in their flaking regions, before and after RDT introduction in Equatorial Guinea. METHODS A total of 566 P. falciparum samples were genotyped to assess the presence of pfhrp2 and pfhrp3 deletions and their flanking genes. The specimens were collected 18 years apart from two provinces of Equatorial Guinea, North Bioko (Insular Region) and Litoral Province (Continental Region). Orthologs of pfhrp2 and pfhrp3 genes from other closely related species were used to compare sequencing data to assess pfhrp2 and pfhrp3 evolution. Additionally, population structure was studied using seven neutral microsatellites. RESULTS This study found that pfhrp2Del and pfhrp3Del were present before the introduction of RDT; however, they increased in frequency after their use, reaching more than 15%. Haplotype networks suggested that pfhrp2Del and pfhrp3Del emerged multiple times. Exon 2 of pfhrp2 and pfhrp3 genes had high variability, but there were no significant changes in amino acid sequences. CONCLUSIONS Baseline sampling before deploying interventions provides a valuable context to interpret changes in genetic markers linked to their efficacy, such as the dynamic of deletions affecting RDT efficacy.
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Affiliation(s)
- Irene Molina-de la Fuente
- Biomedicine and biotechnology Department, University of Alcalá, Ctra.Madrid-Barcelona Km.33,600, 28871, Alcalá de Henares, Spain.
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Luz García
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Vicenta González
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Matilde Riloha
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Consuelo Oki
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Agustín Benito
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Pedro Berzosa
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. PLoS Pathog 2024; 20:e1012013. [PMID: 38870266 PMCID: PMC11206942 DOI: 10.1371/journal.ppat.1012013] [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: 02/01/2024] [Revised: 06/26/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. In low transmission settings, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. We performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n = 1,409) through estimation of identity-by-descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 multi-isolate clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally observed 61 nonsynonymous substitutions that increased markedly in frequency over the study period as well as a novel pfk13 mutation (G718S). However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions, given that clones carrying drug resistance polymorphisms do not demonstrate enhanced persistence or higher abundance than clones carrying polymorphisms of comparable frequency that are unrelated to resistance. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Angela M. Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret Laws
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O. Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lise Musset
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Daniel E. Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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3
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578156. [PMID: 38352461 PMCID: PMC10862847 DOI: 10.1101/2024.01.31.578156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Laws
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lise Musset
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Abdi Moussa R, Papa Mze N, Yonis Arreh H, Abdillahi Hamoud A, Mohamed Alaleh K, Mohamed Aden F, Yonis Omar AR, Osman Abdi W, Kayad Guelleh S, Ahmed Abdi AI, Basco LK, Abdi Khaireh B, Bogreau H. Assessment of the Performance of Lactate Dehydrogenase-Based Rapid Diagnostic Test for Malaria in Djibouti in 2022-2023. Diagnostics (Basel) 2024; 14:262. [PMID: 38337778 PMCID: PMC10854848 DOI: 10.3390/diagnostics14030262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Until 2020, Djiboutian health authorities relied on histidine-rich protein-2 (HRP2)-based rapid diagnostic tests (RDTs) to establish the diagnosis of Plasmodium falciparum. The rapid spread of P. falciparum histidine-rich protein-2 and -3 (pfhrp2/3) gene-deleted parasite strains in Djibouti has led the authorities to switch from HRP2-based RDTs to lactate dehydrogenase (LDH)-based RDTs targeting the plasmodial lactate dehydrogenase (pLDH) specific for P. falciparum and P. vivax (RapiGEN BIOCREDIT Malaria Ag Pf/Pv pLDH/pLDH) in 2021. This study was conducted with the primary objective of evaluating the diagnostic performance of this alternative RDT. Operational constraints related, in particular, to the implementation of this RDT during the COVID-19 pandemic were also considered. The performance of BIOCREDIT Malaria Ag Pf/Pv (pLDH/pLDH) RDT was also compared to our previously published data on the performance of two HRP2-based RDTs deployed in Djibouti in 2018-2020. The diagnosis of 350 febrile patients with suspected malaria in Djibouti city was established using two batches of RapiGEN BIOCREDIT Malaria Ag Pf/Pv (pLDH/pLDH) RDT over a two-year period (2022 and 2023) and confirmed by real-time quantitative polymerase chain reaction. The sensitivity and specificity for the detection of P. falciparum were 88.2% and 100%, respectively. For P. vivax, the sensitivity was 86.7% and the specificity was 100%. Re-training and closer supervision of the technicians between 2022 and 2023 have led to an increased sensitivity to detect P. falciparum (69.8% in 2022 versus 88.2% in 2023; p < 0.01). The receiver operating characteristic curve analysis highlighted a better performance in the diagnosis of P. falciparum with pLDH-based RDTs compared with previous HRP2-based RDTs. In Djibouti, where pfhrp2-deleted strains are rapidly gaining ground, LDH-based RDTs seem to be more suitable for diagnosing P. falciparum than HRP2-based RDTs. Awareness-raising and training for technical staff have also been beneficial.
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Affiliation(s)
- Rahma Abdi Moussa
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France (L.K.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nasserdine Papa Mze
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France (L.K.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Houssein Yonis Arreh
- Laboratoire National de Référence, Hôpital Peltier, Ministère de la Santé, Djibouti ville 98230, Djibouti
| | | | - Kahiya Mohamed Alaleh
- Caisse Nationale de Sécurité Sociale (CNSS), Djibouti ville 98230, Djibouti (K.M.A.)
| | - Fatouma Mohamed Aden
- Caisse Nationale de Sécurité Sociale (CNSS), Djibouti ville 98230, Djibouti (K.M.A.)
| | - Abdoul-Razak Yonis Omar
- Laboratoire de Diagnostic, Centre de Santé Communautaire d’Einguela, Ministère de la Santé, Djibouti ville 98230, Djibouti
| | - Warsama Osman Abdi
- Caisse Nationale de Sécurité Sociale (CNSS), Djibouti ville 98230, Djibouti (K.M.A.)
| | - Samatar Kayad Guelleh
- Programme National de Lutte Contre le Paludisme, Ministère de la Santé, Djibouti ville 98230, Djibouti;
| | - Abdoul-Ilah Ahmed Abdi
- Service de Santé des Armées, Présidence de la République, Djibouti ville 98230, Djibouti;
| | - Leonardo K. Basco
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France (L.K.B.)
| | - Bouh Abdi Khaireh
- UNDP Djibouti, Global Fund to Fight AIDS-TB-Malaria, Djibouti ville 98230, Djibouti;
| | - Hervé Bogreau
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France (L.K.B.)
- IHU-Méditerranée Infection, 13005 Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
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Watson OJ, Tran TNA, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.21.23297352. [PMID: 37905102 PMCID: PMC10615018 DOI: 10.1101/2023.10.21.23297352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the thirteen years since the first report of pfhrp2-deleted parasites in 2010, the World Health Organization (WHO) has found that 40 of 47 countries surveyed worldwide have reported pfhrp2/3 gene deletions. Due to a high prevalence of pfhrp2/3 deletions causing false-negative HRP2 RDTs, in the last five years, Eritrea, Djibouti and Ethiopia have switched or started switching to using alternative RDTs, that target pan-specific-pLDH or P. falciparum specific-pLDH alone of in combination with HRP2. However, manufacturing of alternative RDTs has not been brought to scale and there are no WHO prequalified combination tests that use Pf-pLDH instead of HRP2 for P. falciparum detection. For these reasons, the continued spread of pfhrp2/3 deletions represents a growing public health crisis that threatens efforts to control and eliminate P. falciparum malaria. National malaria control programmes, their implementing partners and test developers desperately seek pfhrp2/3 deletion data that can inform their immediate and future resource allocation. In response, we use a mathematical modelling approach to evaluate the global risk posed by pfhrp2/3 deletions and explore scenarios for how deletions will continue to spread in Africa. We incorporate current best estimates of the prevalence of pfhrp2/3 deletions and conduct a literature review to estimate model parameters known to impact the selection of pfhrp2/3 deletions for each malaria endemic country. We identify 20 countries worldwide to prioritise for surveillance and future deployment of alternative RDT, based on quickly selecting for pfhrp2/3 deletions once established. In scenarios designed to explore the continued spread of deletions in Africa, we identify 10 high threat countries that are most at risk of deletions both spreading to and subsequently being rapidly selected for. If HRP2-based RDTs continue to be relied on for malaria case management, we predict that the major route for pfhrp2 deletions to spread is south out from the current hotspot in the Horn of Africa, moving through East Africa over the next 20 years. We explore the variation in modelled timelines through an extensive parameter sensitivity analysis and despite wide uncertainties, we identify three countries that have not yet switched RDTs (Senegal, Zambia and Kenya) that are robustly identified as high risk for pfhrp2/3 deletions. These results provide a refined and updated prediction model for the emergence of pfhrp2/3 deletions in an effort to help guide pfhrp2/3 policy and prioritise future surveillance efforts and innovation.
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Affiliation(s)
- Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert J Zupko
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tasmin Symons
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | | | | | - Susan Rumisha
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Paulina A Dzianach
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Isaac Kim
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | | | - Lucy Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Peter Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Australia
| | - Azra Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
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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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Sabin S, Jones S, Patel D, Subramaniam G, Kelley J, Aidoo M, Talundzic E. Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer. Sci Rep 2023; 13:2893. [PMID: 36801925 PMCID: PMC9938884 DOI: 10.1038/s41598-022-26935-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/22/2022] [Indexed: 02/20/2023] Open
Abstract
The prevalence of Plasmodium falciparum hrp2 (pfhrp2)-deleted parasites threatens the efficacy of the most used and sensitive malaria rapid diagnostic tests and highlights the need for continued surveillance for this gene deletion. While PCR methods are adequate for determining pfhrp2 presence or absence, they offer a limited view of its genetic diversity. Here, we present a portable sequencing method using the MinION. Pfhrp2 amplicons were generated from individual samples, barcoded, and pooled for sequencing. To overcome potential crosstalk between barcodes, we implemented a coverage-based threshold for pfhrp2 deletion confirmation. Amino acid repeat types were then counted and visualized with custom Python scripts following de novo assembly. We evaluated this assay using well-characterized reference strains and 152 field isolates with and without pfhrp2 deletions, of which 38 were also sequenced on the PacBio platform to provide a standard for comparison. Of 152 field samples, 93 surpassed the positivity threshold, and of those samples, 62/93 had a dominant pfhrp2 repeat type. PacBio-sequenced samples with a dominant repeat-type profile from the MinION sequencing data matched the PacBio profile. This field-deployable assay can be used alone for surveilling pfhrp2 diversity or as a sequencing-based addition to the World Health Organization's existing deletion surveillance protocol.
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Affiliation(s)
- Susanna Sabin
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA. .,Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Sophie Jones
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,Williams Consulting, Catonsville, MD USA
| | - Dhruviben Patel
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,Williams Consulting, Catonsville, MD USA
| | - Gireesh Subramaniam
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,grid.410547.30000 0001 1013 9784Oak Ridge Institute for Science and Education, Oak Ridge, TN USA
| | - Julia Kelley
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Michael Aidoo
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Eldin Talundzic
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
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