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Molina-de la Fuente I, Yimar M, García L, González V, Amor A, Anegagrie M, Benito A, Martínez J, Moreno M, Berzosa P. Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia. Malar J 2022; 21:287. [PMID: 36209103 PMCID: PMC9548178 DOI: 10.1186/s12936-022-04306-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Although rapid diagnostic tests (RDTs) play a key role in malaria-control strategies, their efficacy has been threatened by deletion and genetic variability of the genes pfhrp2/3. This study aims to characterize the deletion, genetic patterns and diversity of these genes and their implication for malaria RDT effectiveness, as well as their genetic evolution in the Amhara region of Ethiopia. Methods The study included 354 isolates from symptomatic patients from the Amhara region of Ethiopia who tested positive by microscopy. Exon 1–2 and exon 2 of genes pfhrp2 and -3 were amplified, and exon 2 was sequenced to analyse the genetic diversity, phylogenetic relationship and epitope availability. Results The deletion frequency in exon 1–2 and exon 2 was 22 and 4.6% for pfhrp2, and 68 and 18% for pfhrp3, respectively. Double deletion frequency for pfhrp2 and pfhrp3 was 1.4%. High genetic diversity, lack of clustering by phylogenetic analysis and evidence of positive selection suggested a diversifying selection for both genes. The amino-acid sequences, classified into different haplotypes, varied widely in terms of frequency of repeats, with novel amino-acid changes. Aminoacidic repetition type 2 and type 7 were the most frequent in all the sequences. The most frequent epitopes among protein sequences were those recognized by MAbs 3A4 and C1-13. Conclusion Deletions and high amino acidic variation in pfhrp2 and pfhrp3 suggest their possible impact on RDT use in the Amhara region, and the high genetic diversity of these genes could be associated with a diversifying selection in Ethiopia. Surveillance of these genes is, therefore, essential to ensure the effectiveness of public health interventions in this region. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04306-3.
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Affiliation(s)
- Irene Molina-de la Fuente
- Department of Biomedicine and Biotechnology, School of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid, Spain. .,Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain. .,Public Health and Epidemiology Research Group, School of Medicine, University of Alcalá, Alcalá de Henares, Madrid, Spain.
| | - Mulat Yimar
- College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Luz García
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Vicenta González
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Arancha Amor
- Mundo Sano Foundations, Institute of Health Carlos III, Madrid, Spain
| | - Melaku Anegagrie
- Mundo Sano Foundations, Institute of Health Carlos III, Madrid, Spain
| | - Agustín Benito
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
| | - Javier Martínez
- Department of Biomedicine and Biotechnology, School of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Marta Moreno
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Pedro Berzosa
- Malaria and Neglected Diseases Laboratory, National Centre of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,CIBERINFECT - CIBER Infectious Diseases (ISCIII), Madrid, Spain
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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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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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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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