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Mwesigwa A, Ocan M, Musinguzi B, Nante RW, Nankabirwa JI, Kiwuwa SM, Kinengyere AA, Castelnuovo B, Karamagi C, Obuku EA, Nsobya SL, Mbulaiteye SM, Byakika-Kibwika P. Plasmodium falciparum genetic diversity and multiplicity of infection based on msp-1, msp-2, glurp and microsatellite genetic markers in sub-Saharan Africa: a systematic review and meta-analysis. Malar J 2024; 23:97. [PMID: 38589874 PMCID: PMC11000358 DOI: 10.1186/s12936-024-04925-y] [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: 12/12/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND In sub-Saharan Africa (SSA), Plasmodium falciparum causes most of the malaria cases. Despite its crucial roles in disease severity and drug resistance, comprehensive data on Plasmodium falciparum genetic diversity and multiplicity of infection (MOI) are sparse in SSA. This study summarizes available information on genetic diversity and MOI, focusing on key markers (msp-1, msp-2, glurp, and microsatellites). The systematic review aimed to evaluate their influence on malaria transmission dynamics and offer insights for enhancing malaria control measures in SSA. METHODS The review was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. Two reviewers conducted article screening, assessed the risk of bias (RoB), and performed data abstraction. Meta-analysis was performed using the random-effects model in STATA version 17. RESULTS The review included 52 articles: 39 cross-sectional studies and 13 Randomized Controlled Trial (RCT)/cohort studies, involving 11,640 genotyped parasite isolates from 23 SSA countries. The overall pooled mean expected heterozygosity was 0.65 (95% CI: 0.51-0.78). Regionally, values varied: East (0.58), Central (0.84), Southern (0.74), and West Africa (0.69). Overall pooled allele frequencies of msp-1 alleles K1, MAD20, and RO33 were 61%, 44%, and 40%, respectively, while msp-2 I/C 3D7 and FC27 alleles were 61% and 55%. Central Africa reported higher frequencies (K1: 74%, MAD20: 51%, RO33: 48%) than East Africa (K1: 46%, MAD20: 42%, RO33: 31%). For msp-2, East Africa had 60% and 55% for I/C 3D7 and FC27 alleles, while West Africa had 62% and 50%, respectively. The pooled allele frequency for glurp was 66%. The overall pooled mean MOI was 2.09 (95% CI: 1.88-2.30), with regional variations: East (2.05), Central (2.37), Southern (2.16), and West Africa (1.96). The overall prevalence of polyclonal Plasmodium falciparum infections was 63% (95% CI: 56-70), with regional prevalences as follows: East (62%), West (61%), Central (65%), and South Africa (71%). CONCLUSION The study shows substantial regional variation in Plasmodium falciparum parasite genetic diversity and MOI in SSA. These findings suggest a need for malaria control strategies and surveillance efforts considering regional-specific factors underlying Plasmodium falciparum infection.
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Affiliation(s)
- Alex Mwesigwa
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Medicine, Kabale University, P. O Box 314, Kabale, Uganda.
| | - Moses Ocan
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Benson Musinguzi
- Departent of Medical Laboratory Science, Faculty of Health Sciences, Muni University, P.O Box 725, Arua, Uganda
| | - Rachel Wangi Nante
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Joaniter I Nankabirwa
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Steven M Kiwuwa
- Department of Biochemistry, School of Biomedical Sciences, College of Health Sciences, Makerere, University, P.O. Box 7072, Kampala, Uganda
| | - Alison Annet Kinengyere
- Albert Cook Library, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Barbara Castelnuovo
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Charles Karamagi
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Ekwaro A Obuku
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel L Nsobya
- Infectious Diseases Research Collaboration, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr, 6E-118, Bethesda, MD, 20892, USA
| | - Pauline Byakika-Kibwika
- Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
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Reda AG, Huwe T, Koepfli C, Assefa A, Tessema SK, Messele A, Golassa L, Mamo H. Amplicon deep sequencing of five highly polymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate population structure in Ethiopia. Malar J 2023; 22:376. [PMID: 38087335 PMCID: PMC10714478 DOI: 10.1186/s12936-023-04814-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Plasmodium falciparum genetic diversity can add information on transmission intensity and can be used to track control and elimination interventions. METHODS Dried blood spots (DBS) were collected from patients who were recruited for a P. falciparum malaria therapeutic efficacy trial in three malaria endemic sites in Ethiopia from October to December 2015, and November to December 2019. qPCR-confirmed infections were subject to amplicon sequencing of polymorphic markers ama1-D3, csp, cpp, cpmp, msp7. Genetic diversity, the proportion of multiclonal infections, multiplicity of infection, and population structure were analysed. RESULTS Among 198 samples selected for sequencing, data was obtained for 181 samples. Mean MOI was 1.38 (95% CI 1.24-1.53) and 17% (31/181) of infections were polyclonal. Mean He across all markers was 0.730. Population structure was moderate; populations from Metema and Metehara 2015 were very similar to each other, but distinct from Wondogent 2015 and Metehara 2019. CONCLUSION The high level of parasite genetic diversity and moderate population structure in this study suggests frequent gene flow of parasites among sites. The results obtained can be used as a baseline for additional parasite genetic diversity and structure studies, aiding in the formulation of appropriate control strategies in Ethiopia.
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Affiliation(s)
- Abeba Gebretsadik Reda
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Tiffany Huwe
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA.
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Ashenafi Assefa
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
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Kojom Foko LP, Jakhan J, Narang G, Singh V. Global polymorphism of Plasmodium falciparum histidine rich proteins 2/3 and impact on malaria rapid diagnostic test detection: a systematic review and meta-analysis. Expert Rev Mol Diagn 2023; 23:925-943. [PMID: 37698448 DOI: 10.1080/14737159.2023.2255136] [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: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/10/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND This review presents an overview of field findings on sequence variation of Plasmodium falciparum histidine-rich proteins 2/3 (PfHRP2/3) for which reference types (1-24) have been identified, and its critical impact on PfHRP2-based rapid diagnostic test (RDT) detection. RESEARCH DESIGN AND METHODS This systematic review and meta-analysis was registered with PROSPERO, CRD42022316027, and conducted as per the PRISMA guidelines, and the methodological quality of studies was assessed. RESULTS Of the 2184 records identified, 34 studies were included mostly from Africa (47.1%) and Asia (35.3%). The reference PfHRP2 types 1, 2, 3, 6, and 7 are invariably found at proportions ≥ 80-100% in all areas with the exception of The Americas where their proportion is very low. The proteins exhibited high diversity of variants/unknown types, especially for types 1, 2, 4, and 7. Eleven major PfHRP2 epitopes were found at pooled proportion > 90%. The existing models to predict RDT detection are greatly limited by the impact of factors such as low (very low) parasitemia, RDT brand, and PfHRP3 cross-reactivity. PfHRP2 length and presence/number of a given reference repeat type/variant did not seem to impact RDT detection. CONCLUSIONS PfHRP2/3 are highly polymorphic and current findings are insufficient, conflicting and not convincing enough to conclude on the role of PfHRP2/3 sequence polymorphism in PfHRP2-based RDT detection.
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Affiliation(s)
- Loick P Kojom Foko
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Jahnvi Jakhan
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Geetika Narang
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Vineeta Singh
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
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Agaba BB, Rugera SP, Mpirirwe R, Atekat M, Okubal S, Masereka K, Erionu M, Adranya B, Nabirwa G, Odong PB, Mukiibi Y, Ssewanyana I, Nabadda S, Muwanguzi E. Asymptomatic malaria infection, associated factors and accuracy of diagnostic tests in a historically high transmission setting in Northern Uganda. Malar J 2022; 21:392. [PMID: 36550492 PMCID: PMC9783970 DOI: 10.1186/s12936-022-04421-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Asymptomatic malaria infections are important parasite reservoirs and could sustain transmission in the population, but they are often unreported. A community-based survey was conducted to investigate the prevalence and factors associated with asymptomatic malaria infections in a historically high transmission setting in northern Uganda. METHODS Using a cross-sectional design, 288 children aged 2-15 years were enrolled and tested for the presence of malaria parasites using rapid diagnostic tests (RDTs) and blood smear microscopy between January to May 2022. Statistical analysis was performed using the exact binomial and Fisher's exact test with p ≤ 0.05 indicating significance. The logistic regression was used to explore factors associated with asymptomatic malaria infections. RESULTS Overall, the prevalence of asymptomatic infection was 34.7% (95% CI 29.2-40.5) with the highest observed in children 5-10 years 45.9% (95% CI 35.0-57.0). Gweri village accounted for 39.1% (95% CI 27.6-51.6) of malaria infections. Median parasite density was 1500 parasites/µl of blood. Plasmodium falciparum was the dominant species (86%) followed by Plasmodium malariae (5%). Factors associated with asymptomatic malaria infection were sleeping under mosquito net (Adjusted Odds Ratio (aOR) 0.27; 95% CI 0.13-0.56), p = 0.001 and presence of village health teams (VHTs) (aOR 0.02; 95% CI 0.01-0.45), p = 0.001. Sensitivity and specificity were higher for the P. falciparum/pLDH RDTs compared to HRP2-only RDTs, 90% (95% CI 86.5-93.5) and 95.2% (95% CI 92.8-97.7), p = 0.001, respectively. CONCLUSION Asymptomatic malaria infections were present in the study population and this varied with place and person in the different age groups. Plasmodium falciparum was the dominant parasite species however the presence of P. malariae and Plasmodium ovale was observed, which may have implication for the choice and deployment of diagnostic tools. Individuals who slept under mosquito net or had presence of functional VHTs were less likely to have asymptomatic malaria infection. P.f/pLDH RDTs performed better than the routinely used HRP2 RDTs. In view of these findings, investigation and reporting of asymptomatic malaria reservoirs through community surveys is recommended for accurate disease burden estimate and better targeting of control.
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Affiliation(s)
- Bosco B. Agaba
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda ,grid.415705.2National Malaria Control Division, Ministry of Health, Kampala, Uganda ,National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda ,grid.463352.50000 0004 8340 3103Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Simon P. Rugera
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ruth Mpirirwe
- grid.11194.3c0000 0004 0620 0548Department of Statistics, Makerere University, Kampala, Uganda
| | - Martha Atekat
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Samuel Okubal
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Khalid Masereka
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Miseal Erionu
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Bosco Adranya
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Gertrude Nabirwa
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Patrick B. Odong
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Yasin Mukiibi
- Uganda Institute of Allied and Management Sciences, Kampala, Uganda
| | - Isaac Ssewanyana
- National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda ,grid.463352.50000 0004 8340 3103Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Susan Nabadda
- National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda
| | - Enoch Muwanguzi
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda ,Uganda Institute of Allied and Management Sciences, Kampala, Uganda
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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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Pinto A, Archaga O, Mejía Á, Escober L, Henríquez J, Montoya A, Valdivia HO, Fontecha G. Evidence of a Recent Bottleneck in Plasmodium falciparum Populations on the Honduran-Nicaraguan Border. Pathogens 2021; 10:pathogens10111432. [PMID: 34832588 PMCID: PMC8617645 DOI: 10.3390/pathogens10111432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 12/04/2022] Open
Abstract
The countries of Central America and the island of Hispaniola have set the goal of eliminating malaria in less than a decade. Although efforts to reduce the malaria burden in the region have been successful, there has been an alarming increase in cases in the Nicaraguan Moskitia since 2014. The continuous decrease in cases between 2000 and 2014, followed by a rapid expansion from 2015 to the present, has generated a potential bottleneck effect in the populations of Plasmodium spp. Consequently, this study aimed to evaluate the genetic diversity of P. falciparum and the decrease in allelic richness in this population. The polymorphic regions of the pfmsp-1 and pfmsp-2 genes of patients with falciparum malaria from Honduras and Nicaragua were analyzed using nested PCR and sequencing. Most of the samples were classified into the K1 allelic subfamily of the pfmsp-1 gene and into the 3D7 subfamily of the pfmsp-2 gene. Despite the low genetic diversity found, more than half of the samples presented a polyclonal K1/RO33 haplotype. No sequence polymorphisms were found within each allelic subfamily. This study describes a notable decrease in the genetic diversity of P. falciparum in the Moskitia region after a bottleneck phenomenon. These results will be useful for future epidemiological investigations and the monitoring of malaria transmission in Central America.
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Affiliation(s)
- Alejandra Pinto
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Osman Archaga
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Ángel Mejía
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Lenin Escober
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa 11101, Honduras; (L.E.); (J.H.)
| | - Jessica Henríquez
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa 11101, Honduras; (L.E.); (J.H.)
| | - Alberto Montoya
- National Center for Diagnosis and Reference, Health Ministry, Managua 11001, Nicaragua;
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima 07006, Peru;
| | - Gustavo Fontecha
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
- Correspondence: ; Tel.: +504-33935443
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