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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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Andika B, Mobegi V, Gathii K, Nyataya J, Maina N, Awinda G, Mutai B, Waitumbi J. Plasmodium falciparum population structure inferred by msp1 amplicon sequencing of parasites collected from febrile patients in Kenya. Malar J 2023; 22:263. [PMID: 37689681 PMCID: PMC10492417 DOI: 10.1186/s12936-023-04700-5] [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: 06/16/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Multiplicity of infection (MOI) is an important measure of Plasmodium falciparum diversity, usually derived from the highly polymorphic genes, such as msp1, msp2 and glurp as well as microsatellites. Conventional methods of deriving MOI lack fine resolution needed to discriminate minor clones. This study used amplicon sequencing (AmpliSeq) of P. falciparum msp1 (Pfmsp1) to measure spatial and temporal genetic diversity of P. falciparum. METHODS 264 P. falciparum positive blood samples collected from areas of differing malaria endemicities between 2010 and 2019 were used. Pfmsp1 gene was amplified and amplicon libraries sequenced on Illumina MiSeq. Sequences were aligned against a reference sequence (NC_004330.2) and clustered to detect fragment length polymorphism and amino acid variations. RESULTS Children < 5 years had higher parasitaemia (median = 23.5 ± 5 SD, p = 0.03) than the > 5-14 (= 25.3 ± 5 SD), and those > 15 (= 25.1 ± 6 SD). Of the alleles detected, 553 (54.5%) were K1, 250 (24.7%) MAD20 and 211 (20.8%) RO33 that grouped into 19 K1 allelic families (108-270 bp), 14 MAD20 (108-216 bp) and one RO33 (153 bp). AmpliSeq revealed nucleotide polymorphisms in alleles that had similar sizes, thus increasing the K1 to 104, 58 for MAD20 and 14 for RO33. By AmpliSeq, the mean MOI was 4.8 (± 0.78, 95% CI) for the malaria endemic Lake Victoria region, 4.4 (± 1.03, 95% CI) for the epidemic prone Kisii Highland and 3.4 (± 0.62, 95% CI) for the seasonal malaria Semi-Arid region. MOI decreased with age: 4.5 (± 0.76, 95% CI) for children < 5 years, compared to 3.9 (± 0.70, 95% CI) for ages 5 to 14 and 2.7 (± 0.90, 95% CI) for those > 15. Females' MOI (4.2 ± 0.66, 95% CI) was not different from males 4.0 (± 0.61, 95% CI). In all regions, the number of alleles were high in the 2014-2015 period, more so in the Lake Victoria and the seasonal transmission arid regions. CONCLUSION These findings highlight the added advantages of AmpliSeq in haplotype discrimination and the associated improvement in unravelling complexity of P. falciparum population structure.
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Affiliation(s)
- Brian Andika
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Victor Mobegi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Kimita Gathii
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Josphat Nyataya
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Naomi Maina
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - George Awinda
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Beth Mutai
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - John Waitumbi
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya.
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Lubinda J, Bi Y, Haque U, Lubinda M, Hamainza B, Moore AJ. Spatio-temporal monitoring of health facility-level malaria trends in Zambia and adaptive scaling for operational intervention. COMMUNICATIONS MEDICINE 2022; 2:79. [PMID: 35789566 PMCID: PMC9249860 DOI: 10.1038/s43856-022-00144-1] [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: 11/30/2020] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Background The spatial and temporal variability inherent in malaria transmission within countries implies that targeted interventions for malaria control in high-burden settings and subnational elimination are a practical necessity. Identifying the spatio-temporal incidence, risk, and trends at different administrative geographies within malaria-endemic countries and monitoring them in near real-time as change occurs is crucial for developing and introducing cost-effective, subnational control and elimination intervention strategies. Methods This study developed intelligent data analytics incorporating Bayesian trend and spatio-temporal Integrated Laplace Approximation models to analyse high-burden over 32 million reported malaria cases from 1743 health facilities in Zambia between 2009 and 2015. Results The results show that at least 5.4 million people live in catchment areas with increasing trends of malaria, covering over 47% of all health facilities, while 5.7 million people live in areas with a declining trend (95% CI), covering 27% of health facilities. A two-scale spatio-temporal trend comparison identified significant differences between health facilities and higher-level districts, and the pattern observed in the southeastern region of Zambia provides the first evidence of the impact of recently implemented localised interventions. Conclusions The results support our recommendation for an adaptive scaling approach when implementing national malaria monitoring, control and elimination strategies and a particular need for stratified subnational approaches targeting high-burden regions with increasing disease trends. Strong clusters along borders with highly endemic countries in the north and south of Zambia underscore the need for coordinated cross-border malaria initiatives and strategies. Malaria is an infectious disease that is widespread in many African countries. Malaria transmission within a country can vary between regions, so tailored interventions for malaria control and elimination targeted to different regions are necessary. To achieve this, it is important to measure and monitor the frequency of malaria infections, its risk, and trends at different geographic administrative scales. This study analysed over 32 million reported malaria cases from 1743 health facilities in Zambia between 2009 and 2015. The results showed an increasing national trend in malaria risk and malaria infection frequency and identified differences between health facility and district trends. These findings support a flexible approach when implementing and expanding national malaria monitoring, control and elimination strategies, especially in areas bordering countries where malaria is widespread, cross-border movement is common, and cross-border initiatives could be beneficial. Lubinda et al. analyse over 32 million health-facility reported malaria cases in Zambia (2009–15) to examine spatially-structured temporal trends. They observe overall increasing trends in risk and rates and highlight the potential benefits of using an adaptive scaling approach in national malaria strategies, and a need for cross-border initiatives.
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Andrianaranjaka VHI, Ravaoarisoa E, Rakotomanga TA, Ralinoro F, Rakoto DAD, Randrianarivo RH, Jeannoda V, Ratsimbasoa A. DNA recovery from used malaria RDT to detect Plasmodium species and to assess Plasmodium falciparum genetic diversity: a pilot study in Madagascar. Malar J 2022; 21:227. [PMID: 35883089 PMCID: PMC9327223 DOI: 10.1186/s12936-022-04246-y] [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: 01/12/2022] [Accepted: 07/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are widely used for malaria diagnosis in Madagascar, where Plasmodium falciparum is the predominant species. Molecular diagnosis is essential for malaria surveillance, but requires additional blood samples for DNA extraction. Used RDTs is an attractive alternative that can be used as a source of DNA. Plasmodium falciparum genetic diversity and multiplicity of infection, usually determined by the genotyping of polymorphic regions of merozoite surface proteins 1 and 2 genes (msp1, msp2), and the repeated region RII of the glutamate-rich protein gene (glurp) have been associated with malaria transmission levels and subsequently with the impact of the deployed control strategies. Thus, the study aims to use RDT as DNA source to detect Plasmodium species, to characterize Plasmodium falciparum genetic diversity and determine the multiplicity of infection. Methods A pilot study was conducted in two sites with different epidemiological patterns: Ankazomborona (low transmission area) and Matanga (high transmission area). On May 2018, used RDT (SD BIOLINE Malaria Ag P.f/Pan, 05FK63) were collected as DNA source. Plasmodium DNA was extracted by simple elution with nuclease free water. Nested-PCR were performed to confirm Plasmodium species and to analyse P. falciparum msp1, msp2 and glurp genes polymorphisms. Results Amongst the 170 obtained samples (N = 74 from Ankazomborona and N = 96 from Matanga), Plasmodium positivity rate was 23.5% (40/170) [95% CI 17.5–30.8%] by nested-PCR with 92.2% (37/40) positive to P. falciparum, 5% (2/40) to Plasmodium vivax and 2.5% (1/40) to P. falciparum/P. vivax mixed infection. Results showed high polymorphisms in P. falciparum msp1, msp2 and glurp genes. Multiple infection rate was 28.6% [95% CI 12.2–52.3%]. The mean of MOI was 1.79 ± 0.74. Conclusion This pilot study highlighted that malaria diagnosis and molecular analysis are possible by using used malaria RDT. A large-scale study needs to be conducted to assess more comprehensively malaria parasites transmission levels and provide new data for guiding the implementation of local strategies for malaria control and elimination. Trial registration Retrospectively registered
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Affiliation(s)
- Voahangy Hanitriniaina I Andrianaranjaka
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar. .,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar.
| | - Elisabeth Ravaoarisoa
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Tovonahary A Rakotomanga
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Fanomezantsoa Ralinoro
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Danielle A Doll Rakoto
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ranjàna H Randrianarivo
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Victor Jeannoda
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Arsène Ratsimbasoa
- Faculté de Médecine, Université de Fianarantsoa, Fianarantsoa, Madagascar.,Centre National d'Application de Recherche Pharmaceutique, Antananarivo, Madagascar
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Mayor A, da Silva C, Rovira-Vallbona E, Roca-Feltrer A, Bonnington C, Wharton-Smith A, Greenhouse B, Bever C, Chidimatembue A, Guinovart C, Proctor JL, Rodrigues M, Canana N, Arnaldo P, Boene S, Aide P, Enosse S, Saute F, Candrinho B. Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol. BMJ Open 2022; 12:e063456. [PMID: 35820756 PMCID: PMC9274532 DOI: 10.1136/bmjopen-2022-063456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Genomic data constitute a valuable adjunct to routine surveillance that can guide programmatic decisions to reduce the burden of infectious diseases. However, genomic capacities remain low in Africa. This study aims to operationalise a functional malaria molecular surveillance system in Mozambique for guiding malaria control and elimination. METHODS AND ANALYSES This prospective surveillance study seeks to generate Plasmodium falciparum genetic data to (1) monitor molecular markers of drug resistance and deletions in rapid diagnostic test targets; (2) characterise transmission sources in low transmission settings and (3) quantify transmission levels and the effectiveness of antimalarial interventions. The study will take place across 19 districts in nine provinces (Maputo city, Maputo, Gaza, Inhambane, Niassa, Manica, Nampula, Zambézia and Sofala) which span a range of transmission strata, geographies and malaria intervention types. Dried blood spot samples and rapid diagnostic tests will be collected across the study districts in 2022 and 2023 through a combination of dense (all malaria clinical cases) and targeted (a selection of malaria clinical cases) sampling. Pregnant women attending their first antenatal care visit will also be included to assess their value for molecular surveillance. We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. Genetic data will be incorporated into epidemiological and transmission models to identify the most informative relationship between genetic features, sources of malaria transmission and programmatic effectiveness of new malaria interventions. Strategic genomic information will be ultimately integrated into the national malaria information and surveillance system to improve the use of the genetic information for programmatic decision-making. ETHICS AND DISSEMINATION The protocol was reviewed and approved by the institutional (CISM) and national ethics committees of Mozambique (Comité Nacional de Bioética para Saúde) and Spain (Hospital Clinic of Barcelona). Project results will be presented to all stakeholders and published in open-access journals. TRIAL REGISTRATION NUMBER NCT05306067.
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Affiliation(s)
- Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Clemente da Silva
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Eduard Rovira-Vallbona
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Caitlin Bever
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Caterina Guinovart
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | - Simone Boene
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
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Oboh MA, Ndiaye T, Diongue K, Ndiaye YD, Sy M, Deme AB, Diallo MA, Yade MS, Volkman SK, Badiane AS, Amambua-Ngwa A, Ndiaye D. Allelic diversity of MSP1 and MSP2 repeat loci correlate with levels of malaria endemicity in Senegal and Nigerian populations. Malar J 2021; 20:38. [PMID: 33436004 PMCID: PMC7805152 DOI: 10.1186/s12936-020-03563-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing the genetic diversity of malaria parasite populations in different endemic settings (from low to high) could be helpful in determining the effectiveness of malaria interventions. This study compared Plasmodium falciparum parasite population diversity from two sites with low (pre-elimination) and high transmission in Senegal and Nigeria, respectively. METHODS Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) and Nigeria (93). Allelic polymorphism at merozoite surface protein 1 (msp1) and merozoite surface protein- 2 (msp2) genes were assessed by nested PCR. RESULTS The most frequent msp1 and msp2 allelic families are the K1 and IC3D7 allelotypes in both Senegal and Nigeria. Multiplicity of infection (MOI) of greater that 1 and thus complex infections was common in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp1/2) than in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles was associated with heavy than with moderate parasite density. Meanwhile, equal proportions of K1 were observed in both heavy and moderate infection types in Nigeria. The IC3D7 subtype allele of the msp2 family was the most frequent in heavily parasitaemic individuals from both countries than in the moderately infected participants. CONCLUSION The unexpectedly low genetic diversity of infections high endemic Nigerian setting compared to the low endemic settings in Senegal is suggestive of possible epidemic outbreak in Nigeria.
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Affiliation(s)
- Mary A Oboh
- Medical Research Council Unit, the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
| | - Tolla Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal.
| | - Khadim Diongue
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Yaye D Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mouhamad Sy
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mamadou A Diallo
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mamadou S Yade
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Aida S Badiane
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit, the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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Ndiaye T, Sy M, Gaye A, Siddle KJ, Park DJ, Bei AK, Deme AB, Mbaye A, Dieye B, Ndiaye YD, Ndiaye IM, Diallo MA, Diongue K, Volkman SK, Badiane AS, Ndiaye D. Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal. Malar J 2020; 19:403. [PMID: 33172455 PMCID: PMC7654156 DOI: 10.1186/s12936-020-03471-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular epidemiology can provide important information regarding the genetic diversity and transmission of Plasmodium falciparum, which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of P. falciparum and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform. METHODS Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-three P. falciparum isolates from two epidemiologically different areas in the South and North of Senegal, was carried out. RESULTS A total of 76 Pfmsp1 and 116 Pfmsp2 clones were identified and 135 different alleles were found, 56 and 79 belonged to the pfmsp1 and pfmsp2 genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For pfmsp1, a high positive Tajima's D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D = - 1.46045) and F-Statistic (Fst) was 0.19505. For pfmsp2, non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas (p = 0.001). CONCLUSION This study revealed a high genetic diversity of pfmsp1 and pfmsp2 genes and low genetic differentiation in P. falciparum population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of P. falciparum infections.
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Affiliation(s)
- Tolla Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal.
| | - Mouhamad Sy
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Amy Gaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | | | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy K Bei
- Yale School of Public Health, 60 College Street, New Haven, CT, 06510, USA
| | - Awa B Deme
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aminata Mbaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Baba Dieye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Yaye Die Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mamadou Alpha Diallo
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Khadim Diongue
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
| | - Aida Sadikh Badiane
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Daouda Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
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8
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Ndiaye T, Sy M, Gaye A, Ndiaye D. Genetic polymorphism of Merozoite Surface Protein 1 (msp1) and 2 (msp2) genes and multiplicity of Plasmodium falciparum infection across various endemic areas in Senegal. Afr Health Sci 2019; 19:2446-2456. [PMID: 32127816 PMCID: PMC7040301 DOI: 10.4314/ahs.v19i3.19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Despite a significant decline in Senegal, malaria remains a burden in various parts of the country. Assessment of multiplicity of Plasmodium falciparum infection and genetic diversity of parasites population could help in monitoring of malaria control. OBJECTIVE To assess genetic diversity and multiplicity of infection in P. falciparum isolates from three areas in Senegal with different malaria transmissions. METHODS 136 blood samples were collected from patients with uncomplicated P. falciparum malaria in Pikine, Kedougou and Thies. Polymorphic loci of msp1 and 2 (Merozoite surface protein-1 and 2) genes were amplified by nested PCR. RESULTS For msp1gene, K1 allelic family was predominant with frequency of 71%. Concerning msp2 gene, IC3D7 allelic family was the most represented with frequency of 83%. Multiclonal isolates found were 36% and 31% for msp1et msp2 genes respectively. The MOI found in all areas was 2.56 and was statistically different between areas (P=0.024). Low to intermediate genetic diversity were found with heterozygosity range (He=0,394-0,637) and low genetic differentiation (Fst msp1= 0.011; Fst msp2=0.017) were observed between P. falciparum population within the country. CONCLUSION Low to moderate genetic diversity of P.falciparum strains and MOI disparities were found in Senegal.
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Affiliation(s)
- Tolla Ndiaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mouhamad Sy
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Amy Gaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Daouda Ndiaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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9
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Stresman G, Bousema T, Cook J. Malaria Hotspots: Is There Epidemiological Evidence for Fine-Scale Spatial Targeting of Interventions? Trends Parasitol 2019; 35:822-834. [PMID: 31474558 DOI: 10.1016/j.pt.2019.07.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
As data at progressively granular spatial scales become available, the temptation is to target interventions to areas with higher malaria transmission - so-called hotspots - with the aim of reducing transmission in the wider community. This paper reviews literature to determine if hotspots are an intrinsic feature of malaria epidemiology and whether current evidence supports hotspot-targeted interventions. Hotspots are a consistent feature of malaria transmission at all endemicities. The smallest spatial unit capable of supporting transmission is the household, where peri-domestic transmission occurs. Whilst the value of focusing interventions to high-burden areas is evident, there is currently limited evidence that local-scale hotspots fuel transmission. As boundaries are often uncertain, there is no conclusive evidence that hotspot-targeted interventions accelerate malaria elimination.
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Affiliation(s)
- Gillian Stresman
- Infection Biology Department, London School of Hygiene and Tropical Medicine, London, UK.
| | - Teun Bousema
- Radboud University Medical Centre, Department of Microbiology, HB Nijmegen, The Netherlands.
| | - Jackie Cook
- Medical Research Council (MRC) Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
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10
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Vera-Arias CA, Castro LE, Gómez-Obando J, Sáenz FE. Diverse origin of Plasmodium falciparum in northwest Ecuador. Malar J 2019; 18:251. [PMID: 31349843 PMCID: PMC6660669 DOI: 10.1186/s12936-019-2891-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ecuador plans to eliminate malaria by 2020, and the country has already seen a decrease in the number of cases from more than 100,000 in 2000 to only 618 in 2015. Around 30% of malaria infections in Ecuador are caused by Plasmodium falciparum. Most malaria population genetics studies performed in Latin America, especially in the Pacific Coast, indicate a high clonality and a clear structure of P. falciparum populations. It was shown that an outbreak of P. falciparum in northwest Ecuador was the result of a clonal expansion of parasites circulating at low levels in the country or re-invading Ecuador from neighbouring territories. However, general characteristics of P. falciparum circulating in the northwest coast of Ecuador have not been determined. The main goal of this study was to genetically characterize the population structure of P. falciparum in coastal Ecuadorian localities bordering with Colombia. METHODS Molecular investigation of 41 samples collected from 2013 to 2016 in San Lorenzo County, northwest Ecuador was performed using seven neutral microsatellite markers. RESULTS The genetic population structure of P. falciparum in northwest Ecuador is clearly defined as three different genetic groups previously reported in Ecuador, Peru and Colombia. CONCLUSIONS The limited number of P. falciparum clonal types that are circulating in northwest Ecuador, are related to ancestral parasite clonal lineages reported in the Pacific Coast. These parasites could be a product of migration from neighbouring regions or residual clonal types circulating in the country in low proportions. Studies of the genetic characterization of P. falciparum in eliminating areas help determine the possible origin of parasites in order to create strategies to prevent the entrance of new lineages and achieve local elimination of malaria.
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Affiliation(s)
- Claudia A Vera-Arias
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076, Apartado: 17-01-2184, Quito, Ecuador
| | | | - Javier Gómez-Obando
- Ministerio de Salud Pública, Distrito de Salud de San Lorenzo, San Lorenzo, Ecuador
| | - Fabián E Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076, Apartado: 17-01-2184, Quito, Ecuador.
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11
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Gnagne AP, Konate A, Bedia-Tanoh AV, Amiah-Droh M, Menan HIE, N'Guetta ASP, Yavo W. Dynamics of Plasmodium falciparum genetic diversity among asymptomatic and symptomatic children in three epidemiological areas in Cote d'Ivoire. Pathog Glob Health 2019; 113:133-142. [PMID: 31144611 DOI: 10.1080/20477724.2019.1624076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Asymptomatic carriers of Plasmodium are considered a reservoir of the parasite in humans. Therefore, in order to be effective, new malaria elimination strategies must take these targets into account. The aim of this study was to analyse genetic diversity of Plasmodium falciparum among schoolchildren in three epidemiological areas in Côte d'Ivoire. This was a cross-sectional study carried out from May 2015 to April 2016 in a primary school in rural and urban areas of San Pedro, Grand-Bassam and Abengourou, during the rainy season and the dry season. A total of 282 Plasmodium falciparum isolates were genotyped using Nested PCR of Pfmsp1 and Pfmsp2 genes. The overall frequency of K1, Mad20 and RO33 alleles was 81.6%, 53.4% and 57% for Pfmsp1 respectively. For Pfmsp2, this frequency was 84.3% and 72.2% for 3D7 and FC27. K1, Mad20 and FC27 Frequencies were significantly higher in Abengourou compared to other sites. Overall, the frequency of MIs was significantly higher in Abengourou for Pfmsp1 and Pfmsp2. However, Mad20 and RO33 alleles were significantly higher in the rainy season. No significant difference was observed between Pfmsp2 alleles in both seasons. Frequency of the 3D7 allele was significantly higher in symptomatic patients. MIs and COI increased with parasitemia for Pfmsp1and Pfmsp2. The data can be added to that available for monitoring and control of P. falciparum malaria. Further studies combining the entomological inoculation rate and the genetic diversity of P. falciparum will allow us to shed light on our understanding of the epidemiology of this parasite.
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Affiliation(s)
- Akpa Paterne Gnagne
- a Centre de Recherche et de Lutte contre le Paludisme , Institut National de Santé Publique , Abidjan , Côte d'Ivoire.,b Laboratoire de Génétique , Université Félix Houphouët Boigny , Abidjan , Côte d'Ivoire
| | - Abibatou Konate
- a Centre de Recherche et de Lutte contre le Paludisme , Institut National de Santé Publique , Abidjan , Côte d'Ivoire.,c Département de Parasitologie-Mycologie , UFR Sciences Pharmaceutiques et Biologique , Abidjan , Côte d'Ivoire
| | - Akoua Valérie Bedia-Tanoh
- a Centre de Recherche et de Lutte contre le Paludisme , Institut National de Santé Publique , Abidjan , Côte d'Ivoire.,c Département de Parasitologie-Mycologie , UFR Sciences Pharmaceutiques et Biologique , Abidjan , Côte d'Ivoire
| | - Mireille Amiah-Droh
- a Centre de Recherche et de Lutte contre le Paludisme , Institut National de Santé Publique , Abidjan , Côte d'Ivoire.,b Laboratoire de Génétique , Université Félix Houphouët Boigny , Abidjan , Côte d'Ivoire
| | - Hervé Ignace Eby Menan
- c Département de Parasitologie-Mycologie , UFR Sciences Pharmaceutiques et Biologique , Abidjan , Côte d'Ivoire
| | | | - William Yavo
- a Centre de Recherche et de Lutte contre le Paludisme , Institut National de Santé Publique , Abidjan , Côte d'Ivoire.,c Département de Parasitologie-Mycologie , UFR Sciences Pharmaceutiques et Biologique , Abidjan , Côte d'Ivoire
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12
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Low genetic diversity and complexity of submicroscopic Plasmodium falciparum infections among febrile patients in low transmission areas in Senegal. PLoS One 2019; 14:e0215755. [PMID: 31022221 PMCID: PMC6483351 DOI: 10.1371/journal.pone.0215755] [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: 11/19/2018] [Accepted: 04/08/2019] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Submicroscopic Plasmodium infections are common in malaria endemic countries, but very little studies have been done in Senegal. This study investigates the genetic diversity and complexity of submicroscopic P. falciparum infections among febrile patients in low transmission areas in Senegal. MATERIALS AND METHODS Hundred and fifty blood samples were collected from febrile individuals living in Dielmo and Ndiop (Senegal) between August 2014 and January 2015, tested for microscopic and sub-microscopic P. falciparum infections and characterized for their genetic diversity and complexity of infections using msp-1 and msp-2 genotyping. RESULTS Submicroscopic P. falciparum infections were 19.6% and 25% in Dielmo and Ndiop, respectively. K1 and 3D7 were the predominant msp-1 and msp-2 allelic types with respective frequencies of 67.36% and 67.10% in microscopic isolates and 58.24% and 78% in submicroscopic ones. Frequencies of msp-1 allelic types were statistically comparable between the studied groups (p>0.05), and were respectively 93.54% vs 87.5% for K1, 60% vs 54.83% for MAD20 and 41.93% vs 22.5% for RO33 while frequencies of msp-2 allelic types were significantly highest in the microscopy group for FC27 (41.93% vs 10%, Fisher's Exact Test, p = 0.001) and 3D7 (61.29% vs 32.5%, Fisher's Exact Test, p = 0.02). Multiplicities of infection were lowest in submicroscopic P. falciparum isolates. CONCLUSIONS The study revealed a high submicroscopic P. falciparum carriage among patients in the study areas, and that submicroscopic P. falciparum isolates had a lower genetic diversity and complexity of malaria infections.
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Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda. Sci Rep 2018; 8:10159. [PMID: 29977002 PMCID: PMC6033881 DOI: 10.1038/s41598-018-28534-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular techniques are not routinely employed for malaria surveillance, while cross-sectional, community-based parasite surveys require significant resources. Here, we describe a novel use of malaria rapid diagnostic tests (RDTs) collected at a single facility as source material for sequencing to esimtate malaria transmission intensity across a relatively large catchment area. We extracted Plasmodium falciparum DNA from RDTs, then amplified and sequenced a region of the apical membrane antigen 1 (pfama1) using targeted amplicon deep sequencing. We determined the multiplicity of infection (MOI) for each sample and examined associations with demographic, clinical, and spatial factors. We successfully genotyped 223 of 287 (77.7%) of the samples. We demonstrated an inverse relationship between the MOI and elevation with individuals presenting from the highest elevation villages harboring infections approximately half as complex as those from the lowest (MOI 1.85 vs. 3.51, AOR 0.25, 95% CI 0.09-0.65, p = 0.004). This study demonstrates the feasibility and validity of using routinely-collected RDTs for molecular surveillance of malaria and has real-world utility, especially as the cost of high-throughpout sequencing continues to decline.
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Affiliation(s)
- Ross M Boyce
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.
| | - Nick Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Travis Fulton
- Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA
| | - Raquel Reyes
- Division of General Medicine & Clinical Epidemiology, University of North Carolina at Chapel Hill, 5039 Old Clinic Building, CB 7110, Chapel Hill, 27599, USA
| | - Michael Matte
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Moses Ntaro
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Edgar Mulogo
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Andreea Waltmann
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, 125 Nashua Street, Suite 722, Boston, 02114, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.,Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA.,Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
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14
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Gueye NSG, Ntoumi F, Vouvoungui C, Kobawila SC, NKombo M, Mouanga AM, Deibert J, Koukouikila-Koussounda F. Plasmodium falciparum merozoite protein-1 genetic diversity and multiplicity of infection in isolates from Congolese children consulting in a pediatric hospital in Brazzaville. Acta Trop 2018; 183:78-83. [PMID: 29626433 DOI: 10.1016/j.actatropica.2018.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 04/01/2018] [Accepted: 04/03/2018] [Indexed: 11/27/2022]
Abstract
As in many sub-Saharan African countries, the burden of malaria has been reduced in the Republic of Congo as a result of massive deployment of insecticide treated nets and availability of artemisinin-combinations therapies (ACTs). High to moderate genetic diversity of msp-1 gene of Plasmodium falciparum (P. falciparum) has been reported from different parts of the world but limited data are available from Central Africa including the Republic of Congo. For this reason, the aim of study was to investigate the P. falciparum genetic diversity and to determine the multiplicity of infection in P. falciparum isolates from Congolese children in order to dispose of an additional parameter to measure the impact malaria control intervention. A total of 229 blood samples were collected from September 2014 to February 2015 in children aged from one to ten years presenting a paediatric hospital Marien NGOUABI located in Northern part of Brazzaville. Inclusion criterion was fever (axillary temperature ≥ 37.5 °C) or history of fever in the preceding 48 h before inclusion in this study. Then thick and thin blood smears were done to detect malaria parasites, to determine parasite density and to identify plasmodial species. Sub-microscopic infection was detected by PCR using the P. falciparum msp-1 gene as molecular marker. The prevalence of microscopic and sub-microscopic infection in this cohort was 10% and 27.5%, respectively. The K1 allelic family was predominant (45% of isolates) whereas the RO33 and MAD20 represented 35% and 20%, respectively of isolates. In this study 48% (38/79) of isolates harbored more than one parasite clone. Overall the multiplicity of infection (MOI) was 1.7. According to type of infection, the MOI was significantly higher in children with microscopic infection (2.5 vs 1.4 for submicroscopic infection, P = .001). When considering age, hemoglobin genotype (AA or AS) and level and parasite density, no association was observed with the MOI. This study reveals that the P. falciparum genetic diversity in isolates from Congolese children is high but with low multiplicity of infection.
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15
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Zhong D, Koepfli C, Cui L, Yan G. Molecular approaches to determine the multiplicity of Plasmodium infections. Malar J 2018; 17:172. [PMID: 29685152 PMCID: PMC5914063 DOI: 10.1186/s12936-018-2322-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/26/2022] Open
Abstract
Multiplicity of infection (MOI), also termed complexity of infection (COI), is defined as the number of genetically distinct parasite strains co-infecting a single host, which is an important indicator of malaria epidemiology. PCR-based genotyping often underestimates MOI. Next generation sequencing technologies provide much more accurate and genome-wide characterization of polyclonal infections. However, complete haplotype characterization of multiclonal infections remains a challenge due to PCR artifacts and sequencing errors, and requires efficient computational tools. In this review, the advantages and limitations of current molecular approaches to determine multiplicity of malaria parasite infection are discussed.
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Affiliation(s)
- Daibin Zhong
- Program in Public Health, University of California, Irvine, CA, 92617, USA.
| | - Cristian Koepfli
- Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, CA, 92617, USA.
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16
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Huang B, Tuo F, Liang Y, Wu W, Wu G, Huang S, Zhong Q, Su XZ, Zhang H, Li M, Bacar A, Abdallah KS, Mliva AMSA, Wang Q, Yang Z, Zheng S, Xu Q, Song J, Deng C. Temporal changes in genetic diversity of msp-1, msp-2, and msp-3 in Plasmodium falciparum isolates from Grande Comore Island after introduction of ACT. Malar J 2018; 17:83. [PMID: 29458365 PMCID: PMC5819244 DOI: 10.1186/s12936-018-2227-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/08/2018] [Indexed: 11/26/2022] Open
Abstract
Background Malaria is still one of the serious public health problems in Grande Comore Island, although the number of annual cases has been greatly reduced in recent years. A better understanding of malaria parasite population diversity and transmission dynamics is critical for assessing the effectiveness of malaria control measures. The objective of this study is to investigate temporal changes in genetic diversity of Plasmodium falciparum populations and multiplicity of infection (MOI) in Grande Comore 10 years after introduction of ACT. Methods A total of 232 P. falciparum clinical isolates were collected from the Grande Comore Island during two sampling periods (118 for 2006‒2007 group, and 114 for 2013‒2016 group). Parasite isolates were characterized for genetic diversity and complexity of infection by genotyping polymorphic regions in merozoite surface protein gene 1 (msp-1), msp-2, and msp-3 using nested PCR and DNA sequencing. Results Three msp-1 alleles (K1, MAD20, and RO33), two msp-2 alleles (FC27 and 3D7), and two msp-3 alleles (K1 and 3D7) were detected in parasites of both sampling periods. The RO33 allele of msp-1 (84.8%), 3D7 allele of msp-2 (90.8%), and K1 allele of msp-3 (66.7%) were the predominant allelic types in isolates from 2006–2007 group. In contrast, the RO33 allele of msp-1 (63.4%), FC27 allele of msp-2 (91.1%), and 3D7 allele of msp-3 (53.5%) were the most prevalent among isolates from the 2013–2016 group. Compared with the 2006‒2007 group, polyclonal infection rates of msp-1 (from 76.7 to 29.1%, P < 0.01) and msp-2 (from 62.4 to 28.3%, P < 0.01) allelic types were significantly decreased in those from 2013‒2016 group. Similarly, the MOIs for both msp-1 and msp-2 were higher in P. falciparum isolates in the 2006–2007 group than those in 2013–2016 group (MOI = 3.11 vs 1.63 for msp-1; MOI = 2.75 vs 1.35 for msp-2). DNA sequencing analyses also revealed reduced numbers of distinct sequence variants in the three genes from 2006‒2007 to 2013‒2016: msp-1, from 32 to 23 (about 28% decline); msp-2 from 29 to 21 (about 28% decline), and msp-3 from 11 to 3 (about 72% decline). Conclusions The present data showed dramatic reduction in genetic diversity and MOI among Grande Comore P. falciparum populations over the course of the study, suggesting a trend of decreasing malaria transmission intensity and genetic diversity in Grande Comore Island. These data provide valuable information for surveillance of P. falciparum infection and for assessing the appropriateness of the current malarial control strategies in the endemic area.
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Affiliation(s)
- Bo Huang
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China.,Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Fei Tuo
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Yuan Liang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Wanting Wu
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Guangchao Wu
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Shiguang Huang
- School of Stomatology, Jinan University, Guangzhou, 510632, Guangdong, People's Republic of China
| | - Qirun Zhong
- Artepharm, Co., Ltd, Guangzhou, 510405, Guangdong, People's Republic of China
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hongying Zhang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Mingqiang Li
- Artepharm, Co., Ltd, Guangzhou, 510405, Guangdong, People's Republic of China
| | - Affane Bacar
- National Malaria Control Programme, BP 500, Moroni, Comoros
| | | | | | - Qi Wang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Zhaoli Yang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Shaoqin Zheng
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China
| | - Qin Xu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Jianping Song
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China. .,Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China.
| | - Changsheng Deng
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China. .,Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510445, Guangdong, People's Republic of China.
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Miller RH, Hathaway NJ, Kharabora O, Mwandagalirwa K, Tshefu A, Meshnick SR, Taylor SM, Juliano JJ, Stewart VA, Bailey JA. A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity. Malar J 2017; 16:490. [PMID: 29246158 PMCID: PMC5732508 DOI: 10.1186/s12936-017-2137-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/06/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali. RESULTS A total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali. CONCLUSIONS Amplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection may perform well for understanding COI, they may offer little geographic or temporal discrimination between parasite populations.
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Affiliation(s)
- Robin H Miller
- Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD, USA
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, 55 Lake Avenue North, Worcester, MA, USA
| | - Oksana Kharabora
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - Kashamuka Mwandagalirwa
- Ecole de Santé Publique, Université de Kinshasa, Commune de Lemba, P.O Box 11850, Kinshasa, Democratic Republic of Congo
| | - Antoinette Tshefu
- Ecole de Santé Publique, Université de Kinshasa, Commune de Lemba, P.O Box 11850, Kinshasa, Democratic Republic of Congo
| | - Steven R Meshnick
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - Steve M Taylor
- Division of Infectious Diseases and Duke Global Health Institute, Duke University Medical Center, 303 Research Drive, Durham, NC, USA
| | - Jonathan J Juliano
- University of North Carolina School of Medicine, 101 Manning Drive, Chapel Hill, NC, USA
| | - V Ann Stewart
- Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, 55 Lake Avenue North, Worcester, MA, USA.
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