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Freville A, Stewart LB, Tetteh KKA, Treeck M, Cortes A, Voss TS, Tarr SJ, Baker DA, Conway DJ. Expression of the MSPDBL2 antigen in a discrete subset of Plasmodium falciparum schizonts is regulated by GDV1 but may not be linked to sexual commitment. mBio 2024; 15:e0314023. [PMID: 38530030 PMCID: PMC11077968 DOI: 10.1128/mbio.03140-23] [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: 11/21/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
The Plasmodium falciparum merozoite surface protein MSPDBL2 is a polymorphic antigen targeted by acquired immune responses, and normally expressed in only a minority of mature schizonts. The potential relationship of MSPDBL2 to sexual commitment is examined, as variable mspdbl2 transcript levels and proportions of MSPDBL2-positive mature schizonts in clinical isolates have previously correlated with levels of many sexual stage parasite gene transcripts, although not with the master regulator ap2-g. It is demonstrated that conditional overexpression of the gametocyte development protein GDV1, which promotes sexual commitment, also substantially increases the proportion of MSPDBL2-positive schizonts in culture. Conversely, truncation of the gdv1 gene is shown to prevent any expression of MSPDBL2. However, across diverse P. falciparum cultured lines, the variable proportions of MSPDBL2 positivity in schizonts do not correlate significantly with variable gametocyte conversion rates, indicating it is not involved in sexual commitment. Confirming this, examining a line with endogenous hemagglutinin-tagged AP2-G showed that the individual schizonts expressing MSPDBL2 are mostly different from those expressing AP2-G. Using a selection-linked integration system, modified P. falciparum lines were engineered to express an intact or disrupted version of MSPDBL2, showing the protein is not required for sexual commitment or early gametocyte development. Asexual parasite multiplication rates were also not affected by expression of either intact or disrupted MSPDBL2 in a majority of schizonts. Occurring alongside sexual commitment, the role of the discrete MSPDBL2-positive schizont subpopulation requires further investigation in natural infections where it is under immune selection. IMPORTANCE Malaria parasites in the blood are remarkably variable, able to switch antigenic targets so they may survive within humans who have already developed specific immune responses. This is one of the challenges in developing vaccines against malaria. MSPDBL2 is a target of naturally acquired immunity expressed in minority proportions of schizonts, the end stages of each 2-day replication cycle in red blood cells which contain merozoites prepared to invade new red blood cells. Results show that the proportion of schizonts expressing MSPDBL2 is positively controlled by the expression of the regulatory gametocyte development protein GDV1. It was previously known that expression of GDV1 leads to increased expression of AP2-G which causes parasites to switch to sexual development, so a surprising finding here is that MSPDBL2-positive parasites are mostly distinct from those that express AP2-G. This discrete antigenic subpopulation of mostly asexual parasites is regulated alongside sexually committed parasites, potentially enabling survival under stress conditions.
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Affiliation(s)
- Aline Freville
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Lindsay B. Stewart
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kevin K. A. Tetteh
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Alfred Cortes
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
- ICREA, Barcelona, Catalonia, Spain
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah J. Tarr
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David A. Baker
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David J. Conway
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Gupta H, Sharma S, Gilyazova I, Satyamoorthy K. Molecular tools are crucial for malaria elimination. Mol Biol Rep 2024; 51:555. [PMID: 38642192 DOI: 10.1007/s11033-024-09496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
The eradication of Plasmodium parasites, responsible for malaria, is a daunting global public health task. It requires a comprehensive approach that addresses symptomatic, asymptomatic, and submicroscopic cases. Overcoming this challenge relies on harnessing the power of molecular diagnostic tools, as traditional methods like microscopy and rapid diagnostic tests fall short in detecting low parasitaemia, contributing to the persistence of malaria transmission. By precisely identifying patients of all types and effectively characterizing malaria parasites, molecular tools may emerge as indispensable allies in the pursuit of malaria elimination. Furthermore, molecular tools can also provide valuable insights into parasite diversity, drug resistance patterns, and transmission dynamics, aiding in the implementation of targeted interventions and surveillance strategies. In this review, we explore the significance of molecular tools in the pursuit of malaria elimination, shedding light on their key contributions and potential impact on public health.
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Affiliation(s)
- Himanshu Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Sonal Sharma
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Irina Gilyazova
- Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, 450054, Russia
- Bashkir State Medical University, Ufa, 450008, Russia
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, 580009, Karnataka, India
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Sollelis L, Howick VM, Marti M. Revisiting the determinants of malaria transmission. Trends Parasitol 2024; 40:302-312. [PMID: 38443304 DOI: 10.1016/j.pt.2024.02.001] [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: 12/20/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Malaria parasites have coevolved with humans over thousands of years, mirroring their migration out of Africa. They persist to this day, despite continuous elimination efforts worldwide. These parasites can adapt to changing environments during infection of human and mosquito, and when expanding the geographical range by switching vector species. Recent studies in the human malaria parasite, Plasmodium falciparum, identified determinants governing the plasticity of sexual conversion rates, sex ratio, and vector competence. Here we summarize the latest literature revealing environmental, epigenetic, and genetic determinants of malaria transmission.
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Affiliation(s)
- Lauriane Sollelis
- Wellcome Center for Integrative Parasitology, Institute of Infection and Immunity University of Glasgow, Glasgow, UK; Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Virginia M Howick
- Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland; Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology, Institute of Infection and Immunity University of Glasgow, Glasgow, UK; Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland.
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Greyling N, van der Watt M, Gwarinda H, van Heerden A, Greenhouse B, Leroy D, Niemand J, Birkholtz LM. Genetic complexity alters drug susceptibility of asexual and gametocyte stages of Plasmodium falciparum to antimalarial candidates. Antimicrob Agents Chemother 2024; 68:e0129123. [PMID: 38259087 PMCID: PMC10916389 DOI: 10.1128/aac.01291-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Malaria elimination requires interventions able to target both the asexual blood stage (ABS) parasites and transmissible gametocyte stages of Plasmodium falciparum. Lead antimalarial candidates are evaluated against clinical isolates to address key concerns regarding efficacy and to confirm that the current, circulating parasites from endemic regions lack resistance against these candidates. While this has largely been performed on ABS parasites, limited data are available on the transmission-blocking efficacy of compounds with multistage activity. Here, we evaluated the efficacy of lead antimalarial candidates against both ABS parasites and late-stage gametocytes side-by-side, against clinical P. falciparum isolates from southern Africa. We additionally correlated drug efficacy to the genetic diversity of the clinical isolates as determined with a panel of well-characterized, genome-spanning microsatellite markers. Our data indicate varying sensitivities of the isolates to key antimalarial candidates, both for ABS parasites and gametocyte stages. While ABS parasites were efficiently killed, irrespective of genetic complexity, antimalarial candidates lost some gametocytocidal efficacy when the gametocytes originated from genetically complex, multiple-clone infections. This suggests a fitness benefit to multiclone isolates to sustain transmission and reduce drug susceptibility. In conclusion, this is the first study to investigate the efficacy of antimalarial candidates on both ABS parasites and gametocytes from P. falciparum clinical isolates where the influence of parasite genetic complexity is highlighted, ultimately aiding the malaria elimination agenda.
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Affiliation(s)
- Nicola Greyling
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Mariëtte van der Watt
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Hazel Gwarinda
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Ashleigh van Heerden
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Bryan Greenhouse
- Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Didier Leroy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Jandeli Niemand
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
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Casanova D, Baptista V, Costa M, Freitas B, Pereira MDNI, Calçada C, Mota P, Kythrich O, Pereira MHJS, Osório NS, Veiga MI. Artemisinin resistance-associated gene mutations in Plasmodium falciparum: A case study of severe malaria from Mozambique. Travel Med Infect Dis 2024; 57:102684. [PMID: 38159875 DOI: 10.1016/j.tmaid.2023.102684] [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: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The effectiveness of artemisinin-based combination therapies (ACT) in treating Plasmodium falciparum, is vital for global malaria control efforts, particularly in sub-Saharan Africa. The examination of imported cases from endemic areas holds implications for malaria chemotherapy on a global scale. METHOD A 45-year-old male presented with high fever, dry cough, diarrhoea and generalized muscle pain, following a two-week trip to Mozambique. P. falciparum infection with hiperparasitemia was confirmed and the patient was treated initially with quinine and doxycycline, then intravenous artesunate. To assess drug susceptibility, ex vivo half-maximal inhibitory concentration assays were conducted, and the isolated P. falciparum genome was deep sequenced. RESULTS The clinical isolate exhibited elevated ex vivo half-maximal inhibitory concentration values to dihydroartemisinin, lumefantrine, mefloquine and piperaquine. Genomic analysis identified a I416V mutation in the P. falciparum Kelch13 (PF3D7_1343700) gene, and several mutations at the Kelch13 interaction candidate genes, pfkics (PF3D7_0813000, PF3D7_1138700, PF3D7_1246300), including the ubiquitin carboxyl-terminal hydrolase 1, pfubp1 (PF3D7_0104300). Mutations at the drug transporters and genes linked to next-generation antimalarial drug resistance were also present. CONCLUSIONS This case highlights the emergence of P. falciparum strains carrying mutations in artemisinin resistance-associated genes in Mozambique, couple with a reduction in ex vivo susceptibility to ACT drugs. Continuous surveillance of mutations linked to drug resistance and regular monitoring of drug susceptibility are imperative to anticipate the spread of potential resistant strains emerging in Mozambique and to maintain effective malaria control strategies.
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Affiliation(s)
- Daniela Casanova
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Vitória Baptista
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Microelectromechanical Systems Research Unit (CMEMS-UMinho), School of Engineering, University of Minho, Campus de Azurém, 4800-058, Guimarães, Portugal
| | - Magda Costa
- Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Bruno Freitas
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria das Neves Imaculada Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Carla Calçada
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Paula Mota
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | - Olena Kythrich
- Clinical Pathology Department, Hospital Senhora da Oliveira, 4835-044, Guimarães, Portugal
| | | | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; ICVS/3B's─PT Government Associate Laboratory, 4806-909, Guimarães/ Braga, Portugal; Clinical Academic Center-Braga (2CA-Braga), 4710-243, Braga, Portugal.
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Gwarinda HB, Tessema SK, Raman J, Greenhouse B, Birkholtz LM. Population structure and genetic connectivity of Plasmodium falciparum in pre-elimination settings of Southern Africa. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1227071. [PMID: 38455947 PMCID: PMC10910941 DOI: 10.3389/fepid.2023.1227071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/17/2023] [Indexed: 03/09/2024]
Abstract
To accelerate malaria elimination in the Southern African region by 2030, it is essential to prevent cross-border malaria transmission. However, countries within the region are highly interconnected due to human migration that aids in the movement of the parasite across geographical borders. It is therefore important to better understand Plasmodium falciparum transmission dynamics in the region, and identify major parasite source and sink populations, as well as cross-border blocks of high parasite connectivity. We performed a meta-analysis using collated parasite allelic data generated by microsatellite genotyping of malaria parasites from Namibia, Eswatini, South Africa, and Mozambique (N = 5,314). The overall number of unique alleles was significantly higher (P ≤ 0.01) in Namibia (mean A = 17.3 ± 1.46) compared to South Africa (mean A = 12.2 ± 1.22) and Eswatini (mean A = 13.3 ± 1.27, P ≤ 0.05), whilst the level of heterozygosity was not significantly different between countries. The proportion of polyclonal infections was highest for Namibia (77%), and lowest for Mozambique (64%). A was significant population structure was detected between parasites from the four countries, and patterns of gene flow showed that Mozambique was the major source area and Eswatini the major sink area of parasites between the countries. This study showed strong signals of parasite population structure and genetic connectivity between malaria parasite populations across national borders. This calls for strengthening the harmonization of malaria control and elimination efforts between countries in the southern African region. This data also proves its potential utility as an additional surveillance tool for malaria surveillance on both a national and regional level for the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance as countries work towards malaria elimination.
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Affiliation(s)
- Hazel B. Gwarinda
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Sofonias K. Tessema
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jaishree Raman
- Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre for Emerging Zoonotic and Parasitic Diseases, A Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of Witwatersrand, Johannesburg, South Africa
| | - Bryan Greenhouse
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
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Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
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Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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Waweru H, Kanoi BN, Kuja JO, Maranga M, Kongere J, Maina M, Kinyua J, Gitaka J. Limited genetic variations of the Rh5-CyRPA-Ripr invasion complex in Plasmodium falciparum parasite population in selected malaria-endemic regions, Kenya. FRONTIERS IN TROPICAL DISEASES 2023; 4:1102265. [PMID: 38406638 PMCID: PMC7615667 DOI: 10.3389/fitd.2023.1102265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
The invasion of human erythrocytes by Plasmodium falciparum merozoites requires interaction between parasite ligands and host receptors. Interaction of PfRh5-CyRPA-Ripr protein complex with basigin, an erythrocyte surface receptor, via PfRh5 is essential for erythrocyte invasion. Antibodies raised against each antigen component of the complex have demonstrated erythrocyte invasion inhibition, making these proteins potential blood-stage vaccine candidates. Genetic polymorphisms present a significant challenge in developing efficacious vaccines, leading to variant-specific immune responses. This study investigated the genetic variations of the PfRh5 complex proteins in P. falciparum isolates from Lake Victoria islands, Western Kenya. Here, twenty-nine microscopically confirmed P. falciparum field samples collected from islands in Lake Victoria between July 2014 and July 2016 were genotyped by whole genome sequencing, and results compared to sequences mined from the GenBank database, from a study conducted in Kilifi, as well as other sequences from the MalariaGEN repository. We analyzed the frequency of polymorphisms in the PfRh5 protein complex proteins, PfRh5, PfCyRPA, PfRipr, and PfP113, and their location mapped on the 3D protein complex structure. We identified a total of 58 variants in the PfRh5 protein complex. PfRh5 protein was the most polymorphic with 30 SNPs, while PfCyRPA was relatively conserved with 3 SNPs. The minor allele frequency of the SNPs ranged between 1.9% and 21.2%. Ten high-frequency alleles (>5%) were observed in PfRh5 at codons 147, 148, 277, 410, and 429 and in PfRipr at codons 190, 255, 259, and 1003. A SNP was located in protein-protein interaction region C203Y and F292V of PfRh5 and PfCyRPA, respectively. Put together, this study revealed low polymorphisms in the PfRh5 invasion complex in the Lake Victoria parasite population. However, the two mutations identified on the protein interaction regions prompts for investigation on their impacts on parasite invasion process to support the consideration of PfRh5 components as potential malaria vaccine candidates.
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Affiliation(s)
- Harrison Waweru
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Bernard N. Kanoi
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Research in Tropical Medicine and Community Development, Nairobi, Kenya
| | - Josiah O. Kuja
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mary Maranga
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - James Kongere
- Centre for Research in Tropical Medicine and Community Development, Nairobi, Kenya
| | - Michael Maina
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Johnson Kinyua
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jesse Gitaka
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Research in Tropical Medicine and Community Development, Nairobi, Kenya
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Stewart LB, Freville A, Voss TS, Baker DA, Awandare GA, Conway DJ. Plasmodium falciparum Sexual Commitment Rate Variation among Clinical Isolates and Diverse Laboratory-Adapted Lines. Microbiol Spectr 2022; 10:e0223422. [PMID: 36409095 PMCID: PMC9769538 DOI: 10.1128/spectrum.02234-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/20/2022] [Indexed: 11/23/2022] Open
Abstract
Asexual blood-stage malaria parasites must produce sexual progeny to infect mosquitoes. It is important to understand the scope and causes of intraspecific variation in sexual commitment rates, particularly for the major human parasite P. falciparum. First, two alternative assay methods of measuring sexual commitment were compared to test a genetically modified P. falciparum line with elevated commitment rates inducible by overexpression of GDV1. The methods yielded correlated measurements with higher sensitivity and precision being achieved by one employing detection of the early gametocyte differentiation marker Pfs16. Thus, this was used to survey a diverse range of parasite lines and test each in multiple biological replicate assays in a serum-free medium supplemented with Albumax. There were differences among six recent clinical isolates from Ghana in their mean rates of sexual commitment per cycle, ranging from 3.3% to 12.2%. Among 13 diverse long-term laboratory-adapted lines, mean sexual commitment rates for most ranged from 4.7% to 13.4%, a few had lower rates with means from 0.3 to 1.6%, and one with a nonfunctional ap2-g gene always showed zero commitment. Among a subset of lines tested for the effects of exogenous choline to suppress commitment, there were significant differences. As expected, there was no effect in a line that had lost the gdv1 gene and that had generally low commitment, whereas the others showed quantitatively variable but significant responses to choline, suggesting potential trait variation. The results indicated the value of performing multiple replicate assays for understanding the variation of this key reproductive trait that likely affects transmission. IMPORTANCE Only sexual-stage malaria parasites are transmitted from human blood to mosquitoes. Thus, it is vital to understand variations in sexual commitment rates because these may be modifiable or susceptible to blocking. Two different methods of commitment rate measurement were first compared, demonstrating higher sensitivity and precision by the detection of an early differentiation marker, which was subsequently used to survey diverse lines. Clinical isolates from Ghana showed significant variation in mean per-cycle commitment rates and variation among biological replicates. Laboratory-adapted lines of diverse origins had a wider range with most being within the range observed for the clinical isolates, while a minority consistently had lower or zero rates. There was quantitative variation in the effects when adding choline to suppress commitment, indicating differing responsiveness of parasites to this environmental modification. Performing multiple assay replicates and comparisons of diverse isolates was important to understand this trait and its potential effects on transmission.
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Affiliation(s)
- Lindsay B. Stewart
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Aline Freville
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, University of Basel, Basal, Switzerland
| | - David A. Baker
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - David J. Conway
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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10
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Highly Variable Expression of Merozoite Surface Protein MSPDBL2 in Diverse Plasmodium falciparum Clinical Isolates and Transcriptome Scans for Correlating Genes. mBio 2022; 13:e0194822. [PMID: 35950755 PMCID: PMC9426457 DOI: 10.1128/mbio.01948-22] [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] [Indexed: 11/30/2022] Open
Abstract
The merozoite surface protein MSPDBL2 of Plasmodium falciparum is under strong balancing selection and is a target of naturally acquired antibodies. Remarkably, MSPDBL2 is expressed in only a minority of mature schizonts of any cultured parasite line, and mspdbl2 gene transcription increases in response to overexpression of the gametocyte development inducer GDV1, so it is important to understand its natural expression. Here, MSPDBL2 in mature schizonts was analyzed in the first ex vivo culture cycle of 96 clinical isolates from 4 populations with various levels of infection endemicity in different West African countries, by immunofluorescence microscopy with antibodies against a conserved region of the protein. In most isolates, less than 1% of mature schizonts were positive for MSPDBL2, but the frequency distribution was highly skewed, as nine isolates had more than 3% schizonts positive and one had 73% positive. To investigate whether the expression of other gene loci correlated with MSPDBL2 expression, whole-transcriptome sequencing was performed on schizont-enriched material from 17 of the isolates with a wide range of proportions of schizonts positive. Transcripts of particular genes were highly significantly positively correlated with MSPDBL2 positivity in schizonts as well as with mspdbl2 gene transcript levels, showing overrepresentation of genes implicated previously as involved in gametocytogenesis but not including the gametocytogenesis master regulator ap2-g. Single-cell transcriptome analysis of a laboratory-adapted clone showed that most individual parasites expressing mspdbl2 did not express ap2-g, consistent with MSPDBL2 marking a developmental subpopulation that is distinct but likely to co-occur alongside sexual commitment. IMPORTANCE These findings contribute to understanding malaria parasite antigenic and developmental variation, focusing on the merozoite surface protein encoded by the single locus under strongest balancing selection. Analyzing the initial ex vivo generation of parasites grown from a wide sample of clinical infections, we show a unique and highly skewed pattern of natural expression frequencies of MSPDBL2, distinct from that of any other antigen. Bulk transcriptome analysis of a range of clinical isolates showed significant overrepresentation of sexual development genes among those positively correlated with MSPDBL2 protein and mspdbl2 gene expression, indicating the MSPDBL2-positive subpopulation to be often coincident with parasites developing sexually in preparation for transmission. Single-cell transcriptome data confirm the absence of a direct correlation with the ap2-g master regulator of sexual development, indicating that the MSPDBL2-positive subpopulation has a separate function in asexual survival and replication under conditions that promote terminal sexual differentiation.
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11
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Declines in prevalence alter the optimal level of sexual investment for the malaria parasite Plasmodium falciparum. Proc Natl Acad Sci U S A 2022; 119:e2122165119. [PMID: 35867831 PMCID: PMC9335338 DOI: 10.1073/pnas.2122165119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Like most human pathogens, the malaria parasite Plasmodium falciparum experiences strong selection pressure from public health interventions such as drug treatment. While most commonly studied in the context of drug targets and related pathways, parasite adaptation to control measures likely extends to phenotypes beyond drug resistance. Here, we use modeling to explore how control measures can reduce levels of within-host competition between P. falciparum genotypes and favor higher rates of sexual investment. We validate these predictions with longitudinally sampled genomic data from French Guiana during a period of malaria decline and find that the most strongly selected genes are enriched for transcription factors involved in commitment to and development of the parasite’s sexual gametocyte form. Successful infectious disease interventions can result in large reductions in parasite prevalence. Such demographic change has fitness implications for individual parasites and may shift the parasite’s optimal life history strategy. Here, we explore whether declining infection rates can alter Plasmodium falciparum’s investment in sexual versus asexual growth. Using a multiscale mathematical model, we demonstrate how the proportion of polyclonal infections, which decreases as parasite prevalence declines, affects the optimal sexual development strategy: Within-host competition in multiclone infections favors a greater investment in asexual growth whereas single-clone infections benefit from higher conversion to sexual forms. At the same time, drug treatment also imposes selection pressure on sexual development by shortening infection length and reducing within-host competition. We assess these models using 148 P. falciparum parasite genomes sampled in French Guiana over an 18-y period of intensive intervention (1998 to 2015). During this time frame, multiple public health measures, including the introduction of new drugs and expanded rapid diagnostic testing, were implemented, reducing P. falciparum malaria cases by an order of magnitude. Consistent with this prevalence decline, we see an increase in the relatedness among parasites, but no single clonal background grew to dominate the population. Analyzing individual allele frequency trajectories, we identify genes that likely experienced selective sweeps. Supporting our model predictions, genes showing the strongest signatures of selection include transcription factors involved in the development of P. falciparum’s sexual gametocyte form. These results highlight how public health interventions impose wide-ranging selection pressures that affect basic parasite life history traits.
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12
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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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13
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An In Silico Analysis of Malaria Pre-Erythrocytic-Stage Antigens Interpreting Worldwide Genetic Data to Suggest Vaccine Candidate Variants and Epitopes. Microorganisms 2022; 10:microorganisms10061090. [PMID: 35744609 PMCID: PMC9231253 DOI: 10.3390/microorganisms10061090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Failure to account for genetic diversity of antigens during vaccine design may lead to vaccine escape. To evaluate the vaccine escape potential of antigens used in vaccines currently in development or clinical testing, we surveyed the genetic diversity, measured population differentiation, and performed in silico prediction and analysis of T-cell epitopes of ten such Plasmodium falciparum pre-erythrocytic-stage antigens using whole-genome sequence data from 1010 field isolates. Of these, 699 were collected in Africa (Burkina Faso, Cameroon, Guinea, Kenya, Malawi, Mali, and Tanzania), 69 in South America (Brazil, Colombia, French Guiana, and Peru), 59 in Oceania (Papua New Guinea), and 183 in Asia (Cambodia, Myanmar, and Thailand). Antigens surveyed include cell-traversal protein for ookinetes and sporozoites, circumsporozoite protein, liver-stage antigens 1 and 3, sporozoite surface proteins P36 and P52, sporozoite asparagine-rich protein-1, sporozoite microneme protein essential for cell traversal-2, and upregulated-in-infectious-sporozoite 3 and 4 proteins. The analyses showed that a limited number of these protein variants, when combined, would be representative of worldwide parasite populations. Moreover, predicted T-cell epitopes were identified that could be further explored for immunogenicity and protective efficacy. Findings can inform the rational design of a multivalent malaria vaccine.
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14
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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15
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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Affiliation(s)
- Myo T. Naung
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Elijah Martin
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Jacob Munro
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Somya Mehra
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Andrew J. Guy
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - G. L. Abby Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Livingstone Tavul
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel Hetzel
- Swiss Tropical Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dominic Kwiatkowski
- Sanger Institute, Hinxton, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Division of Parasites and Insect Vectors, Pasteur Institute, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
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16
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Oduma CO, Koepfli C. Plasmodium falciparum and Plasmodium vivax Adjust Investment in Transmission in Response to Change in Transmission Intensity: A Review of the Current State of Research. Front Cell Infect Microbiol 2021; 11:786317. [PMID: 34956934 PMCID: PMC8692836 DOI: 10.3389/fcimb.2021.786317] [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: 09/30/2021] [Accepted: 11/19/2021] [Indexed: 12/02/2022] Open
Abstract
Malaria parasites can adjust the proportion of parasites that develop into gametocytes, and thus the probability for human-to-vector transmission, through changes in the gametocyte conversion rate. Understanding the factors that impact the commitment of malaria parasites to transmission is required to design better control interventions. Plasmodium spp. persist across countries with vast differences in transmission intensities, and in sites where transmission is highly seasonal. Mounting evidence shows that Plasmodium spp. adjusts the investment in transmission according to seasonality of vector abundance, and transmission intensity. Various techniques to determine the investment in transmission are available, i.e., short-term culture, where the conversion rate can be measured most directly, genome and transcriptome studies, quantification of mature gametocytes, and mosquito feeding assays. In sites with seasonal transmission, the proportion of gametocytes, their densities and infectivity are higher during the wet season, when vectors are plentiful. When countries with pronounced differences in transmission intensity were compared, the investment in transmission was higher when transmission was low, thus maximizing the parasite’s chances to be transmitted to mosquitoes. Increased transmissibility of residual infections after a successful reduction of malaria transmission levels need to be considered when designing intervention measures.
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Affiliation(s)
- Colins O Oduma
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya.,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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17
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Usui M, Williamson KC. Stressed Out About Plasmodium falciparum Gametocytogenesis. Front Cell Infect Microbiol 2021; 11:790067. [PMID: 34926328 PMCID: PMC8674873 DOI: 10.3389/fcimb.2021.790067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 11/21/2022] Open
Abstract
Blocking malaria transmission is critical to malaria control programs but remains a major challenge especially in endemic regions with high levels of asymptomatic infections. New strategies targeting the transmissible sexual stages of the parasite, called gametocytes, are needed. This review focuses on P. falciparum gametocytogenesis in vivo and in vitro. Highlighting advances made elucidating genes required for gametocyte production and identifying key questions that remain unanswered such as the factors and regulatory mechanisms that contribute to gametocyte induction, and the mechanism of sequestration. Tools available to begin to address these issues are also described to facilitate advances in our understanding of this important stage of the life cycle.
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Affiliation(s)
- Miho Usui
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kim C Williamson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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18
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Grace CA, Forrester S, Silva VC, Carvalho KSS, Kilford H, Chew YP, James S, Costa DL, Mottram JC, Costa CCHN, Jeffares DC. Candidates for Balancing Selection in Leishmania donovani Complex Parasites. Genome Biol Evol 2021; 13:6448231. [PMID: 34865011 PMCID: PMC8717319 DOI: 10.1093/gbe/evab265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
The Leishmania donovani species complex is the causative agent of visceral leishmaniasis, which cause 20–40,000 fatalities a year. Here, we conduct a screen for balancing selection in this species complex. We used 384 publicly available L. donovani and L. infantum genomes, and sequence 93 isolates of L. infantum from Brazil to describe the global diversity of this species complex. We identify five genetically distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We find that signals of balancing selection are generally not shared between populations, consistent with transient adaptive events, rather than long-term balancing selection. We then apply multiple diversity metrics to identify candidate genes with robust signatures of balancing selection, identifying a curated set of 24 genes with robust signatures. These include zeta toxin, nodulin-like, and flagellum attachment proteins. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides genes for further study.
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Affiliation(s)
- Cooper Alastair Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Sarah Forrester
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Vladimir Costa Silva
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Kátia Silene Sousa Carvalho
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Hannah Kilford
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Yen Peng Chew
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom.,Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sally James
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Dorcas L Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Jeremy C Mottram
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Carlos C H N Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Daniel C Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
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19
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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20
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Koepfli C, Nguitragool W, de Almeida ACG, Kuehn A, Waltmann A, Kattenberg E, Ome-Kaius M, Rarau P, Obadia T, Kazura J, Monteiro W, Darcy AW, Wini L, Bassat Q, Felger I, Sattabongkot J, Robinson LJ, Lacerda M, Mueller I. Identification of the asymptomatic Plasmodium falciparum and Plasmodium vivax gametocyte reservoir under different transmission intensities. PLoS Negl Trop Dis 2021; 15:e0009672. [PMID: 34449764 PMCID: PMC8428688 DOI: 10.1371/journal.pntd.0009672] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 09/09/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Background Understanding epidemiological variables affecting gametocyte carriage and density is essential to design interventions that most effectively reduce malaria human-to-mosquito transmission. Methodology/Principal findings Plasmodium falciparum and P. vivax parasites and gametocytes were quantified by qPCR and RT-qPCR assays using the same methodologies in 5 cross-sectional surveys involving 16,493 individuals in Brazil, Thailand, Papua New Guinea, and Solomon Islands. The proportion of infections with detectable gametocytes per survey ranged from 44–94% for P. falciparum and from 23–72% for P. vivax. Blood-stage parasite density was the most important predictor of the probability to detect gametocytes. In moderate transmission settings (prevalence by qPCR>5%), parasite density decreased with age and the majority of gametocyte carriers were children. In low transmission settings (prevalence<5%), >65% of gametocyte carriers were adults. Per survey, 37–100% of all individuals positive for gametocytes by RT-qPCR were positive by light microscopy for asexual stages or gametocytes (overall: P. falciparum 178/348, P. vivax 235/398). Conclusions/Significance Interventions to reduce human-to-mosquito malaria transmission in moderate-high endemicity settings will have the greatest impact when children are targeted. In contrast, all age groups need to be included in control activities in low endemicity settings to achieve elimination. Detection of infections by light microscopy is a valuable tool to identify asymptomatic blood stage infections that likely contribute most to ongoing transmission at the time of sampling. Plasmodium vivax and Plasmodium falciparum cause the vast majority of all human malaria cases. Across all transmission settings, a large proportion of infections of the two species remain asymptomatic. These infections are not diagnosed and treated by control programs focusing on clinical cases. They can carry gametocytes, the sexual stage of the parasite that establishes infections in mosquitos, thus asymptomatic infections contribute to transmission. In order to determine who is likely to contribute to transmission, gametocyte densities were measured by sensitive molecular methods in afebrile individuals in four countries. The proportion of infections with gametocytes varied greatly among surveys, and was higher in regions that had experienced low transmission for extended periods of time. In moderate-high transmission settings, gametocyte densities were particularly high in children below six years, highlighting the importance that interventions to reduce transmission include this age group. The majority of gametocyte carriers was positive by light microscopy. The comprehensive data on gametocyte carriage presented here lays the foundation for the development of more effective screen and treat activities to reduce malaria transmission.
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Affiliation(s)
- Cristian Koepfli
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- University of Notre Dame, Eck Institute for Global Health, Department of Biological Sciences, Notre Dame, Indiana, United States of America
- * E-mail:
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anne Cristine Gomes de Almeida
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
- Universidade do Estado do Amazonas, Manaus, Brazil
| | - Andrea Kuehn
- ISGlobal, Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
| | - Andreea Waltmann
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Eline Kattenberg
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Maria Ome-Kaius
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Patricia Rarau
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Thomas Obadia
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
- Unité Malaria: parasites et Hôtes, Département Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
| | - James Kazura
- Centre for Global Health & Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Wuelton Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
- Universidade do Estado do Amazonas, Manaus, Brazil
| | - Andrew W. Darcy
- National Health Training and Research Institute, Ministry of Health, Honiara, Solomon Islands
| | - Lyndes Wini
- Vector Borne Diseases Program, Ministry of Health, Honiara, Solomon Islands
| | - Quique Bassat
- ISGlobal, Hospital Clínic—Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Leanne J. Robinson
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Marcus Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Unité Malaria: parasites et Hôtes, Département Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
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21
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Whitlock AOB, Juliano JJ, Mideo N. Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread. PLoS Comput Biol 2021; 17:e1008577. [PMID: 34280179 PMCID: PMC8321109 DOI: 10.1371/journal.pcbi.1008577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/29/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
Although drug resistance in Plasmodium falciparum typically evolves in regions of low transmission, resistance spreads readily following introduction to regions with a heavier disease burden. This suggests that the origin and the spread of resistance are governed by different processes, and that high transmission intensity specifically impedes the origin. Factors associated with high transmission, such as highly immune hosts and competition within genetically diverse infections, are associated with suppression of resistant lineages within hosts. However, interactions between these factors have rarely been investigated and the specific relationship between adaptive immunity and selection for resistance has not been explored. Here, we developed a multiscale, agent-based model of Plasmodium parasites, hosts, and vectors to examine how host and parasite dynamics shape the evolution of resistance in populations with different transmission intensities. We found that selection for antigenic novelty (“immune selection”) suppressed the evolution of resistance in high transmission settings. We show that high levels of population immunity increased the strength of immune selection relative to selection for resistance. As a result, immune selection delayed the evolution of resistance in high transmission populations by allowing novel, sensitive lineages to remain in circulation at the expense of the spread of a resistant lineage. In contrast, in low transmission settings, we observed that resistant strains were able to sweep to high population prevalence without interference. Additionally, we found that the relationship between immune selection and resistance changed when resistance was widespread. Once resistance was common enough to be found on many antigenic backgrounds, immune selection stably maintained resistant parasites in the population by allowing them to proliferate, even in untreated hosts, when resistance was linked to a novel epitope. Our results suggest that immune selection plays a role in the global pattern of resistance evolution. Drug resistance in the malaria parasite, Plasmodium falciparum, presents an ongoing public health challenge, but aspects of its evolution are poorly understood. Although antimalarial resistance is common worldwide, it can typically be traced to just a handful of evolutionary origins. Counterintuitively, although Sub Saharan Africa bears 90% of the global malaria burden, resistance typically originates in regions where transmission intensity is low. In high transmission regions, infections are genetically diverse, and hosts have significant standing adaptive immunity, both of which are known to suppress the frequency of resistance within infections. However, interactions between immune-driven selection, transmission intensity, and resistance have not been investigated. Using a multiscale, agent-based model, we found that high transmission intensity slowed the evolution of resistance via its effect on host population immunity. High host immunity strengthened selection for antigenic novelty, interfering with selection for resistance and allowing sensitive lineages to suppress resistant lineages in untreated hosts. However, once resistance was common in the circulating parasite population, immune selection maintained it in the population at a high prevalence. Our findings provide a novel explanation for observations about the origin of resistance and suggest that adaptive immunity is a critical component of selection.
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Affiliation(s)
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Canada
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22
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441 DOI: 10.12688/wellcomeopenres.16168.1] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
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23
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441.2 DOI: 10.12688/wellcomeopenres.16168.2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
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24
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Ndwiga L, Osoti V, Ochwedo KO, Wamae K, Bejon P, Rayner JC, Githinji G, Ochola-Oyier LI. The Plasmodium falciparum Rh5 invasion protein complex reveals an excess of rare variant mutations. Malar J 2021; 20:278. [PMID: 34162366 PMCID: PMC8220363 DOI: 10.1186/s12936-021-03815-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 06/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The invasion of the red blood cells by Plasmodium falciparum merozoites involves the interplay of several proteins that are also targets for vaccine development. The proteins PfRh5-PfRipr-PfCyRPA-Pfp113 assemble into a complex at the apical end of the merozoite and are together essential for erythrocyte invasion. They have also been shown to induce neutralizing antibodies and appear to be less polymorphic than other invasion-associated proteins, making them high priority blood-stage vaccine candidates. Using available whole genome sequencing data (WGS) and new capillary sequencing data (CS), this study describes the genetic polymorphism in the Rh5 complex in P. falciparum isolates obtained from Kilifi, Kenya. METHODS 162 samples collected in 2013 and 2014 were genotyped by capillary sequencing (CS) and re-analysed WGS from 68 culture-adapted P. falciparum samples obtained from a drug trial conducted from 2005 to 2007. The frequency of polymorphisms in the merozoite invasion proteins, PfRh5, PfRipr, PfCyRPA and PfP113 were examined and where possible polymorphisms co-occurring in the same isolates. RESULTS From a total 70 variants, including 2 indels, 19 SNPs [27.1%] were identified by both CS and WGS, while an additional 15 [21.4%] and 36 [51.4%] SNPs were identified only by either CS or WGS, respectively. All the SNPs identified by CS were non-synonymous, whereas WGS identified 8 synonymous and 47 non-synonymous SNPs. CS identified indels in repeat regions in the p113 gene in codons 275 and 859 that were not identified in the WGS data. The minor allele frequencies of the SNPs ranged between 0.7 and 34.9% for WGS and 1.1-29.6% for CS. Collectively, 12 high frequency SNPs (> 5%) were identified: four in Rh5 codon 147, 148, 203 and 429, two in p113 at codons 7 and 267 and six in Ripr codons 190, 259, 524, 985, 1003 and 1039. CONCLUSION This study reveals that the majority of the polymorphisms are rare variants and confirms a low level of genetic polymorphisms in all proteins within the Rh5 complex.
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Affiliation(s)
- Leonard Ndwiga
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
| | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
| | - Kevin Omondi Ochwedo
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Kevin Wamae
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
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25
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:843. [PMID: 34070769 PMCID: PMC8228830 DOI: 10.3390/genes12060843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth-the number of Plasmodium species' genomes sequenced-and in depth-massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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Affiliation(s)
| | - Gareth D. Weedall
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
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26
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Shah Z, Naung MT, Moser KA, Adams M, Buchwald AG, Dwivedi A, Ouattara A, Seydel KB, Mathanga DP, Barry AE, Serre D, Laufer MK, Silva JC, Takala-Harrison S. Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria. PLoS Genet 2021; 17:e1009576. [PMID: 34033654 PMCID: PMC8184011 DOI: 10.1371/journal.pgen.1009576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/07/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. Immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode possible targets of naturally acquired immunity that should be validated immunologically and further characterized for their potential as vaccine candidates.
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Affiliation(s)
- Zalak Shah
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Myo T. Naung
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Kara A. Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Andrea G. Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Karl B. Seydel
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Don P. Mathanga
- University of Malawi College of Medicine, Malaria Alert Centre, Blantyre, Malawi
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- Disease Elimination and Maternal and Child Health, Burnet Institute, Melbourne, Victoria, Australia
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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27
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Abera D, Kibet CK, Degefa T, Amenga-Etego L, Bargul JL, Golassa L. Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia. Malar J 2021; 20:129. [PMID: 33663492 PMCID: PMC7934276 DOI: 10.1186/s12936-021-03660-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/20/2021] [Indexed: 11/12/2022] Open
Abstract
Background Plasmodium falciparum parasite populations in Ethiopia have been experiencing local selective pressures from drugs and immunity, leading to evolutionary adaptation. However, there was a paucity of data on genomic characterization and evolutionary adaptations of P. falciparum isolates from the central area of Ethiopia. Methods Whole-genome analysis of 25 P. falciparum isolates from central Ethiopia, specifically from West Arsi, were studied to determine their genetic diversity, population structures, and signatures of selection in known drug resistance alleles against global isolates from Cambodia, Thailand, DR Congo, and Malawi. Results A total of 18,517 high-quality single-nucleotide polymorphisms (SNPs) were identified in Ethiopian P. falciparum isolates. About 84% of the Ethiopian P. falciparum isolates had a FWS value > 0.95 showing a dominant single genotype infection in most isolates at the time of collection with little potential for out-crossing as expected in areas with low transmission intensity. Within-host diversity of Ethiopian infections was significantly different from East African (p < 0.001), but not Southeast Asian infections (P > 0.05). A significant population structure has been observed by PCA and population differentiation between Ethiopian parasites and East African (Fst ~ 10%) and Southeast Asian populations (Fst ~ 18%), suggesting limited gene flow and the independent evolution of the Ethiopian parasite population. Moreover, a total of 125 genes under balancing selection was found that include ama1, trap, eba175, and lsa3, previously identified as targets of human host immunity. Recent directional selection analysis using integrated standardized haplotype score (IHS) did not detect any selection signatures in the Pfcrt, Pfdhfr, Pfdhps, Pfmdr1, and PfK13 genes. However, known drug resistance-conferring mutations analysis showed that at least one SNP marker was fixed in these genes, but not in Pfdhps and PfK13. Conclusion Plasmodium falciparum populations in the central region of Ethiopia was structurally diverged from both Southeast Asian and other East African populations. Malaria infections in Ethiopia had low within-host diversity, and parasites carry fixed chloroquine resistance markers despite the withdrawal of this drug for the treatment of P. falciparum. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03660-y.
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Affiliation(s)
- Deriba Abera
- Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.,School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Caleb K Kibet
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Teshome Degefa
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Joel L Bargul
- Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.,International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
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Shi SM, Shi TQ, Chen SB, Cui YB, Kassegne K, Okpeku M, Chen JH, Shen HM. Genome-Wide Scans for Ghanaian Plasmodium falciparum Genes Under Selection From Local and Chinese Host Populations. Front Cell Infect Microbiol 2021; 11:630797. [PMID: 33718278 PMCID: PMC7947188 DOI: 10.3389/fcimb.2021.630797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/07/2021] [Indexed: 01/02/2023] Open
Abstract
Initial malarial infection mostly causes symptomatic illness in humans. Infection that is not fatal induces complete protection from severe illness and death, and thus complete protection from severe illness or death is granted with sufficient exposure. However, malaria parasite immunity necessitates constant exposure. Therefore, it is important to evaluate lowered immunity and recurrent susceptibility to symptomatic disease in lower transmission areas. We aimed to investigate selection pressure based on transmission levels, antimalarial drug use, and environmental factors. We whole genome sequenced (WGS) P. falciparum clinical samples from Chinese hosts working in Ghana and compared the results with the WGS data of isolates from native Ghanaians downloaded from pf3k. The P. falciparum samples were generally clustered according to their geographic origin, and Chinese imported samples showed a clear African origin with a slightly different distribution from the native Ghanaian samples. Moreover, samples collected from two host populations showed evidence of differences in the intensity of selection. Compared with native Ghanaian samples, the China-imported isolates exhibited a higher proportion of monoclonal infections, and many genes associated with RBC invasion and immune evasion were found to be under less selection pressure. There was no significant difference in the selection of drug-resistance genes due to a similar artemisinin-based combination therapy medication profile. Local selection of malarial parasites is considered to be a result of differences in the host immunity or disparity in the transmission opportunities of the host. In China, most P. falciparum infections were imported from Africa, and under these circumstances, distinct local selective pressures may be caused by varying acquired immunity and transmission intensity. This study revealed the impact of host switching on the immune system, and it may provide a better understanding of the mechanisms that enable clinical immunity to malaria.
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Affiliation(s)
- Shan-Mei Shi
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Tian-Qi Shi
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Kokouvi Kassegne
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Moses Okpeku
- Discipline of Genetics, School of Life Science, University of Kwazulu-Natal, Durban, South Africa
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention⁃Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, National Centre for International Research on Tropical Diseases, WHO Collaborating Center for Tropical Diseases, Shanghai, China
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Gwarinda HB, Tessema SK, Raman J, Greenhouse B, Birkholtz LM. Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa. Malar J 2021; 20:96. [PMID: 33593382 PMCID: PMC7885214 DOI: 10.1186/s12936-021-03635-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterized the genetic diversity of parasites circulating within the Vhembe District. METHODS A total of 1153 falciparum-positive rapid diagnostic tests (RDTs) were randomly collected from seven clinics within the district, over three consecutive years (2016, 2017 and 2018) during the wet and dry malaria transmission seasons. Using 26 neutral microsatellite markers, differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), inbreeding metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation, and were associated with temporal and geospatial variances. RESULTS A total of 747 (65%) samples were successfully genotyped. Moderate to high genetic diversity (mean He = 0.74 ± 0.03) was observed in the parasite population. This was ascribed to high allelic richness (mean A = 12.2 ± 1.2). The majority of samples (99%) had unique multi-locus genotypes, indicating high genetic diversity in the sample set. Complex infections were observed in 66% of samples (mean MOI = 2.13 ± 0.04), with 33% of infections showing high within-host diversity as described by the Fws metric. Low, but significant LD (standardised index of association, ISA = 0.08, P < 0.001) was observed that indicates recombination of distinct clones. Limited impact of temporal (FST range - 0.00005 to 0.0003) and spatial (FST = - 0.028 to 0.023) variation on genetic diversity existed during the sampling timeframe and study sites respectively. CONCLUSIONS Consistent with the Vhembe District's classification as a 'high' transmission setting within South Africa, P. falciparum diversity in the area was moderate to high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This data can be used as a reference point for the assessment of the effectiveness of on-going interventions over time, the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance.
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Affiliation(s)
- Hazel B Gwarinda
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - Sofonias K Tessema
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jaishree Raman
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Gauteng, South Africa.,Wits Research Institute for Malaria, Faculty of Health Sciences,, University of Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa.
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Myers KN, Conn D, Brown AMV. Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest. mSystems 2021; 6:e01048-20. [PMID: 33531407 PMCID: PMC7857533 DOI: 10.1128/msystems.01048-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.
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Affiliation(s)
- Kaitlyn N Myers
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Daniel Conn
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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Kassegne K, Komi Koukoura K, Shen HM, Chen SB, Fu HT, Chen YQ, Zhou XN, Chen JH, Cheng Y. Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes. Front Immunol 2020; 11:552698. [PMID: 33193320 PMCID: PMC7645038 DOI: 10.3389/fimmu.2020.552698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022] Open
Abstract
Malaria is a public health concern worldwide, and Togo has proven to be no exception. Effective approaches to provide information on biological insights for disease elimination are therefore a research priority. Local selection on malaria pathogens is due to multiple factors including host immunity. We undertook genome-wide analysis of sequence variation on a sample of 10 Plasmodium falciparum (Pf) clinical isolates from Togo to identify local-specific signals of selection. Paired-end short-read sequences were mapped and aligned onto > 95% of the 3D7 Pf reference genome sequence in high fold coverage. Data on 266 963 single nucleotide polymorphisms were obtained, with average nucleotide diversity π = 1.79 × 10−3. Both principal component and neighbor-joining tree analyses showed that the Togo parasites clustered according to their geographic (Africa) origin. In addition, the average genome-wide diversity of Pf from Togo was much higher than that from other African samples. Tajima’s D value of the Togo isolates was −0.56, suggesting evidence of directional selection and/or recent population expansion. Against this background, within-population analyses identifying loci of balancing and recent positive selections evidenced that host immunity has been the major selective agent. Importantly, 87 and 296 parasite antigen genes with Tajima’s D values > 1 and in the top 1% haplotype scores, respectively, include a significant representation of membrane proteins at the merozoite stage that invaded red blood cells (RBCs) and parasitized RBCs surface proteins that play roles in immunoevasion, adhesion, or rosetting. This is consistent with expectations that elevated signals of selection due to allele-specific acquired immunity are likely to operate on antigenic targets. Collectively, our data suggest a recent expansion of Pf population in Togo and evidence strong host immune selection on membrane/surface antigens reflected in signals of balancing/positive selection of important gene loci. Findings from this study provide a fundamental basis to engage studies for effective malaria control in Togo.
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Affiliation(s)
- Kokouvi Kassegne
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Komi Komi Koukoura
- Laboratoire des Sciences Biomédicales, Alimentaires et Santé Environnementale, Département des Analyses Biomédicales, Ecole Supérieure des Techniques Biologiques et Alimentaires, Université de Lomé, Lomé, Togo
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Hai-Tian Fu
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yong-Quan Chen
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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Roh ME, Tessema SK, Murphy M, Nhlabathi N, Mkhonta N, Vilakati S, Ntshalintshali N, Saini M, Maphalala G, Chen A, Wilheim J, Prach L, Gosling R, Kunene S, S Hsiang M, Greenhouse B. High Genetic Diversity of Plasmodium falciparum in the Low-Transmission Setting of the Kingdom of Eswatini. J Infect Dis 2020; 220:1346-1354. [PMID: 31190073 PMCID: PMC6743842 DOI: 10.1093/infdis/jiz305] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To better understand transmission dynamics, we characterized Plasmodium falciparum genetic diversity in Eswatini, where transmission is low and sustained by importation. METHODS Twenty-six P. falciparum microsatellites were genotyped in 66% of confirmed cases (2014-2016; N = 582). Population and within-host diversity were used to characterize differences between imported and locally acquired infections. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone. RESULTS Parasite population in Eswatini was highly diverse (expected heterozygosity [HE] = 0.75) and complex: 67% polyclonal infections, mean multiplicity of infection (MOI) 2.2, and mean within-host infection fixation index (FWS) 0.84. Imported cases had comparable diversity to local cases but exhibited higher MOI (2.4 vs 2.0; P = .004) and lower mean FWS (0.82 vs 0.85; P = .03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections. CONCLUSIONS In contrast to the common perception that P. falciparum diversity declines with decreasing transmission intensity, Eswatini isolates exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.
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Affiliation(s)
- Michelle E Roh
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Sofonias K Tessema
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Maxwell Murphy
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | | | | | | | | | - Manik Saini
- Clinton Health Access Initiative, Mbabane, Eswatini
| | | | - Anna Chen
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Jordan Wilheim
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Lisa Prach
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco
| | - Roly Gosling
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | | | - Michelle S Hsiang
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Pediatrics, University of California, San Francisco.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco.,Chan Zuckerberg Biohub, San Francisco, California
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Bungei JK, Mobegi VA, Nyanjom SG. Single-nucleotide polymorphism characterization of gametocyte development 1 gene in Plasmodium falciparum isolates from Baringo, Uasin Gishu, and Nandi Counties, Kenya. Heliyon 2020; 6:e03453. [PMID: 32154414 PMCID: PMC7056661 DOI: 10.1016/j.heliyon.2020.e03453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/18/2020] [Accepted: 02/17/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Plasmodium falciparum relies on gametocytogenesis to transmit from humans to mosquitoes. Gametocyte development 1 (Pfgdv1) is an upstream activator and epigenetic controller of gametocytogenesis. The emergence of drug resistance is a major public health concern and this requires the development of new strategies that target the transmission of malaria. As a putative drug target, Pfgdv1 has not been characterized to identify its polymorphisms and alleles under selection and how such polymorphisms influence protein structure. METHODS This study characterized single-nucleotide polymorphisms (SNPs) in primary sequences (n = 30) of Pfgdv1 gene generated from thirty blood samples collected from patients infected with P. falciparum and secondary sequences (n = 216) retrieved from PlasmoDB. ChromasPro, MUSCLE, Tajima's D statistic, SLAC, and STRUM were used in editing raw sequences, performing multiple sequence alignment (MSA), identifying signatures of selection, detecting codon sites under selection pressure, and determining the effect of SNPs, respectively. RESULTS MSA of primary and secondary sequences established the existence of five SNPs, consisting of four non-synonymous substitutions (nsSNPs) (p.P217H, p.R398Q, p.H417N, and p.D497E), and a synonymous substitution (p.S514S). The analysis of amino acid changes reveals that p.P217H, p.R398Q, and p.H417N comprise non-conservative changes. Tajima's D statistic showed that these SNPs were under balancing selection, while SLAC analysis identified p.P217H to be under the strongest positive selection. . Further analysis based on thermodynamics indicated that p.P217H has a destabilizing effect, while p.R398Q and p.D497E have stabilizing effects on the protein structure. CONCLUSIONS The existence of four nsSNPs implies that Pfgdv1 has a minimal diversity in the encoded protein. Selection analysis demonstrates that these nsSNPs are under balancing selection in both local and global populations. However, p.P217H exhibits positive directional selection consistent with previous reports where it showed differentiatial selection of P. falciparum in low and high transmission regions. Therefore, in-silico prediction and experimental determination of protein structure are necessary to evaluate Pfgdv1 as a target candidate for drug design and development.
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Affiliation(s)
- Josephat K. Bungei
- Department of Biochemistry, JKUAT, Kenya
- Department of Biochemistry, School of Medicine, University of Nairobi, Kenya
| | - Victor A. Mobegi
- Department of Biochemistry, School of Medicine, University of Nairobi, Kenya
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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Ajibaye O, Osuntoki AA, Balogun EO, Olukosi YA, Iwalokun BA, Oyebola KM, Hikosaka K, Watanabe YI, Ebiloma GU, Kita K, Amambua-Ngwa A. Genetic polymorphisms in malaria vaccine candidate Plasmodium falciparum reticulocyte-binding protein homologue-5 among populations in Lagos, Nigeria. Malar J 2020; 19:6. [PMID: 31906953 PMCID: PMC6945540 DOI: 10.1186/s12936-019-3096-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/26/2019] [Indexed: 01/26/2023] Open
Abstract
Background Vaccines are the most reliable alternative to elicit sterile immunity against malaria but their development has been hindered by polymorphisms and strain-specificity in previously studied antigens. New vaccine candidates are therefore urgently needed. Highly conserved Plasmodium falciparum reticulocyte-binding protein homologue-5 (PfRH5) has been identified as a potential candidate for anti-disease vaccine development. PfRH5 is essential for erythrocyte invasion by merozoites and crucial for parasite survival. However, there is paucity of data on the extent of genetic variations on PfRH5 in field isolates of Plasmodium falciparum. This study described genetic polymorphisms at the high affinity binding polypeptides (HABPs) 36718, 36727, 36728 of PfRH5 in Nigerian isolates of P. falciparum. This study tested the hypothesis that only specific conserved B and T cell epitopes on PfRH5 HABPs are crucial for vaccine development. Methods One hundred and ninety-five microscopically confirmed P. falciparum samples collected in a prospective cross-sectional study of three different populations in Lagos, Nigeria. Genetic diversity and haplotype construct of Pfrh5 gene were determined using bi-directional sequencing approach. Tajima’s D and the ratio of nonsynonymous vs synonymous mutations were utilized to estimate the extent of balancing and directional selection in the pfrh5 gene. Results Sequence analysis revealed three haplotypes of PfRH5 with negative Tajima’s D and dN/dS value of − 1.717 and 0.011 ± 0.020, respectively. A single nucleotide polymorphism, SNP (G → A) at position 608 was observed, which resulted in a change of the amino acid cysteine at position 203 to tyrosine. Haplotype and nucleotide diversities were 0.318 ± 0.016 and 0.0046 ± 0.0001 while inter-population genetic differentiation ranged from 0.007 to 0.037. Five polypeptide variants were identified, the most frequent being KTKYH with a frequency of 51.3%. One B-cell epitope, 151 major histocompatibility complex (MHC) class II T-cell epitopes, four intrinsically unstructured regions (IURs) and six MHC class I T-cell epitopes were observed in the study. Phylogenetic analysis of the sequences showed clustering and evidence of evolutionary relationship with 3D7, PAS-2 and FCB-2 RH5 sequences. Conclusions This study has revealed low level of genetic polymorphisms in PfRH5 antigen with B- and T-cell epitopes in intrinsically unstructured regions along the PfRH5 gene in Lagos, Nigeria. A broader investigation is however required in other parts of the country to support the possible inclusion of PfRH5 in a cross-protective multi-component vaccine.
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Affiliation(s)
- Olusola Ajibaye
- Department of Biochemistry & Nutrition, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria. .,Department of Biochemistry, College of Medicine, University of Lagos, Idi-Araba, Lagos, Nigeria.
| | - Akinniyi A Osuntoki
- Department of Biochemistry, College of Medicine, University of Lagos, Idi-Araba, Lagos, Nigeria
| | - Emmanuel O Balogun
- Department of Biochemistry, Ahmadu Bello University, 2222, Zaria, Nigeria.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yetunde A Olukosi
- Department of Biochemistry & Nutrition, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Bamidele A Iwalokun
- Department of Biochemistry & Nutrition, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Kolapo M Oyebola
- Department of Biochemistry & Nutrition, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.,Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - Kenji Hikosaka
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yoh-Ichi Watanabe
- Department of Biochemistry, Ahmadu Bello University, 2222, Zaria, Nigeria
| | - Godwin U Ebiloma
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Alfred Amambua-Ngwa
- Medical Research Council at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
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Tessema SK, Raman J, Duffy CW, Ishengoma DS, Amambua-Ngwa A, Greenhouse B. Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa. Malar J 2019; 18:268. [PMID: 31477139 PMCID: PMC6720407 DOI: 10.1186/s12936-019-2880-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/11/2019] [Indexed: 01/13/2023] Open
Abstract
Next-generation sequencing (NGS) technologies are increasingly being used to address a diverse range of biological and epidemiological questions. The current understanding of malaria transmission dynamics and parasite movement mainly relies on the analyses of epidemiologic data, e.g. case counts and self-reported travel history data. However, travel history data are often not routinely collected or are incomplete, lacking the necessary level of accuracy. Although genetic data from routinely collected field samples provides an unprecedented opportunity to track the spread of malaria parasites, it remains an underutilized resource for surveillance due to lack of local awareness and capacity, limited access to sensitive laboratory methods and associated computational tools and difficulty in interpreting genetic epidemiology data. In this review, the potential roles of NGS in better understanding of transmission patterns, accurately tracking parasite movement and addressing the emerging challenges of imported malaria in low transmission settings of sub-Saharan Africa are discussed. Furthermore, this review highlights the insights gained from malaria genomic research and challenges associated with integrating malaria genomics into existing surveillance tools to inform control and elimination strategies.
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Affiliation(s)
- Sofonias K Tessema
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Jaishree Raman
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Disease, Sandringham, Gauteng, South Africa
| | - Craig W Duffy
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - Deus S Ishengoma
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | | | - Bryan Greenhouse
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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Zhu SJ, Hendry JA, Almagro-Garcia J, Pearson RD, Amato R, Miles A, Weiss DJ, Lucas TC, Nguyen M, Gething PW, Kwiatkowski D, McVean G. The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria. eLife 2019; 8:e40845. [PMID: 31298657 PMCID: PMC6684230 DOI: 10.7554/elife.40845] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Furthermore, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.
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Affiliation(s)
- Sha Joe Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Jason A Hendry
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Jacob Almagro-Garcia
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard D Pearson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Roberto Amato
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Alistair Miles
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Daniel J Weiss
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Tim Cd Lucas
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Michele Nguyen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Peter W Gething
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Dominic Kwiatkowski
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
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Plasmodium falciparum sexual differentiation in malaria patients is associated with host factors and GDV1-dependent genes. Nat Commun 2019; 10:2140. [PMID: 31086187 PMCID: PMC6514009 DOI: 10.1038/s41467-019-10172-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 04/12/2019] [Indexed: 01/06/2023] Open
Abstract
Plasmodium sexual differentiation is required for malaria transmission, yet much remains unknown about its regulation. Here, we quantify early gametocyte-committed ring (gc-ring) stage, P. falciparum parasites in 260 uncomplicated malaria patient blood samples 10 days before maturation to transmissible stage V gametocytes using a gametocyte conversion assay (GCA). Seventy six percent of the samples have gc-rings, but the ratio of gametocyte to asexual-committed rings (GCR) varies widely (0–78%). GCR correlates positively with parasitemia and is negatively influenced by fever, not hematocrit, age or leukocyte counts. Higher expression levels of GDV1-dependent genes, ap2-g, msrp1 and gexp5, as well as a gdv1 allele encoding H217 are associated with high GCR, while high plasma lysophosphatidylcholine levels are associated with low GCR in the second study year. The results provide a view of sexual differentiation in the field and suggest key regulatory roles for clinical factors and gdv1 in gametocytogenesis in vivo. Here, the authors quantify early gametocyte-committed ring (gc-ring) stage Plasmodium falciparum parasites in 260 malaria patients 10 days before maturation to transmissible stage V gametocytes, and show that the ratio of circulating gc-rings is positively correlated with parasitemia and negatively correlated with body temperature.
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Ochola-Oyier LI, Wamae K, Omedo I, Ogola C, Matharu A, Musabyimana JP, Njogu FK, Marsh K. Few Plasmodium falciparum merozoite ligand and erythrocyte receptor pairs show evidence of balancing selection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:235-245. [PMID: 30735814 PMCID: PMC6403450 DOI: 10.1016/j.meegid.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/16/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023]
Abstract
Erythrocyte surface proteins have been identified as receptors of Plasmodium falciparum merozoite proteins. The ligand-receptor interactions enable the parasite to invade human erythrocytes, initiating the clinical symptoms of malaria. These interactions are likely to have had an evolutionary impact on the genes that encode the ligand and receptor proteins. We used sequence data from Kilifi, Kenya to detect departures from neutrality in a paired analysis of P. falciparum merozoite ligands and their erythrocyte receptor genes from the same population. We genotyped parasite and human DNA obtained from 93 individuals with severe malaria. We examined six merozoite ligands EBA175, EBL1, EBA140, MSP1, Rh4 and Rh5, and their corresponding erythrocyte receptors, glycophorin (Gyp) A, GypB, GypC, band 3, complement receptor (CR) 1 and basigin, focusing on the regions involved in the ligand-receptor interactions. Positive Tajima's D values (>1) were observed only in the MSP1 C-terminal region and EBA175 region II, while negative values (<-1) were observed in EBL-1 region II, Rh4, basigin exons 3 and 5, CR1 exon 5, Gyp B exons 2, 3 and 4 and Gyp C exon 2. Additionally, ebl-1 region II and basigin exon 3 showed extreme negative values in all three tests, Tajima's D, Fu & Li D* and F*, ≤ - 2. A large majority of the erythrocyte receptor and merozoite genes have a negative Tajima's D even when compared with previously published whole genome data. Thus, highlighting EBA175 region II and MSP1-33, as outlier genes with a positive Tajima's D (>1). Both these genes contain multiple polymorphisms, which in the case of EBA175 may counteract receptor polymorphisms and/or evade host immune responses and in MSP1 the polymorphisms may primarily evade host immune responses.
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MESH Headings
- Alleles
- Child
- Child, Preschool
- Erythrocytes/metabolism
- Erythrocytes/parasitology
- Female
- Gene Frequency
- Host-Parasite Interactions
- Humans
- Infant
- Infant, Newborn
- Ligands
- Malaria, Falciparum/genetics
- Malaria, Falciparum/metabolism
- Malaria, Falciparum/parasitology
- Male
- Merozoites/metabolism
- Models, Molecular
- Plasmodium falciparum/classification
- Plasmodium falciparum/physiology
- Polymorphism, Genetic
- Protein Conformation
- Protozoan Proteins/genetics
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- Lynette Isabella Ochola-Oyier
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya; Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya.
| | - Kevin Wamae
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Irene Omedo
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Christabel Ogola
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Abneel Matharu
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Jean Pierre Musabyimana
- Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, Chiromo Campus, University of Nairobi, P. O. Box 30197, Nairobi, Kenya
| | - Francis K Njogu
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - Kevin Marsh
- KEMRI-Wellcome Trust Collaborative Programme, P.O. Box 230, 80108 Kilifi, Kenya
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41
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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42
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Shen HM, Chen SB, Cui YB, Xu B, Kassegne K, Abe EM, Wang Y, Chen JH. Whole-genome sequencing and analysis of Plasmodium falciparum isolates from China-Myanmar border area. Infect Dis Poverty 2018; 7:118. [PMID: 30445995 PMCID: PMC6240207 DOI: 10.1186/s40249-018-0493-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND China has made progress in malaria control and aims to eliminate malaria nationwide, but implementing effective interventions along the border regions remain a huge task. The Plasmodium falciparum cases imported from Southeast Asia has frequently reported especially in the China-Myanmar border (CMB) area. Though, information is scant on P. falciparum genetic variability in this area. METHODS This study reported P. falciparum isolates genome sequence of six clinical isolates in the CMB area. Furthermore, we estimated the nucleotide diversity, Watterson's estimator and Tajima's D value for the whole genome mutation rate in slide window. RESULTS Our data were aligned onto 96.05-98.61% of the reference 3D7 genome in high fold coverages. Principal component analysis result showed that P. falciparum clustered generally according to their geographic origin. A total of 91 genes were identified as positive selection with Ka/Ks ratio significantly higher than 1, and most of them were multigene families encoding variant surface antigens (VSAs) such as var, rif and stevor. The enrichment of the positive selection on VSA genes implied that the environment complexity subjected CMB's P. falciparum to more pressure for survival. CONCLUSIONS Our research suggests that greater genetic diversity in CMB area and the positive selection signals in VSA genes, which allow P. falciparum to fit the host immune system well and aggravate the difficulty of treatment. Meanwhile, results obtained from this study will provide the fundamental basis for P. falciparum population genomic research in CMB area.
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Affiliation(s)
- Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Kokouvi Kassegne
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Eniola Michael Abe
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
| | - Yue Wang
- Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013 China
- Department of Microbiology and Microbial Engineering, School of Life Science, Fudan University, Shanghai, 200433 China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases, Shanghai, 200025 China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025 China
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Cole R, Viney M. The population genetics of parasitic nematodes of wild animals. Parasit Vectors 2018; 11:590. [PMID: 30424774 PMCID: PMC6234597 DOI: 10.1186/s13071-018-3137-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022] Open
Abstract
Parasitic nematodes are highly diverse and common, infecting virtually all animal species, and the importance of their roles in natural ecosystems is increasingly becoming apparent. How genes flow within and among populations of these parasites - their population genetics - has profound implications for the epidemiology of host infection and disease, and for the response of parasite populations to selection pressures. The population genetics of nematode parasites of wild animals may have consequences for host conservation, or influence the risk of zoonotic disease. Host movement has long been recognised as an important determinant of parasitic nematode population genetic structure, and recent research has also highlighted the importance of nematode life histories, environmental conditions, and other aspects of host ecology. Commonly, factors influencing parasitic nematode population genetics have been studied in isolation, such that an integrated view of the drivers of population genetic structure of parasitic nematodes is still lacking. Here, we seek to provide a comprehensive, broad, and integrative picture of these factors in parasitic nematodes of wild animals that will be a useful resource for investigators studying non-model parasitic nematodes in natural ecosystems. Increasingly, new methods of analysing the population genetics of nematodes are becoming available, and we consider the opportunities that these afford in resolving hitherto inaccessible questions of the population genetics of these important animals.
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Affiliation(s)
- Rebecca Cole
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
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44
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Plasmodium genomics: an approach for learning about and ending human malaria. Parasitol Res 2018; 118:1-27. [PMID: 30402656 DOI: 10.1007/s00436-018-6127-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
Malaria causes high levels of morbidity and mortality in human beings worldwide. According to the World Health Organization (WHO), about half a million people die of this disease each year. Malaria is caused by six species of parasites belonging to the Plasmodium genus: P. falciparum, P. knowlesi, P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. Currently, malaria is being kept under control with varying levels of elimination success in different countries. The development of new molecular tools as well as the use of next-generation sequencing (NGS) technologies and novel bioinformatic approaches has improved our knowledge of malarial epidemiology, diagnosis, treatment, vaccine development, and surveillance strategies. In this work, the genetics and genomics of human malarias have been analyzed. Since the first P. falciparum genome was sequenced in 2002, various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.
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45
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Nkhoma SC, Banda RL, Khoswe S, Dzoole-Mwale TJ, Ward SA. Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:414-424. [PMID: 30145390 PMCID: PMC6219893 DOI: 10.1016/j.meegid.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
Malaria-infected individuals often harbor mixtures of genetically distinct parasite genotypes. We studied intra-host dynamics of parasite genotypes co-infecting asymptomatic adults in an area of intense malaria transmission in Chikhwawa, Malawi. Serial blood samples (5 ml) were collected over seven consecutive days from 25 adults with asymptomatic Plasmodium falciparum malaria and analyzed to determine whether a single peripheral blood sample accurately captures within-host parasite diversity. Blood samples from three of the participants were also analyzed by limiting dilution cloning and SNP genotyping of the parasite clones isolated to examine both the number and relatedness of co-infecting parasite haplotypes. We observed rapid turnover of co-infecting parasite genotypes in 88% of the individuals sampled (n = 22) such that the genetic composition of parasites infecting these individuals changed dramatically over the course of seven days of follow up. Nineteen of the 25 individuals sampled (76%) carried multiple parasite genotypes at baseline. Analysis of serial blood samples from three of the individuals revealed that they harbored 6, 12 and 17 distinct parasite haplotypes respectively. Approximately 70% of parasite haplotypes recovered from the three extensively sampled individuals were unrelated (proportion of shared alleles <83.3%) and were deemed to have primarily arisen from superinfection (inoculation of unrelated parasite haplotypes through multiple mosquito bites). The rest were related at the half-sib level or greater and were deemed to have been inoculated into individual human hosts via parasite co-transmission from single mosquito bites. These findings add further to the growing weight of evidence indicating that a single blood sample poorly captures within-host parasite diversity and underscore the importance of repeated blood sampling to accurately capture within-host parasite ecology. Our data also demonstrate a more pronounced role for parasite co-transmission in generating within-host parasite diversity in high transmission settings than previously assumed. Taken together, these findings have important implications for understanding the evolution of drug resistance, malaria transmission, parasite virulence, allocation of gametocyte sex ratios and acquisition of malaria immunity.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; Wellcome Trust-Liverpool-Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool L69 3GF, UK.
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tamika J Dzoole-Mwale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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46
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Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray L, Stewart LB, D'Alessandro U, Otto TD, Kwiatkowski DP, Conway DJ. Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Sci Rep 2018; 8:15763. [PMID: 30361631 PMCID: PMC6202401 DOI: 10.1038/s41598-018-34078-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3'-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
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Affiliation(s)
- Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | | | | | - Mahamadou Diakite
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) and Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherches en Santé Publique (INRSP), Nouakchott, Mauritania
| | - Sarah J Tarr
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lee Murray
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lindsay B Stewart
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Umberto D'Alessandro
- MRC Gambia Unit, Fajara, The Gambia
- Disease Control Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK.
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Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia. Sci Rep 2018; 8:9687. [PMID: 29946063 PMCID: PMC6018809 DOI: 10.1038/s41598-018-28017-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022] Open
Abstract
Genome sequences of 247 Plasmodium falciparum isolates collected in The Gambia in 2008 and 2014 were analysed to identify changes possibly related to the scale-up of antimalarial interventions that occurred during this period. Overall, there were 15 regions across the genomes with signatures of positive selection. Five of these were sweeps around known drug resistance and antigenic loci. Signatures at antigenic loci such as thrombospodin related adhesive protein (Pftrap) were most frequent in eastern Gambia, where parasite prevalence and transmission remain high. There was a strong temporal differentiation at a non-synonymous SNP in a cysteine desulfarase (Pfnfs) involved in iron-sulphur complex biogenesis. During the 7-year period, the frequency of the lysine variant at codon 65 (Pfnfs-Q65K) increased by 22% (10% to 32%) in the Greater Banjul area. Between 2014 and 2015, the frequency of this variant increased by 6% (20% to 26%) in eastern Gambia. IC50 for lumefantrine was significantly higher in Pfnfs-65K isolates. This is probably the first evidence of directional selection on Pfnfs or linked loci by lumefantrine. Given the declining malaria transmission, the consequent loss of population immunity, and sustained drug pressure, it is important to monitor Gambian P. falciparum populations for further signs of adaptation.
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48
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Simam J, Rono M, Ngoi J, Nyonda M, Mok S, Marsh K, Bozdech Z, Mackinnon M. Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa. BMC Genomics 2018; 19:372. [PMID: 29783949 PMCID: PMC5963192 DOI: 10.1186/s12864-018-4689-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment. RESULTS In a survey of 183 fresh field isolates from three populations in Eastern Africa with different malaria transmission intensities, we identified 94 CNV loci using microarrays. All CNVs had low population frequencies (minor allele frequency < 5%) but each parasite isolate carried an average of 8 CNVs. Nine CNVs showed high levels of population differentiation (FST > 0.3) and nine exhibited significant clines in population frequency across a gradient in transmission intensity. The clearest example of this was a large deletion on chromosome 9 previously reported only in laboratory-adapted isolates. This deletion was present in 33% of isolates from a population with low and highly seasonal malaria transmission, and in < 9% of isolates from populations with higher transmission. Subsets of CNVs were strongly correlated in their population frequencies, implying co-selection. CONCLUSIONS These results support the hypothesis that CNVs are the target of selection in natural populations of P. falciparum. Their environment-specific patterns observed here imply an important role for them in conferring adaptability to the parasite thus enabling it to persist in its highly diverse ecological environment.
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Affiliation(s)
| | - Martin Rono
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Pwani University Bioscience Research Centre, Pwani University, Kilifi, Kenya
| | - Joyce Ngoi
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Mary Nyonda
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University, New York, USA
| | - Kevin Marsh
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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49
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Guy AJ, Irani V, Richards JS, Ramsland PA. Structural patterns of selection and diversity for Plasmodium vivax antigens DBP and AMA1. Malar J 2018; 17:183. [PMID: 29720179 PMCID: PMC5930944 DOI: 10.1186/s12936-018-2324-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/18/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Plasmodium vivax is a significant contributor to the global malaria burden, and a vaccine targeting vivax malaria is urgently needed. An understanding of the targets of functional immune responses during the course of natural infection will aid in the development of a vaccine. Antibodies play a key role in this process, with responses against particular epitopes leading to immune selection pressure on these epitopes. A number of techniques exist to estimate levels of immune selection pressure on particular epitopes, with a sliding window analysis often used to determine particular regions likely to be under immune pressure. However, such analysis neglects protein three-dimensional structural information. With this in mind, a newly developed tool, BioStructMap, was applied to two key antigens from Plasmodium vivax: PvAMA1 and PvDBP Region II. This tool incorporates structural information into tests of selection pressure. RESULTS Sequences from a number of populations were analysed, examining spatially-derived nucleotide diversity and Tajima's D over protein structures for PvAMA1 and PvDBP. Structural patterns of nucleotide diversity were similar across all populations examined, with Domain I of PvAMA1 having the highest nucleotide diversity and displaying significant signatures of immune selection pressure (Tajima's D > 0). Nucleotide diversity for PvDBP was highest bordering the dimerization and DARC-binding interface, although there was less evidence of immune selection pressure on PvDBP compared with PvAMA1. This study supports previous work that has identified Domain I as the main target of immune-mediated selection pressure for PvAMA1, and also supports studies that have identified functional epitopes within PvDBP Region II. CONCLUSIONS The BioStructMap tool was applied to leading vaccine candidates from P. vivax, to examine structural patterns of selection and diversity across a number of geographic populations. There were striking similarities in structural patterns of diversity across multiple populations. Furthermore, whilst regions of high diversity tended to surround conserved binding interfaces, a number of protein regions with very low diversity were also identified, and these may be useful targets for further vaccine development, given previous evidence of functional antibody responses against these regions.
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Affiliation(s)
- Andrew J Guy
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Immunology, Monash University, Melbourne, Australia
| | - Vashti Irani
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Jack S Richards
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia. .,Department of Medicine, University of Melbourne, Melbourne, Australia. .,Department of Infectious Diseases, Monash University, Melbourne, Australia. .,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia.
| | - Paul A Ramsland
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia. .,Department of Immunology, Monash University, Melbourne, Australia. .,School of Science, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia. .,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia.
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50
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Early AM, Lievens M, MacInnis BL, Ockenhouse CF, Volkman SK, Adjei S, Agbenyega T, Ansong D, Gondi S, Greenwood B, Hamel M, Odero C, Otieno K, Otieno W, Owusu-Agyei S, Asante KP, Sorgho H, Tina L, Tinto H, Valea I, Wirth DF, Neafsey DE. Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections. Nat Commun 2018; 9:1381. [PMID: 29643376 PMCID: PMC5895824 DOI: 10.1038/s41467-018-03807-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/14/2018] [Indexed: 12/28/2022] Open
Abstract
Host immunity exerts strong selective pressure on pathogens. Population-level genetic analysis can identify signatures of this selection, but these signatures reflect the net selective effect of all hosts and vectors in a population. In contrast, analysis of pathogen diversity within hosts provides information on individual, host-specific selection pressures. Here, we combine these complementary approaches in an analysis of the malaria parasite Plasmodium falciparum using haplotype sequences from thousands of natural infections in sub-Saharan Africa. We find that parasite genotypes show preferential clustering within multi-strain infections in young children, and identify individual amino acid positions that may contribute to strain-specific immunity. Our results demonstrate that natural host defenses to P. falciparum act in an allele-specific manner to block specific parasite haplotypes from establishing blood-stage infections. This selection partially explains the extreme amino acid diversity of many parasite antigens and suggests that vaccines targeting such proteins should account for allele-specific immunity. Host immune responses exert selective pressure on Plasmodium falciparum. Here, the authors show that allele-specific immunity impacts the antigenic diversity of individual malaria infections. This process partially explains the extreme amino acid diversity of many parasite antigens and suggests that vaccines should account for allele-specific immunity.
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Affiliation(s)
- Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | | | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | - Sarah K Volkman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Simmons College, School of Nursing and Health Sciences, Boston, MA, 02115, USA
| | - Samuel Adjei
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, KNUST - Kumasi, Ghana
| | - Tsiri Agbenyega
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, KNUST - Kumasi, Ghana
| | - Daniel Ansong
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, KNUST - Kumasi, Ghana
| | - Stacey Gondi
- KEMRI-Walter Reed Project, Kombewa, 40102, Kenya
| | - Brian Greenwood
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Mary Hamel
- KEMRI/CDC Research and Public Health Collaboration, Kisumu, 40100, Kenya
| | - Chris Odero
- KEMRI/CDC Research and Public Health Collaboration, Kisumu, 40100, Kenya
| | - Kephas Otieno
- KEMRI/CDC Research and Public Health Collaboration, Kisumu, 40100, Kenya
| | | | - Seth Owusu-Agyei
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,Kintampo Health Research Centre, Kintampo, 200, Ghana.,University of Health and Allied Science, PMB 31, Ho, Volta Region, Ghana
| | | | - Hermann Sorgho
- Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso/Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Lucas Tina
- KEMRI-Walter Reed Project, Kombewa, 40102, Kenya
| | - Halidou Tinto
- Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso/Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Innocent Valea
- Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso/Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Dyann F Wirth
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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