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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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2
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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3
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Eccleston RC, Manko E, Campino S, Clark TG, Furnham N. A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife 2023; 12:e84756. [PMID: 38132182 PMCID: PMC10807863 DOI: 10.7554/elife.84756] [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: 11/07/2022] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogen evolution of drug resistance often occurs in a stepwise manner via the accumulation of multiple mutations that in combination have a non-additive impact on fitness, a phenomenon known as epistasis. The evolution of resistance via the accumulation of point mutations in the DHFR genes of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) has been studied extensively and multiple studies have shown epistatic interactions between these mutations determine the accessible evolutionary trajectories to highly resistant multiple mutations. Here, we simulated these evolutionary trajectories using a model of molecular evolution, parameterised using Rosetta Flex ddG predictions, where selection acts to reduce the target-drug binding affinity. We observe strong agreement with pathways determined using experimentally measured IC50 values of pyrimethamine binding, which suggests binding affinity is strongly predictive of resistance and epistasis in binding affinity strongly influences the order of fixation of resistance mutations. We also infer pathways directly from the frequency of mutations found in isolate data, and observe remarkable agreement with the most likely pathways predicted by our mechanistic model, as well as those determined experimentally. This suggests mutation frequency data can be used to intuitively infer evolutionary pathways, provided sufficient sampling of the population.
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Affiliation(s)
- Ruth Charlotte Eccleston
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Emilia Manko
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Taane G Clark
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
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4
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Phelan JE, Turkiewicz A, Manko E, Thorpe J, Vanheer LN, van de Vegte-Bolmer M, Ngoc NTH, Binh NTH, Thieu NQ, Gitaka J, Nolder D, Beshir KB, Dombrowski JG, Di Santi SM, Bousema T, Sutherland CJ, Campino S, Clark TG. Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. Genome Med 2023; 15:96. [PMID: 37950308 PMCID: PMC10636944 DOI: 10.1186/s13073-023-01247-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. RESULTS The online and command line versions of Malaria-Profiler detect ~ 250 markers from genome sequences covering Plasmodium speciation, likely geographical source, and resistance to chloroquine, sulfadoxine-pyrimethamine (SP), and other anti-malarial drugs for P. falciparum, but also providing mutations for orthologous resistance genes in other species. The predictive performance of the mutation library was assessed using 9321 clinical isolates with WGS and geographical data, with most being single-species infections (P. falciparum 7152/7462, P. vivax 1502/1661, P. knowlesi 143/151, P. malariae 18/18, P. ovale ssp. 5/5), but co-infections were identified (456/9321; 4.8%). The accuracy of the predicted geographical profiles was high to both continental (96.1%) and regional levels (94.6%). For P. falciparum, markers were identified for resistance to chloroquine (49.2%; regional range: 24.5% to 100%), sulfadoxine (83.3%; 35.4- 90.5%), pyrimethamine (85.4%; 80.0-100%) and combined SP (77.4%). Markers associated with the partial resistance of artemisinin were found in WGS from isolates sourced from Southeast Asia (30.6%). CONCLUSIONS Malaria-Profiler is a user-friendly tool that can rapidly and accurately predict the geographical regional source and anti-malarial drug resistance profiles across large numbers of samples with WGS data. The software is flexible with modifiable bioinformatic pipelines. For example, it is possible to select the sequencing platform, display specific variants, and customise the format of outputs. With the increasing application of next-generation sequencing platforms on Plasmodium DNA, Malaria-Profiler has the potential to be integrated into point-of-care and surveillance settings, thereby assisting malaria control. Malaria-Profiler is available online (bioinformatics.lshtm.ac.uk/malaria-profiler) and as standalone software ( https://github.com/jodyphelan/malaria-profiler ).
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Affiliation(s)
- Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Anna Turkiewicz
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Emilia Manko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Joseph Thorpe
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Marga van de Vegte-Bolmer
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Nguyen Thi Hong Ngoc
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Thi Huong Binh
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Quang Thieu
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Gen. Kago Rd, Thika, Kenya
| | - Debbie Nolder
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Khalid B Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, Univ. of São Paulo, São Paulo, Brazil
| | - Silvia Maria Di Santi
- School of Medicine, Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil
| | - Teun Bousema
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, LSHTM, London, WC1E 7HT, UK.
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5
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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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6
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Nkosi-Gondwe T, Robberstad B, Opoka R, Kalibbala D, Rujumba J, Galileya LT, Akun P, Nambatya W, Ssenkusu J, TerKuile F, Phiri K, Idro R. Dihydroartemisinin-piperaquine or sulphadoxine-pyrimethamine for the chemoprevention of malaria in children with sickle cell anaemia in eastern and southern Africa (CHEMCHA): a protocol for a multi-centre, two-arm, double-blind, randomised, placebo-controlled superiority trial. Trials 2023; 24:257. [PMID: 37016392 PMCID: PMC10074896 DOI: 10.1186/s13063-023-07274-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND An estimated 300,000 babies are born with sickle cell anaemia (SCA) annually. Affected children have chronic ill health and suffer premature death. Febrile illnesses such as malaria commonly precipitate acute crises in children with SCA. Thus, chemoprophylaxis for malaria is an important preventive strategy, but current regimes are either sub-optimally effective (e.g. monthly sulphadoxine-pyrimethamine, SP) or difficult to adhere to (e.g. daily proguanil). We propose dihydroartemisinin-piperaquine (DP) as the agent with the most potential to be used across Africa. METHODS This will be a randomised, double-blind, parallel-group superiority trial of weekly single-day courses of DP compared to monthly single-day courses of SP in children with SCA. The study will be conducted in eastern (Uganda) and southern (Malawi) Africa using randomisation stratified by body weight and study centre. Participants will be randomised using an allocation of 1:1 to DP or SP. We will investigate the efficacy, safety, acceptability and uptake and cost-effectiveness of malaria chemoprevention with weekly courses of DP vs monthly SP in 548 to 824 children with SCA followed up for 12-18 months. We will also assess toxicity from cumulative DP dosing and the development of resistance. Participant recruitment commenced on 30 April 2021; follow-up is ongoing. DISCUSSION At the end of this study, findings will be used to inform regional health policy. This manuscript is prepared from protocol version 2.1 dated 1 January 2022. TRIAL REGISTRATION The trial was registered at ClinicalTrials.gov, NCT04844099 . Registered on 08 April 2021.
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Affiliation(s)
| | | | - Robert Opoka
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Joseph Rujumba
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Pamela Akun
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Winnie Nambatya
- Makerere University College of Health Sciences, Kampala, Uganda
| | - John Ssenkusu
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Kamija Phiri
- Training and Research Unit of Excellence, Blantyre, Malawi
| | - Richard Idro
- Makerere University College of Health Sciences, Kampala, Uganda.
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7
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Osborne A, Manko E, Takeda M, Kaneko A, Kagaya W, Chan C, Ngara M, Kongere J, Kita K, Campino S, Kaneko O, Gitaka J, Clark TG. Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya. Sci Rep 2021; 11:19809. [PMID: 34615917 PMCID: PMC8494747 DOI: 10.1038/s41598-021-99192-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Characterising the genomic variation and population dynamics of Plasmodium falciparum parasites in high transmission regions of Sub-Saharan Africa is crucial to the long-term efficacy of regional malaria elimination campaigns and eradication. Whole-genome sequencing (WGS) technologies can contribute towards understanding the epidemiology and structural variation landscape of P. falciparum populations, including those within the Lake Victoria basin, a region of intense transmission. Here we provide a baseline assessment of the genomic diversity of P. falciparum isolates in the Lake region of Kenya, which has sparse genetic data. Lake region isolates are placed within the context of African-wide populations using Illumina WGS data and population genomic analyses. Our analysis revealed that P. falciparum isolates from Lake Victoria form a cluster within the East African parasite population. These isolates also appear to have distinct ancestral origins, containing genome-wide signatures from both Central and East African lineages. Known drug resistance biomarkers were observed at similar frequencies to those of East African parasite populations, including the S160N/T mutation in the pfap2mu gene, which has been associated with delayed clearance by artemisinin-based combination therapy. Overall, our work provides a first assessment of P. falciparum genetic diversity within the Lake Victoria basin, a region targeting malaria elimination.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Mika Takeda
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wataru Kagaya
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Chim Chan
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Mtakai Ngara
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - James Kongere
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Centre for Research in Tropical Medicine and Community Development (CRTMCD), Hospital Road Next to Kenyatta National Hospital, Nairobi, Kenya
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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8
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Yamauchi M, Hirai M, Tachibana SI, Mori T, Mita T. Fitness of sulfadoxine-resistant Plasmodium berghei harboring a single mutation in dihydropteroate synthase (DHPS). Acta Trop 2021; 222:106049. [PMID: 34273314 DOI: 10.1016/j.actatropica.2021.106049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/30/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022]
Abstract
Genetic changes conferring drug resistance are generally believed to impose fitness costs to pathogens in the absence of the drug. However, the fitness of resistant parasites against sulfadoxine/pyrimethamine has been inconclusive in Plasmodium falciparum. This is because resistance is conferred by the complex combination of mutations in dihydropteroate synthase (dhps) and dihydrofolate reductase (dhfr), which makes it difficult to separately assess the extent and magnitude of the costs imposed by mutations in dhps and dhfr. To assess the fitness costs imposed by sulfadoxine resistance alone, we generated a transgenic rodent malaria parasite, P. berghei clone harboring an A394G mutation in dhps (PbDHPS-A394G), corresponding to the causative mutation for sulfadoxine resistance in P. falciparum (PfDHPS-A437G). A four-day suppressive test confirmed that the PbDHPS-A394G clone was resistant to sulfadoxine. PbDHPS-A394G and wild-type clones showed similar growth rates and gametocyte production. This observation was confirmed in competitive experiments in which PbDHPS-A394G and wild-type clones were co-infected into mice to directly assess the survival competition between them. In the mosquitoes, there were no significant differences in oocyst production between PbDHPS-A394G and wild-type. These results indicate that the PbDHPS-A394G mutation alters the parasites to sulfadoxine resistance but may not impose fitness disadvantages during the blood stages in mice and oocyst formation in mosquitoes. These results partly explain the persistence of the PfDHPS-A437G mutant in the natural parasite populations.
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9
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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: 43] [Impact Index Per Article: 14.3] [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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10
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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: 41] [Impact Index Per Article: 13.7] [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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11
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Deelder W, Benavente ED, Phelan J, Manko E, Campino S, Palla L, Clark TG. Using deep learning to identify recent positive selection in malaria parasite sequence data. Malar J 2021; 20:270. [PMID: 34126997 PMCID: PMC8201710 DOI: 10.1186/s12936-021-03788-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/29/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and their spread. With the increasing use of whole-genome sequencing (WGS) of Plasmodium DNA, the potential of deep learning models to detect loci under recent positive selection, historically signals of drug resistance, was evaluated. METHODS A deep learning-based approach (called "DeepSweep") was developed, which can be trained on haplotypic images from genetic regions with known sweeps, to identify loci under positive selection. DeepSweep software is available from https://github.com/WDee/Deepsweep . RESULTS Using simulated genomic data, DeepSweep could detect recent sweeps with high predictive accuracy (areas under ROC curve > 0.95). DeepSweep was applied to Plasmodium falciparum (n = 1125; genome size 23 Mbp) and Plasmodium vivax (n = 368; genome size 29 Mbp) WGS data, and the genes identified overlapped with two established extended haplotype homozygosity methods (within-population iHS, across-population Rsb) (~ 60-75% overlap of hits at P < 0.0001). DeepSweep hits included regions proximal to known drug resistance loci for both P. falciparum (e.g. pfcrt, pfdhps and pfmdr1) and P. vivax (e.g. pvmrp1). CONCLUSION The deep learning approach can detect positive selection signatures in malaria parasite WGS data. Further, as the approach is generalizable, it may be trained to detect other types of selection. With the ability to rapidly generate WGS data at low cost, machine learning approaches (e.g. DeepSweep) have the potential to assist parasite genome-based surveillance and inform malaria control decision-making.
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Affiliation(s)
- Wouter Deelder
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Dalberg Advisors, 7 Rue de Chantepoulet, CH-1201, Geneva, Switzerland
| | | | - Jody Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Emilia Manko
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Luigi Palla
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, Rome, Italy
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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12
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Chaturvedi R, Chhibber-Goel J, Verma I, Gopinathan S, Parvez S, Sharma A. Geographical spread and structural basis of sulfadoxine-pyrimethamine drug-resistant malaria parasites. Int J Parasitol 2021; 51:505-525. [PMID: 33775670 DOI: 10.1016/j.ijpara.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022]
Abstract
The global spread of sulfadoxine (Sdx, S) and pyrimethamine (Pyr, P) resistance is attributed to increasing number of mutations in DHPS and DHFR enzymes encoded by malaria parasites. The association between drug resistance mutations and SP efficacy is complex. Here we provide an overview of the geographical spread of SP resistance mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) encoded dhps and dhfr genes. In addition, we have collated the mutation data and mapped it on to the three-dimensional structures of DHPS and DHFR which have become available. Data from genomic databases and 286 studies were collated to provide a comprehensive landscape of mutational data from 2005 to 2019. Our analyses show that the Pyr-resistant double mutations are widespread in Pf/PvDHFR (P. falciparum ∼61% in Asia and the Middle East, and in the Indian sub-continent; in P. vivax ∼33% globally) with triple mutations prevailing in Africa (∼66%) and South America (∼33%). For PfDHPS, triple mutations dominate South America (∼44%), Asia and the Middle East (∼34%) and the Indian sub-continent (∼27%), while single mutations are widespread in Africa (∼45%). Contrary to the status for P. falciparum, Sdx-resistant single point mutations in PvDHPS dominate globally. Alarmingly, highly resistant quintuple and sextuple mutations are rising in Africa (PfDHFR-DHPS) and Asia (Pf/PvDHFR-DHPS). Structural analyses of DHFR and DHPS proteins in complexes with substrates/drugs have revealed that resistance mutations map proximal to Sdx and Pyr binding sites. Thus new studies can focus on discovery of novel inhibitors that target the non-substrate binding grooves in these two validated malaria parasite drug targets.
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Affiliation(s)
- Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ishika Verma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sreehari Gopinathan
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Suhel Parvez
- Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; National Institute of Malaria Research, Dwarka, New Delhi, India.
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13
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:genes12060843. [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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14
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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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15
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Da Veiga Leal S, Ward D, Campino S, Benavente ED, Ibrahim A, Claret T, Isaías V, Monteiro D, Clark TG, Gonçalves L, Valdez T, da Luz Lima Mendonça M, Silveira H, Nogueira F. Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak. Malar J 2021; 20:172. [PMID: 33789667 PMCID: PMC8011132 DOI: 10.1186/s12936-021-03708-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cape Verde is an archipelago located off the West African coast and is in a pre-elimination phase of malaria control. Since 2010, fewer than 20 Plasmodium falciparum malaria cases have been reported annually, except in 2017, when an outbreak in Praia before the rainy season led to 423 autochthonous cases. It is important to understand the genetic diversity of circulating P. falciparum to inform on drug resistance, potential transmission networks and sources of infection, including parasite importation. METHODS Enrolled subjects involved malaria patients admitted to Dr Agostinho Neto Hospital at Praia city, Santiago island, Cape Verde, between July and October 2017. Neighbours and family members of enrolled cases were assessed for the presence of anti-P. falciparum antibodies. Sanger sequencing and real-time PCR was used to identify SNPs in genes associated with drug resistance (e.g., pfdhfr, pfdhps, pfmdr1, pfk13, pfcrt), and whole genome sequencing data were generated to investigate the population structure of P. falciparum parasites. RESULTS The study analysed 190 parasite samples, 187 indigenous and 3 from imported infections. Malaria cases were distributed throughout Praia city. There were no cases of severe malaria and all patients had an adequate clinical and parasitological response after treatment. Anti-P. falciparum antibodies were not detected in the 137 neighbours and family members tested. No mutations were detected in pfdhps. The triple mutation S108N/N51I/C59R in pfdhfr and the chloroquine-resistant CVIET haplotype in the pfcrt gene were detected in almost all samples. Variations in pfk13 were identified in only one sample (R645T, E668K). The haplotype NFD for pfmdr1 was detected in the majority of samples (89.7%). CONCLUSIONS Polymorphisms in pfk13 associated with artemisinin-based combination therapy (ACT) tolerance in Southeast Asia were not detected, but the majority of the tested samples carried the pfmdr1 haplotype NFD and anti-malarial-associated mutations in the the pfcrt and pfdhfr genes. The first whole genome sequencing (WGS) was performed for Cape Verdean parasites that showed that the samples cluster together, have a very high level of similarity and are close to other parasites populations from West Africa.
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Affiliation(s)
- Silvania Da Veiga Leal
- Laboratório de Entomologia Médica, Largo Do Desastre da Assistência, Instituto Nacional de Saúde Pública, Chã de Areia, Praia 719, Cape Verde.
| | - Daniel Ward
- Department of Infection and Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Department of Infection and Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Department of Infection and Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Amy Ibrahim
- Department of Infection and Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Tânia Claret
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Varela Isaías
- Laboratório de Entomologia Médica, Largo Do Desastre da Assistência, Instituto Nacional de Saúde Pública, Chã de Areia, Praia 719, Cape Verde
| | - Davidson Monteiro
- Laboratório de Entomologia Médica, Largo Do Desastre da Assistência, Instituto Nacional de Saúde Pública, Chã de Areia, Praia 719, Cape Verde
| | - Taane G Clark
- Department of Infection and Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
| | - Luzia Gonçalves
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
- Centro de Estatística E Aplicações da Universidade de Lisboa (CEAUL), Campo Grande, Bloco C6, Piso 4, 1749-016, Lisbon, Portugal
| | - Tomas Valdez
- Ministério da Saúde E da Segurança, Palácio Do Governo, nº47, Praia, Cape Verde
| | - Maria da Luz Lima Mendonça
- Laboratório de Entomologia Médica, Largo Do Desastre da Assistência, Instituto Nacional de Saúde Pública, Chã de Areia, Praia 719, Cape Verde
| | - Henrique Silveira
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
| | - Fatima Nogueira
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008, Lisbon, Portugal
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16
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Labama Otuli N, Marini Djang'eing'a R, Losimba Likwela J, Bosenge Nguma JD, Maindo Alongo MA, Ahuka Ona Longombe A, Mbutu Mango B, M N Bono D, L Mokili J, Manga Okenge JP. Efficacy and safety of malarial prophylaxis with mefloquine during pregnancy in Kisangani, Democratic Republic of Congo: A randomized clinical trial. Br J Clin Pharmacol 2021; 87:3115-3126. [PMID: 33398890 DOI: 10.1111/bcp.14720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
AIMS Kisangani is an area with intense malaria transmission and sulfadoxine-pyrimethamine resistance. Alternative antimalaria prophylaxis medication and protocols are needed, particularly with pregnant individuals. In this study, we compare the tolerance and effectiveness of mefloquine regimen as a split dose with a meal vs. sulfadoxine-pyrimethamine for the intermittent preventive treatment in pregnant individuals in Kisangani. METHODS This study was conducted from 15 May to 30 November 2019 as a single-blind, randomized clinical trial comparing 2 regimens of intermittent preventive treatment during pregnancy. The first regimen consisted of 4 doses of sulfadoxine-pyrimethamine, and the second of 2 doses of mefloquine taken as a split dose with meal. RESULTS The occurrence of major or minor side-effects among patients treated with mefloquine and those treated with sulfadoxine-pyrimethamine were not statistically significant (major side effects: Fisher exact = 0.5014; minor side effects: P = .0961). Intermittent preventive treatment using mefloquine significantly reduced the risk of placental malaria (risk ratio [RR]: 0.4315, 95% confidence interval [CI]: 0.2201-0.8460), maternal peripheral parasitaemia (RR: 0.4397, 95% CI: 0.2377-0.8132) and low birth weight (RR: 0.4708, 95% CI: 0.2455-0.9029). CONCLUSION Splitting dose and intake with a meal increased mefloquine tolerability while keeping its efficacy higher compared to sulfadoxine-pyrimethamine. Intermittent preventive treatment during pregnancy using mefloquine reduces the risk of placental malaria, maternal peripheral parasitaemia and low birth weight, compared to sulfadoxine-pyrimethamine. Thus, mefloquine is a good alternative to intermittent preventive treatment in pregnancy.
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Affiliation(s)
- Noël Labama Otuli
- Department of Gynaecology-Obstetrics, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, 2012, Democratic Republic of the Congo
| | - Roland Marini Djang'eing'a
- Department of Pharmacy, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, Democratic Republic of Congo, 2012, Democratic Republic of Congo.,Laboratory of Analytical Pharmaceutical Chemistry, CIRM, Department of Pharmacy, University of Liege, Liège, Belgium
| | - Joris Losimba Likwela
- Department of Public Health, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, Democratic Republic of Congo
| | - Jean-Didier Bosenge Nguma
- Department of Gynaecology-Obstetrics, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, 2012, Democratic Republic of the Congo
| | - Mike-Antoine Maindo Alongo
- Department of Gynaecology-Obstetrics, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, 2012, Democratic Republic of the Congo
| | - Albert Ahuka Ona Longombe
- Department of Surgery, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, Democratic Republic of Congo
| | - Bernard Mbutu Mango
- Institut Supérieur des Techniques Médicales de Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - John L Mokili
- Viral Information Institute, Department of Biology, San Diego State University, Californie, USA
| | - Jean-Pascal Manga Okenge
- Department of Gynaecology-Obstetrics, Faculty of Medicine and Pharmacy, Kisangani University, Kisangani, 2012, Democratic Republic of the Congo
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17
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Turkiewicz A, Manko E, Sutherland CJ, Diez Benavente E, Campino S, Clark TG. Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance. PLoS Genet 2020; 16:e1009268. [PMID: 33382691 PMCID: PMC7774857 DOI: 10.1371/journal.pgen.1009268] [Citation(s) in RCA: 13] [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: 08/29/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum parasites resistant to antimalarial treatments have hindered malaria disease control. Sulfadoxine-pyrimethamine (SP) was used globally as a first-line treatment for malaria after wide-spread resistance to chloroquine emerged and, although replaced by artemisinin combinations, is currently used as intermittent preventive treatment of malaria in pregnancy and in young children as part of seasonal malaria chemoprophylaxis in sub-Saharan Africa. The emergence of SP-resistant parasites has been predominantly driven by cumulative build-up of mutations in the dihydrofolate reductase (pfdhfr) and dihydropteroate synthetase (pfdhps) genes, but additional amplifications in the folate pathway rate-limiting pfgch1 gene and promoter, have recently been described. However, the genetic make-up and prevalence of those amplifications is not fully understood. We analyse the whole genome sequence data of 4,134 P. falciparum isolates across 29 malaria endemic countries, and reveal that the pfgch1 gene and promoter amplifications have at least ten different forms, occurring collectively in 23% and 34% in Southeast Asian and African isolates, respectively. Amplifications are more likely to be present in isolates with a greater accumulation of pfdhfr and pfdhps substitutions (median of 1 additional mutations; P<0.00001), and there was evidence that the frequency of pfgch1 variants may be increasing in some African populations, presumably under the pressure of SP for chemoprophylaxis and anti-folate containing antibiotics used for the treatment of bacterial infections. The selection of P. falciparum with pfgch1 amplifications may enhance the fitness of parasites with pfdhfr and pfdhps substitutions, potentially threatening the efficacy of this regimen for prevention of malaria in vulnerable groups. Our work describes new pfgch1 amplifications that can be used to inform the surveillance of SP drug resistance, its prophylactic use, and future experimental work to understand functional mechanisms.
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Affiliation(s)
- Anna Turkiewicz
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emilia Manko
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Colin J. Sutherland
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ernest Diez Benavente
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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18
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Moser KA, Madebe RA, Aydemir O, Chiduo MG, Mandara CI, Rumisha SF, Chaky F, Denton M, Marsh PW, Verity R, Watson OJ, Ngasala B, Mkude S, Molteni F, Njau R, Warsame M, Mandike R, Kabanywanyi AM, Mahende MK, Kamugisha E, Ahmed M, Kavishe RA, Greer G, Kitojo CA, Reaves EJ, Mlunde L, Bishanga D, Mohamed A, Juliano JJ, Ishengoma DS, Bailey JA. Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes. Mol Ecol 2020; 30:100-113. [PMID: 33107096 DOI: 10.1111/mec.15706] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/25/2020] [Accepted: 10/13/2020] [Indexed: 02/05/2023]
Abstract
High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programmes, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania countrywide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, approximately separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from nearby districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts (including two infections carrying pfk13-R561H), and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared.
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Affiliation(s)
- Kara A Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | | | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Mercy G Chiduo
- National Institute for Medical Research, Tanga, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Tanga, Tanzania.,Kilimanjaro Christian Medical Centre/Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Susan F Rumisha
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Frank Chaky
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Patrick W Marsh
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.,MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | - Ritha Njau
- World Health Organization Country Office, Dar es Salaam, Tanzania
| | - Marian Warsame
- Gothenburg University, Gothenburg, Sweden.,Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Renata Mandike
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | | | - Erasmus Kamugisha
- Catholic University of Health and Allied Sciences/Bugando Medical Centre, Mwanza, Tanzania
| | - Maimuna Ahmed
- Catholic University of Health and Allied Sciences/Bugando Medical Centre, Mwanza, Tanzania
| | - Reginald A Kavishe
- Kilimanjaro Christian Medical Centre/Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - George Greer
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Chonge A Kitojo
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Erik J Reaves
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Linda Mlunde
- Jhpiego/Boresha Afya Project, Dar es Salaam, Tanzania
| | | | - Ally Mohamed
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.,Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.,Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Vic, Australia.,Harvard T.H. Chan School of Public health, Harvard University, Boston, MA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
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19
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Jiang T, Cheng W, Yao Y, Tan H, Wu K, Li J. Molecular surveillance of anti-malarial resistance Pfdhfr and Pfdhps polymorphisms in African and Southeast Asia Plasmodium falciparum imported parasites to Wuhan, China. Malar J 2020; 19:434. [PMID: 33238987 PMCID: PMC7691106 DOI: 10.1186/s12936-020-03509-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
Background Anti-malarial drug resistance is a severe challenge for eventual control and global elimination of malaria. Resistance to sulfadoxine-pyrimethamine (SP) increases as mutations accumulate in the Pfdhfr and Pfdhps genes. This study aimed to assess the polymorphisms and prevalence of mutation in these genes in the Plasmodium falciparum infecting migrant workers returning to Wuhan, China. Methods Blood samples were collected for 9 years (2011–2019). Parasite genomic DNA was extracted from blood spots on filter paper. The mutations were evaluated by nested PCR and sequencing. The single-nucleotide polymorphisms (SNPs) and haplotypes of the Pfdhfr and Pfdhps genes were analysed. Results Pfdhfr codon 108 showed a 94.7% mutation rate, while for Pfdhps, the rate for codon 437 was 79.0%. In total, five unique haplotypes at the Pfdhfr locus and 11 haplotypes at the Pfdhps locus were found while the Pfdhfr-Pfdhps combined loci revealed 28 unique haplotypes. A triple mutant (IRNI) of Pfdhfr was the most prevalent haplotype (84.4%). For Pfdhps, a single mutant (SGKAA) and a double mutant (SGEAA) were detected at frequencies of 37.8 and 22.3%, respectively. Among the combined haplotypes, a quadruple mutant (IRNI-SGKAA) was the most common, with a 30.0% frequency, followed by a quintuplet mutant (IRNI-SGEAA) with a frequency of 20.4%. Conclusion The high prevalence and saturation of Pfdhfr haplotypes and the medium prevalence of Pfdhps haplotypes demonstrated in the present data will provide support for predicting the status and progression of antifolate resistance in malaria-endemic regions and imported malaria in nonendemic areas. Additional interventions to evaluate and prevent SP resistance should be continuously considered.
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Affiliation(s)
- Tingting Jiang
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Weijia Cheng
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yi Yao
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Huabing Tan
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China.,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Kai Wu
- Department of Schistosomiasis and Endemic Diseases, Wuhan City Center for Disease Prevention and Control, Wuhan, 430015, China.
| | - Jian Li
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China. .,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China.
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20
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Cowell AN, Winzeler EA. The genomic architecture of antimalarial drug resistance. Brief Funct Genomics 2019; 18:314-328. [PMID: 31119263 PMCID: PMC6859814 DOI: 10.1093/bfgp/elz008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 11/15/2022] Open
Abstract
Plasmodium falciparum and Plasmodium vivax, the two protozoan parasite species that cause the majority of cases of human malaria, have developed resistance to nearly all known antimalarials. The ability of malaria parasites to develop resistance is primarily due to the high numbers of parasites in the infected person's bloodstream during the asexual blood stage of infection in conjunction with the mutability of their genomes. Identifying the genetic mutations that mediate antimalarial resistance has deepened our understanding of how the parasites evade our treatments and reveals molecular markers that can be used to track the emergence of resistance in clinical samples. In this review, we examine known genetic mutations that lead to resistance to the major classes of antimalarial medications: the 4-aminoquinolines (chloroquine, amodiaquine and piperaquine), antifolate drugs, aryl amino-alcohols (quinine, lumefantrine and mefloquine), artemisinin compounds, antibiotics (clindamycin and doxycycline) and a napthoquinone (atovaquone). We discuss how the evolution of antimalarial resistance informs strategies to design the next generation of antimalarial therapies.
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Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases and Global Health, Department of Medicine, University of California, San Diego, Gilman Dr., La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, USA
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21
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Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, William T, Yeo TW, de Sessions PF, Ramaprasad A, Ibrahim A, Charleston J, Hibberd ML, Pain A, Moon RW, Auburn S, Ling LY, Anstey NM, Clark TG, Campino S. Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations. Sci Rep 2019; 9:9873. [PMID: 31285495 PMCID: PMC6614422 DOI: 10.1038/s41598-019-46398-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/28/2019] [Indexed: 12/19/2022] Open
Abstract
The zoonotic Plasmodium knowlesi parasite is the most common cause of human malaria in Malaysia. Genetic analysis has shown that the parasites are divided into three subpopulations according to their geographic origin (Peninsular or Borneo) and, in Borneo, their macaque host (Macaca fascicularis or M. nemestrina). Whilst evidence suggests that genetic exchange events have occurred between the two Borneo subpopulations, the picture is unclear in less studied Peninsular strains. One difficulty is that P. knowlesi infected individuals tend to present with low parasitaemia leading to samples with insufficient DNA for whole genome sequencing. Here, using a parasite selective whole genome amplification approach on unprocessed blood samples, we were able to analyse recent genomes sourced from both Peninsular Malaysia and Borneo. The analysis provides evidence that recombination events are present in the Peninsular Malaysia parasite subpopulation, which have acquired fragments of the M. nemestrina associated subpopulation genotype, including the DBPβ and NBPXa erythrocyte invasion genes. The NBPXb invasion gene has also been exchanged within the macaque host-associated subpopulations of Malaysian Borneo. Our work provides strong evidence that exchange events are far more ubiquitous than expected and should be taken into consideration when studying the highly complex P. knowlesi population structure.
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Affiliation(s)
- Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ana Rita Gomes
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Matthew Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Harriet Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bridget E Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia.,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300, Kota Kinabalu, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300, Kota Kinabalu, Sabah, Malaysia.,Clinical Research Centre, Queen Elizabeth Hospital, 88300, Kota Kinabalu, Sabah, Malaysia.,Jesselton Medical Centre, 88300, Kota Kinabalu, Sabah, Malaysia
| | - Tsin Wen Yeo
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Abhinay Ramaprasad
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Amy Ibrahim
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Genomics Institute, Biopolis, Singapore
| | - Arnab Pain
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Robert W Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom. .,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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22
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An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene. Sci Rep 2019; 9:8287. [PMID: 31164664 PMCID: PMC6547842 DOI: 10.1038/s41598-019-44599-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
The evolution of genetic mechanisms for host immune evasion and anti-malarial resistance has enabled the Plasmodium falciparum malaria parasite to inflict high morbidity and mortality on human populations. Most studies of P. falciparum genetic diversity have focused on single-nucleotide polymorphisms (SNPs), assisting the identification of drug resistance-associated loci such as the chloroquine related crt and sulfadoxine-pyrimethamine related dhfr. Whilst larger structural variants are known to impact adaptation, for example, mdr1 duplications with anti-malarial resistance, no large-scale, genome-wide study on clinical isolates has been undertaken using whole genome sequencing data. By applying a structural variant detection pipeline across whole genome sequence data from 2,855 clinical isolates in 21 malaria-endemic countries, we identified >70,000 specific deletions and >600 duplications. Most structural variants are rare (48.5% of deletions and 94.7% of duplications are found in single isolates) with 2.4% of deletions and 0.2% of duplications found in >5% of global isolates. A subset of variants was present at high frequency in drug-resistance related genes including mdr1, the gch1 promoter region, and a putative novel duplication of crt. Regional-specific variants were identified, and a companion visualisation tool has been developed to assist web-based investigation of these polymorphisms by the wider scientific community.
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23
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He Y, Campino S, Diez Benavente E, Warhurst DC, Beshir KB, Lubis I, Gomes AR, Feng J, Jiazhi W, Sun X, Huang F, Tang LH, Sutherland CJ, Clark TG. Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area. PLoS One 2019; 14:e0213686. [PMID: 30883571 PMCID: PMC6422288 DOI: 10.1371/journal.pone.0213686] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/26/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Malaria reduction and future elimination in China is made more difficult by the importation of cases from neighboring endemic countries, particularly Myanmar, Laos, and Vietnam, and increased travel to Africa by Chinese nationals. The increasing prevalence of artemisinin resistant parasites across Southeast Asia highlights the importance of monitoring the parasite importation into China. Artemisinin resistance in the Mekong region is associated with variants of genes encoding the K13 kelch domain protein (pf13k), found in specific genetic backgrounds, including certain alleles of genes encoding the chloroquine resistance transporter (pfcrt) and multidrug resistance transporter PgH1 (pfmdr1). METHODS In this study we investigated the prevalence of drug resistance markers in 72 P. falciparum samples from uncomplicated malaria infections in Tengchong and Yingjiang, counties on the Yunnan-Myanmar border. Variants of pf13k, pfcrt and pfmdr1 are described. RESULTS Almost all parasites harboured chloroquine-resistant alleles of pfcrt, whereas pfmdr1 was more diverse. Major mutations in the K13 propeller domain associated with artemisinin resistance in the Mekong region (C580Y, R539T and Y493H) were absent, but F446I and two previously undescribed mutations (V603E and V454I) were identified. Protein structural modelling was carried out in silico on each of these K13 variants, based on recently published crystal structures for the K13 propeller domain. Whereas F446I was predicted to elicit a moderate destabilisation of the propeller structure, the V603E substitution is likely to lead to relatively high protein instability. We plotted these stability estimates, and those for all previously described variants, against published values for in vivo parasitaemia half-life, and found that quadratic regression generates a useful predictive algorithm. CONCLUSION This study provides a baseline of P. falciparum resistance-associated mutations prevalent at the China-Myanmar border. We also show that protein modelling can be used to generate testable predictions as to the impact of pfk13 mutations on in vivo (and potentially in vitro) artemisinin susceptibility.
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Affiliation(s)
- Yan He
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, Shanghai, People’s Republic of China
- WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, People’s Republic of China
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C. Warhurst
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Khalid B. Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Inke Lubis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ana Rita Gomes
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jun Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, Shanghai, People’s Republic of China
- WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, People’s Republic of China
| | - Wang Jiazhi
- Yunnan Institute of Parasitic Diseases, Provincial Centre of Malaria Research, Provincial Collaborative Innovation Centre for Public Health and Disease Prevention and Control, Provincial Key Laboratory of Vector-borne Diseases Control and Research, Puer, China
| | - Xiaodong Sun
- Tengchong County Centers for Disease Control and Prevention, Guanghua village, Tiancheng district, Tengchong, Yunnan Province, China
| | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, Shanghai, People’s Republic of China
- WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, People’s Republic of China
| | - Lin-hua Tang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, Shanghai, People’s Republic of China
- WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, People’s Republic of China
| | - Colin J. Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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24
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SV-Pop: population-based structural variant analysis and visualization. BMC Bioinformatics 2019; 20:136. [PMID: 30866793 PMCID: PMC6417133 DOI: 10.1186/s12859-019-2718-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background Genetic structural variation underpins a multitude of phenotypes, with significant implications for a range of biological outcomes. Despite their crucial role, structural variants (SVs) are often neglected and overshadowed by single nucleotide polymorphisms (SNPs), which are used in large-scale analysis such as genome-wide association and population genetic studies. Results To facilitate the high-throughput analysis of structural variation we have developed an analytical pipeline and visualisation tool, called SV-Pop. The utility of this pipeline was then demonstrated through application with a large, multi-population P. falciparum dataset. Conclusions Designed to facilitate downstream analysis and visualisation post-discovery, SV-Pop allows for straightforward integration of multi-population analysis, method and sample-based concordance metrics, and signals of selection.
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25
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Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. Sci Rep 2018; 8:15429. [PMID: 30337594 PMCID: PMC6193930 DOI: 10.1038/s41598-018-33767-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/06/2018] [Indexed: 12/24/2022] Open
Abstract
Malaria infection during pregnancy, caused by the sequestering of Plasmodium falciparum parasites in the placenta, leads to high infant mortality and maternal morbidity. The parasite-placenta adherence mechanism is mediated by the VAR2CSA protein, a target for natural occurring immunity. Currently, vaccine development is based on its ID1-DBL2Xb domain however little is known about the global genetic diversity of the encoding var2csa gene, which could influence vaccine efficacy. In a comprehensive analysis of the var2csa gene in >2,000 P. falciparum field isolates across 23 countries, we found that var2csa is duplicated in high prevalence (>25%), African and Oceanian populations harbour a much higher diversity than other regions, and that insertions/deletions are abundant leading to an underestimation of the diversity of the locus. Further, ID1-DBL2Xb haplotypes associated with adverse birth outcomes are present globally, and African-specific haplotypes exist, which should be incorporated into vaccine design.
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26
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Osei M, Ansah F, Matrevi SA, Asante KP, Awandare GA, Quashie NB, Duah NO. Amplification of GTP-cyclohydrolase 1 gene in Plasmodium falciparum isolates with the quadruple mutant of dihydrofolate reductase and dihydropteroate synthase genes in Ghana. PLoS One 2018; 13:e0204871. [PMID: 30265714 PMCID: PMC6162080 DOI: 10.1371/journal.pone.0204871] [Citation(s) in RCA: 6] [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: 08/01/2018] [Accepted: 09/14/2018] [Indexed: 11/19/2022] Open
Abstract
Sulfadoxine-pyrimethamine (SP) is used as malaria chemoprophylaxis for pregnant women and children in Ghana. Plasmodium falciparum resistance to SP is linked to mutations in the dihydropteroate synthase gene (pfdhps), dihydrofolate reductase gene (pfdhfr) and amplification of GTP cyclohydrolase 1 (pfgch1) gene. The pfgch1 duplication is associated with pfdhfr L164, a crucial mutant for high level pyrimethamine resistance which is rare in Ghana. The presence of amplified pfgch1 in Ghanaian isolates could be an indicator of the evolution of the L164 mutant. This study therefore determined the pfgch1 copy number variations and SP resistance mutations in clinical isolates from Ghana. One hundred and ninety-two (192) blood samples collected from children aged ≤14 years with uncomplicated malaria in 2013-14 and 2015-16 were used. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the pfgch1 copy number and nested PCR-Sanger sequencing used to detect mutations in pfdhps and pfdhfr genes. Twelve parasites (6.3%) harbored double copies of the pfgch1 gene out of the 192 samples. Of the 12, 75% had the pfdhfr I51-R59-N108, 92% had the pfdhps G437 mutant, 8% had the pfdhps E540 and 67% had the SP resistance haplotype IRNG. No L164 was detected in samples with amplified pfgch1. The rare T108 mutant associated with cycloguanil resistance showed predominance (60%) over N108 in the 2015-16 isolates. The observation of parasites with increased copy number of pfgch1 gene is indicative of the future evolution of the rare quadruple pfdhfr mutant, I51-R59-N108-L164, in Ghanaian parasites. Mutant pfdhps isolates also had increased gch1 copy number suggestive that it may also facilitate sulphadoxine resistance. The selection of parasites with pfgch1 gene amplification will enhance the sustenance and persistence of parasites with SP resistance in the country. Policy makers need to begin the search for a replacement chemoprophylaxis drug for malaria vulnerable groups in Ghana.
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Affiliation(s)
- Musah Osei
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Sena A. Matrevi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | | | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Neils B. Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- Centre for Tropical Clinical Pharmacology and Therapeutics, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nancy O. Duah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
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Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. PLoS Genet 2018; 14:e1007279. [PMID: 29791438 PMCID: PMC5988311 DOI: 10.1371/journal.pgen.1007279] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/05/2018] [Accepted: 02/26/2018] [Indexed: 12/30/2022] Open
Abstract
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections. Using the inferred IBD status at genomic locations, we have also developed a novel statistic for identifying loci under positive selection and propose relatedness networks as a means of exploring shared haplotypes within populations. We evaluate the performance of our methodologies for detecting IBD and selection, including comparisons with existing tools, then perform an exploratory analysis of whole genome sequencing data from a global Plasmodium falciparum dataset of more than 2500 genomes. This analysis identifies Southeast Asia as having many highly related isolates, possibly as a result of both reduced transmission from intensified control efforts and population bottlenecks following the emergence of antimalarial drug resistance. Many signals of selection are also identified, most of which overlap genes that are known to be associated with drug resistance, in addition to two novel signals observed in multiple countries that have yet to be explored in detail. Additionally, we investigate relatedness networks over the selected loci and determine that one of these sweeps has spread between continents while the other has arisen independently in different countries. IBD analysis of microorganisms using isoRelate can be used for exploring population structure, positive selection and haplotype distributions, and will be a valuable tool for monitoring disease control and elimination efforts of many diseases. There are growing concerns over the emergence of antimicrobial drug resistance, which threatens the efficacy of treatments for infectious diseases such as malaria. As such, it is important to understand the dynamics of resistance by investigating population structure, natural selection and disease transmission in microorganisms. The study of disease dynamics has been hampered by the lack of suitable statistical models for analysis of isolates containing multiple infections. We introduce a statistical model that uses population genomic data to identify genomic regions (loci) that are inherited from a common ancestor, in the presence of multiple infections. We demonstrate its potential for biological discovery using a global Plasmodium falciparum dataset. We identify low genetic diversity in isolates from Southeast Asia, possibly from clonal expansion following intensified control efforts after the emergence of artemisinin resistance. We also identify loci under positive selection, most of which contain genes that have been associated with antimalarial drug resistance. We discover two loci under strong selection in multiple countries throughout Southeast Asia and Africa where the selection pressure is currently unknown. We find that the selection pressure at one of these loci has originated from gene flow, while the other loci has originated from multiple independent events.
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28
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Ravenhall M, Campino S, Sepúlveda N, Manjurano A, Nadjm B, Mtove G, Wangai H, Maxwell C, Olomi R, Reyburn H, Drakeley CJ, Riley EM, Clark TG. Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania. PLoS Genet 2018; 14:e1007172. [PMID: 29381699 PMCID: PMC5806895 DOI: 10.1371/journal.pgen.1007172] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/09/2018] [Accepted: 12/29/2017] [Indexed: 01/07/2023] Open
Abstract
Significant selection pressure has been exerted on the genomes of human populations exposed to Plasmodium falciparum infection, resulting in the acquisition of mechanisms of resistance against severe malarial disease. Many host genetic factors, including sickle cell trait, have been associated with reduced risk of developing severe malaria, but do not account for all of the observed phenotypic variation. Identification of novel inherited risk factors relies upon high-resolution genome-wide association studies (GWAS). We present findings of a GWAS of severe malaria performed in a Tanzanian population (n = 914, 15.2 million SNPs). Beyond the expected association with the sickle cell HbS variant, we identify protective associations within two interleukin receptors (IL-23R and IL-12RBR2) and the kelch-like protein KLHL3 (all P<10-6), as well as near significant effects for Major Histocompatibility Complex (MHC) haplotypes. Complementary analyses, based on detecting extended haplotype homozygosity, identified SYNJ2BP, GCLC and MHC as potential loci under recent positive selection. Through whole genome sequencing of an independent Tanzanian cohort (parent-child trios n = 247), we confirm the allele frequencies of common polymorphisms underlying associations and selection, as well as the presence of multiple structural variants that could be in linkage with these SNPs. Imputation of structural variants in a region encompassing the glycophorin genes on chromosome 4, led to the characterisation of more than 50 rare variants, and individually no strong evidence of associations with severe malaria in our primary dataset (P>0.3). Our approach demonstrates the potential of a joint genotyping-sequencing strategy to identify as-yet unknown susceptibility loci in an African population with well-characterised malaria phenotypes. The regions encompassing these loci are potential targets for the design of much needed interventions for preventing or treating malarial disease.
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Affiliation(s)
- Matt Ravenhall
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nuno Sepúlveda
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Statistics and Applications, University of Lisbon, Lisbon, Portugal
| | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
- National Institute for Medical Research, Mwanza, Tanzania
| | - Behzad Nadjm
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - George Mtove
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Hannah Wangai
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Caroline Maxwell
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Raimos Olomi
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Hugh Reyburn
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Christopher J. Drakeley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Eleanor M. Riley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania
| | - Taane G. Clark
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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29
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Herrmann FC, Sivakumar N, Jose J, Costi MP, Pozzi C, Schmidt TJ. In Silico Identification and In Vitro Evaluation of Natural Inhibitors of Leishmania major Pteridine Reductase I. Molecules 2017; 22:molecules22122166. [PMID: 29211037 PMCID: PMC6149668 DOI: 10.3390/molecules22122166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 12/29/2022] Open
Abstract
In a continuation of our computational efforts to find new natural inhibitors of a variety of target enzymes from parasites causing neglected tropical diseases (NTDs), we now report on 15 natural products (NPs) that we have identified as inhibitors of Leishmania major pteridine reductase I (LmPTR1) through a combination of in silico and in vitro investigations. Pteridine reductase (PTR1) is an enzyme of the trypanosomatid parasites’ peculiar folate metabolism, and has previously been validated as a drug target. Initially, pharmacophore queries were created based on four 3D structures of LmPTR1 using co-crystallized known inhibitors as templates. Each of the pharmacophore queries was used to virtually screen a database of 1100 commercially available natural products. The resulting hits were submitted to molecular docking analyses in the substrate binding site of the respective protein structures used for the pharmacophore design. This approach led to the in silico identification of a total of 18 NPs with predicted binding affinity to LmPTR1. These compounds were subsequently tested in vitro for inhibitory activity towards recombinant LmPTR1 in a spectrophotometric inhibition assay. Fifteen out of the 18 tested compounds (hit rate = 83%) showed significant inhibitory activity against LmPTR1 when tested at a concentration of 50 µM. The IC50 values were determined for the six NPs that inhibited the target enzyme by more than 50% at 50 µM, with sophoraflavanone G being the most active compound tested (IC50 = 19.2 µM). The NPs identified and evaluated in the present study may represent promising lead structures for the further rational drug design of more potent inhibitors against LmPTR1.
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Affiliation(s)
- Fabian C Herrmann
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
| | - Nirina Sivakumar
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, Correnstrasse 48, D-48149 Muenster, Germany.
| | - Maria P Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy.
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Thomas J Schmidt
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
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30
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Lynch CA, Pearce R, Pota H, Egwang C, Egwang T, Bhasin A, Cox J, Abeku TA, Roper C. Travel and the emergence of high-level drug resistance in Plasmodium falciparum in southwest Uganda: results from a population-based study. Malar J 2017; 16:150. [PMID: 28415996 PMCID: PMC5392983 DOI: 10.1186/s12936-017-1812-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/08/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The I164L mutation on the dhfr gene confers high level resistance to sulfadoxine-pyrimethamine (SP) but it is rare in Africa except in a cluster of reports where prevalence >10% in highland areas of southwest Uganda and eastern Rwanda. The occurrence of the dhfr I164L mutation was investigated in community surveys in this area and examined the relationship to migration. METHODS A cross-sectional prevalence survey was undertaken in among villages within the catchment areas of two health facilities in a highland site (Kabale) and a highland fringe site (Rukungiri) in 2007. Sociodemographic details, including recent migration, were collected for each person included in the study. A total of 206 Plasmodium falciparum positive subjects were detected by rapid diagnostic test; 203 in Rukungiri and 3 in Kabale. Bloodspot samples were taken and were screened for dhfr I164L. RESULTS Sequence analysis confirmed the presence of the I164L mutations in twelve P. falciparum positive samples giving an estimated prevalence of 8.6% in Rukungiri. Of the three parasite positive samples in Kabale, none had I164L mutations. Among the twelve I164L positives three were male, ages ranged from 5 to 90 years of age. None of those with the I164L mutation had travelled in the 8 weeks prior to the survey, although three were from households from which at least one household member had travelled during that period. Haplotypes were determined in non-mixed infections and showed the dhfr I164L mutation occurs in both as a N51I + S108N + I164L haplotype (n = 2) and N51I + C59R + S108N + I164L haplotype (n = 5). Genotyping of flanking microsatellite markers showed that the I164L occurred independently on the triple mutant (N51I, C59R + S108N) and double mutant (N51I + S108N) background. CONCLUSIONS There is sustained local transmission of parasites with the dhfr I164L mutation in Rukungiri and no evidence to indicate its occurrence is associated with recent travel to highly resistant neighbouring areas. The emergence of a regional cluster of I164L in SW Uganda and Rwanda indicates that transmission of I164L is facilitated by strong drug pressure in low transmission areas potentially catalysed in those areas by travel and the importation of parasites from relatively higher transmission settings.
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Affiliation(s)
- Caroline A Lynch
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
| | - Richard Pearce
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Hirva Pota
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Amit Bhasin
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jonathan Cox
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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31
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Gomes AR, Ravenhall M, Benavente ED, Talman A, Sutherland C, Roper C, Clark TG, Campino S. Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:174-180. [PMID: 28376349 PMCID: PMC5379905 DOI: 10.1016/j.ijpddr.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/19/2022]
Abstract
Drug resistance is a recurrent problem in the fight against malaria. Genetic and epidemiological surveillance of antimalarial resistant parasite alleles is crucial to guide drug therapies and clinical management. New antimalarial compounds are currently at various stages of clinical trials and regulatory evaluation. Using ∼2000 Plasmodium falciparum genome sequences, we investigated the genetic diversity of eleven gene-targets of promising antimalarial compounds and assessed their potential efficiency across malaria endemic regions. We determined if the loci are under selection prior to the introduction of new drugs and established a baseline of genetic variance, including potential resistant alleles, for future surveillance programmes. Genetic diversity of 11gene-targets of new antimalarial compounds was investigated. Genetic data was analysed for 18 malaria endemic countries. No signals of selective pressure was observed. A mutation linked to resistance to a new antimalarial was found in African parasites. Amino-acid changes close to reported antimalarial resistant mutations were detected.
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Affiliation(s)
- Ana Rita Gomes
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Ravenhall
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Arthur Talman
- Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Colin Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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