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Thiam F, Diop G, Coulonges C, Derbois C, Mbengue B, Thiam A, Nguer CM, Zagury JF, Deleuze JF, Dieye A. G6PD and HBB polymorphisms in the Senegalese population: prevalence, correlation with clinical malaria. PeerJ 2022; 10:e13487. [PMID: 35811813 PMCID: PMC9266585 DOI: 10.7717/peerj.13487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/03/2022] [Indexed: 01/24/2023] Open
Abstract
Background Host genetic factors contribute to the variability of malaria phenotypes and can allow a better understanding of mechanisms involved in susceptibility and/or resistance to Plasmodium falciparum infection outcomes. Several genetic polymorphisms were reported to be prevalent among populations living in tropical malaria-endemic regions and induce protection against malaria. The present study aims to investigate the prevalence of HBB (chr11) and G6PD (chrX) deficiencies polymorphisms among Senegalese populations and their associations with the risk for severe Plasmodium falciparum malaria occurrence. Methods We performed a retrospective study with 437 samples, 323 patients recruited in hospitals located in three different endemic areas where malaria episodes were confirmed and 114 free malaria controls. The patients enrolled were classified into two groups: severe malaria (SM) (153 patients) and uncomplicated malaria (UM) (170 patients). PCR and DNA sequencing assessed host genetic polymorphisms in HBB and G6PD. Using a multivariate regression and additive model, estimates of the impact of human HBB and G6PD polymorphisms on malaria incidence were performed. Results Six frequent SNPs with minor allele frequencies (MAF) > 3% were detected in the HBB gene (rs7946748, rs7480526, rs10768683, rs35209591, HbS (rs334) and rs713040) and two in the G6PD gene (rs762515 and rs1050828 (G6PD-202 G > A). Analysis of selected HbS polymorphism showed significant association with protective effect against severe malaria with a significant p-value = 0.033 (OR 0.38, 95% CI [0.16-0.91]) for SM vs. UM comparison. Surprisingly, our study did not identify the protective effect of variant HbC polymorphism against severe malaria. Finally, we found some of the polymorphisms, like HbS (rs334), are associated with age and biological parameters like eosinophils, basophils, lymphocytes etc. Conclusion Our data report HBB and G6PD polymorphisms in the Senegalese population and their correlation with severe/mild malaria and outcome. The G6PD and HBB deficiencies are widespread in West Africa endemic malaria regions such as The Gambia, Mali, and Burkina Faso. The study shows the critical role of genetic factors in malaria outcomes. Indeed, genetic markers could be good tools for malaria endemicity prognosis.
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Affiliation(s)
- Fatou Thiam
- Groupe de Recherche Biotechnologie Appliquée et Bioprocédés Environnementaux (GRBA-BE), Laboratoire Eau, Energie, Environnement et Procédés Industriels (LE3PI), Département de Génie Chimique et Biologie Appliquée, Ecole Supérieure Polytechnique, Université Cheikh Anta DIOP de Dakar, Dakar Fann, Dakar, Sénégal
| | - Gora Diop
- Unité Postulante de Biologie Génétique, Génomique et Bio-informatique (G2B), Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar Fann, Dakar, Sénégal,Pole d’Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, Dakar, Sénégal
| | - Cedric Coulonges
- Equipe GBA «Génomique, Bioinformatique & Applications », Conservatoire National des Arts et Métiers, Paris, France
| | - Céline Derbois
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Babacar Mbengue
- Service d’Immunologie, Faculté de Médecine, de Pharmacie et d’Odontostomatologie, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Alassane Thiam
- Pole d’Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, Dakar, Sénégal
| | - Cheikh Momar Nguer
- Groupe de Recherche Biotechnologie Appliquée et Bioprocédés Environnementaux (GRBA-BE), Laboratoire Eau, Energie, Environnement et Procédés Industriels (LE3PI), Département de Génie Chimique et Biologie Appliquée, Ecole Supérieure Polytechnique, Université Cheikh Anta DIOP de Dakar, Dakar Fann, Dakar, Sénégal
| | - Jean Francois Zagury
- Equipe GBA «Génomique, Bioinformatique & Applications », Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-Francois Deleuze
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Alioune Dieye
- Service d’Immunologie, Faculté de Médecine, de Pharmacie et d’Odontostomatologie, Université Cheikh Anta DIOP, Dakar, Sénégal
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Dos Santos RO, da Cruz MGS, Lopes SCP, Oliveira LB, Nogueira PA, Lima ES, Soares IS, Kano FS, de Carvalho AT, Costa FTM, Ganoza CA, de Lacerda MVG, Lalwani P. A First Plasmodium vivax Natural Infection Induces Increased Activity of the Interferon Gamma-Driven Tryptophan Catabolism Pathway. Front Microbiol 2020; 11:400. [PMID: 32256470 PMCID: PMC7089964 DOI: 10.3389/fmicb.2020.00400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
The human immune response that controls Plasmodium infection in the liver and blood stages of the parasite life cycle is composed by both pro- and anti-inflammatory programs. Pro-inflammatory responses primarily mediated by IFN-γ controls the infection, but also induce tolerogenic mechanisms to limit host damage, including the tryptophan (TRP) catabolism pathway mediated by the enzyme Indoleamine 2,3-Dioxygenase (IDO1), an enzyme that catalyzes the degradation of TRP to kynurenines (KYN). Here we assessed total serum kynurenines and cytokine dynamics in a cohort of natural Plasmodium vivax human infection and compared them to those of endemic healthy controls and other febrile diseases. In acute malaria, the absolute free kynurenine (KYN) serum levels and the KYN to TRP (KYN/TRP) ratio were significantly elevated in patients compared to healthy controls. Individuals with a diagnosis of a first malaria episode had higher serum KYN levels than individuals with a previous malaria episode. We observed an inverse relationship between the serum levels of IFN-γ and IL-10 in patients with a first malaria episode compared to those of subjects with previous history of malaria. Kynurenine elevation was positively correlated with serum IFN-γ levels in acute infection, whereas, it was negatively correlated with parasite load and P. vivax LDH levels. Overall, the differences observed between infected individuals depended on the number of Plasmodium infections. The decrease in the KYN/TRP ratio in malaria-experienced subjects coincided with the onset of anti-P. vivax IgG. These results suggest that P. vivax infection induces a strong anti-inflammatory program in individuals with first time malaria, which fades with ensuing protective immunity after subsequent episodes. Understanding the tolerance mechanisms involved in the initial exposure would help in defining the balance between protective and pathogenic immune responses necessary to control infection and to improve vaccination strategies.
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Affiliation(s)
| | | | | | | | | | - Emerson Silva Lima
- Faculdade de Ciências Farmacêuticas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
| | - Irene Silva Soares
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Flora Satiko Kano
- Instituto René Rachou (IRR), Fiocruz Minas Gerais, Belo Horizonte, Brazil
| | | | - Fabio Trindade Maranhão Costa
- Departamento de Genética, Evolução, Imunologia e Microbiologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Christian A Ganoza
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Marcus Vinicius Guimarães de Lacerda
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Manaus, Brazil.,Fundação de Medicina Tropical, Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Pritesh Lalwani
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Manaus, Brazil
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Pfeffer DA, Lucas TCD, May D, Harris J, Rozier J, Twohig KA, Dalrymple U, Guerra CA, Moyes CL, Thorn M, Nguyen M, Bhatt S, Cameron E, Weiss DJ, Howes RE, Battle KE, Gibson HS, Gething PW. malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project. Malar J 2018; 17:352. [PMID: 30290815 PMCID: PMC6173876 DOI: 10.1186/s12936-018-2500-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/29/2018] [Indexed: 12/20/2022] Open
Abstract
Background The Malaria Atlas Project (MAP) has worked to assemble and maintain a global open-access database of spatial malariometric data for over a decade. This data spans various formats and topics, including: geo-located surveys of malaria parasite rate; global administrative boundary shapefiles; and global and regional rasters representing the distribution of malaria and associated illnesses, blood disorders, and intervention coverage. MAP has recently released malariaAtlas, an R package providing a direct interface to MAP’s routinely-updated malariometric databases and research outputs. Methods and results The current paper reviews the functionality available in malariaAtlas and highlights its utility for spatial epidemiological analysis of malaria. malariaAtlas enables users to freely download, visualise and analyse global malariometric data within R. Currently available data types include: malaria parasite rate and vector occurrence point data; subnational administrative boundary shapefiles; and a large suite of rasters covering a diverse range of metrics related to malaria research. malariaAtlas is here used in two mock analyses to illustrate how this data may be incorporated into a standard R workflow for spatial analysis. Conclusions malariaAtlas is the first open-access R-interface to malariometric data, providing a new and reproducible means of accessing such data within a freely available and commonly used statistical software environment. In this way, the malariaAtlas package aims to contribute to the environment of data-sharing within the malaria research community. Electronic supplementary material The online version of this article (10.1186/s12936-018-2500-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel A Pfeffer
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Timothy C D Lucas
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.
| | - Daniel May
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Joseph Harris
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Jennifer Rozier
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Katherine A Twohig
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Ursula Dalrymple
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Carlos A Guerra
- Sanaria Institute for Global Health & Tropical Medicine, Rockville, MD, 20850, USA
| | - Catherine L Moyes
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Mike Thorn
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Michele Nguyen
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Samir Bhatt
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Ewan Cameron
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Daniel J Weiss
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Rosalind E Howes
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Katherine E Battle
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Harry S Gibson
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Peter W Gething
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
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Howes RE, Battle KE, Mendis KN, Smith DL, Cibulskis RE, Baird JK, Hay SI. Global Epidemiology of Plasmodium vivax. Am J Trop Med Hyg 2016; 95:15-34. [PMID: 27402513 PMCID: PMC5198891 DOI: 10.4269/ajtmh.16-0141] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023] Open
Abstract
Plasmodium vivax is the most widespread human malaria, putting 2.5 billion people at risk of infection. Its unique biological and epidemiological characteristics pose challenges to control strategies that have been principally targeted against Plasmodium falciparum Unlike P. falciparum, P. vivax infections have typically low blood-stage parasitemia with gametocytes emerging before illness manifests, and dormant liver stages causing relapses. These traits affect both its geographic distribution and transmission patterns. Asymptomatic infections, high-risk groups, and resulting case burdens are described in this review. Despite relatively low prevalence measurements and parasitemia levels, along with high proportions of asymptomatic cases, this parasite is not benign. Plasmodium vivax can be associated with severe and even fatal illness. Spreading resistance to chloroquine against the acute attack, and the operational inadequacy of primaquine against the multiple attacks of relapse, exacerbates the risk of poor outcomes among the tens of millions suffering from infection each year. Without strategies accounting for these P. vivax-specific characteristics, progress toward elimination of endemic malaria transmission will be substantially impeded.
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Affiliation(s)
- Rosalind E. Howes
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Katherine E. Battle
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kamini N. Mendis
- Global Malaria Program, World Health Organization, Geneva, Switzerland
| | - David L. Smith
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
- Sanaria Institute for Global Health and Tropical Medicine, Rockville, Maryland
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington
| | | | - J. Kevin Baird
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon I. Hay
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
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Moyes CL, Temperley WH, Henry AJ, Burgert CR, Hay SI. Providing open access data online to advance malaria research and control. Malar J 2013; 12:161. [PMID: 23680401 PMCID: PMC3662599 DOI: 10.1186/1475-2875-12-161] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/10/2013] [Indexed: 11/12/2022] Open
Abstract
Background To advance research on malaria, the outputs from existing studies and the data that fed into them need to be made freely available. This will ensure new studies can build on the work that has gone before. These data and results also need to be made available to groups who are developing public health policies based on up-to-date evidence. The Malaria Atlas Project (MAP) has collated and geopositioned over 50,000 parasite prevalence and vector occurrence survey records contributed by over 3,000 sources including research groups, government agencies and non-governmental organizations worldwide. This paper describes the results of a project set up to release data gathered, used and generated by MAP. Methods Requests for permission to release data online were sent to 236 groups who had contributed unpublished prevalence (parasite rate) surveys. An online explorer tool was developed so that users can visualize the spatial distribution of the vector and parasite survey data before downloading it. In addition, a consultation group was convened to provide advice on the mode and format of release for data generated by MAP’s modelling work. New software was developed to produce a suite of publication-quality map images for download from the internet for use in external publications. Conclusion More than 40,000 survey records can now be visualized on a set of dynamic maps and downloaded from the MAP website on a free and unrestricted basis. As new data are added and new permissions to release existing data come in, the volume of data available for download will increase. The modelled data output from MAP’s own analyses are also available online in a range of formats, including image files and GIS surface data, for use in advocacy, education, further research and to help parameterize or validate other mathematical models.
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Affiliation(s)
- Catherine L Moyes
- Department of Zoology, Spatial Ecology and Epidemiology Group, Tinbergen Building, South Parks Road, Oxford, OX 1 3PS, UK.
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