51
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Rougeron V, Tiedje KE, Chen DS, Rask TS, Gamboa D, Maestre A, Musset L, Legrand E, Noya O, Yalcindag E, Renaud F, Prugnolle F, Day KP. Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance. Ecol Evol 2017; 7:9376-9390. [PMID: 29187975 PMCID: PMC5696401 DOI: 10.1002/ece3.3425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/07/2017] [Accepted: 08/19/2017] [Indexed: 11/11/2022] Open
Abstract
Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.
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Affiliation(s)
- Virginie Rougeron
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Kathryn E Tiedje
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Donald S Chen
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA
| | - Thomas S Rask
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt and Departamento de Ciencias Celulares y Moleculares Facultad de Ciencias y Filosofia Universidad Peruana Cayetano Heredia Lima Peru
| | - Amanda Maestre
- Grupo Salud y Comunidad Facultad de Medicina Universidad de Antioquía Medellín Colombia
| | - Lise Musset
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana
| | - Eric Legrand
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana.,Unit of Genetics and Genomics on Insect Vectors Institut Pasteur Paris France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria Instituto de Altos Estudios en Salud "Dr. Arnoldo Gabaldón" Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical Universidad Central de Venezuela Caracas Venezuela
| | - Erhan Yalcindag
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Karen P Day
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
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52
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Hamilton WL, Claessens A, Otto TD, Kekre M, Fairhurst RM, Rayner JC, Kwiatkowski D. Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Res 2017; 45:1889-1901. [PMID: 27994033 PMCID: PMC5389722 DOI: 10.1093/nar/gkw1259] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/01/2016] [Indexed: 01/31/2023] Open
Abstract
For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution.
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Affiliation(s)
- William L Hamilton
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0SP, UK
| | - Antoine Claessens
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Mihir Kekre
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Dominic Kwiatkowski
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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53
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Johri P, Krenek S, Marinov GK, Doak TG, Berendonk TU, Lynch M. Population Genomics of Paramecium Species. Mol Biol Evol 2017; 34:1194-1216. [PMID: 28204679 DOI: 10.1093/molbev/msx074] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington, IN
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | | | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
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Palinauskas V, Bernotienė R, Žiegytė R, Bensch S, Valkiūnas G. Experimental evidence for hybridization of closely related lineages in Plasmodium relictum. Mol Biochem Parasitol 2017; 217:1-6. [PMID: 28803842 DOI: 10.1016/j.molbiopara.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 05/02/2017] [Accepted: 08/05/2017] [Indexed: 02/02/2023]
Abstract
Over 50 avian Plasmodium species have been described. However, PCR-based information shows much broader diversity of genetic lineages in these parasites. This discrepancy indicates insufficient knowledge about taxonomic diversity and boundaries of a single species in avian Plasmodium species. In recent taxonomy, most of genetically closely related lineages that share the same morphology and development patterns are attributed to the same biological species, but there is no information if these lineages are able to cross. This information is crucial to understand if these lineages form single or multiple evolutionary units. Due to presence of sexual process and sporogonic development of Plasmodium parasites in mosquitoes, self and cross-fertilization can occur and be identified during the oocyst stage. We initiated in vivo hybridization experiments of two widespread Plasmodium relictum lineages (pSGS1 and pGRW11) in experimentally infected Culex pipiens pipiens form molestus mosquitoes. To study putative hybrid oocysts, we used a laser microdissection technique together with PCR-based analyses of mitochondrial and nuclear genes. We demonstrate that both pSGS1 and pGRW11 lineages develop in infected mosquitoes in parallel, but also form hybrid oocysts of these two lineages. Our results are in accord to a recent global phylogeographic study of P. relictum that suggested that cross-fertilization between pSGS1 and pGRW11 might occur. This information helps to understand population structure, gene flow and the evolutionary process of haemosporidian parasites.
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Affiliation(s)
| | - Rasa Bernotienė
- Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania
| | - Rita Žiegytė
- Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania
| | - Staffan Bensch
- Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden
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55
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Oppenheim SJ, Rosenfeld JA, DeSalle R. Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors. BMC Genomics 2017; 18:205. [PMID: 28241792 PMCID: PMC5327517 DOI: 10.1186/s12864-017-3590-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/13/2017] [Indexed: 11/24/2022] Open
Abstract
Background The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. Results The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Conclusions Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they generate. We believe that efforts to maximize the amount of information obtained from automated annotation can help address the functional annotation deficit that most evolutionary biologists now face, and here demonstrate the value of such an approach. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3590-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara J Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Jeffrey A Rosenfeld
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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56
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Zin NM, Baba MS, Zainal-Abidin AH, Latip J, Mazlan NW, Edrada-Ebel R. Gancidin W, a potential low-toxicity antimalarial agent isolated from an endophytic Streptomyces SUK10. Drug Des Devel Ther 2017; 11:351-363. [PMID: 28223778 PMCID: PMC5308589 DOI: 10.2147/dddt.s121283] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Endophytic Streptomyces strains are potential sources for novel bioactive molecules. In this study, the diketopiperazine gancidin W (GW) was isolated from the endophytic actinobacterial genus Streptomyces, SUK10, obtained from the bark of Shorea ovalis tree, and it was tested in vivo against Plasmodium berghei PZZ1/100. GW exhibited an inhibition rate of nearly 80% at 6.25 and 3.125 μg kg-1 body weight on day four using the 4-day suppression test method on male ICR strain mice. Comparing GW at both concentrations with quinine hydrochloride and normal saline as positive and negative controls, respectively, 50% of the mice treated with 3.125 μg kg-1 body weight managed to survive for more than 11 months after infection, which almost reached the life span of normal mice. Biochemical tests of selected enzymes and proteins in blood samples of mice treated with GW were also within normal levels; in addition, no abnormalities or injuries were found on internal vital organs. These findings indicated that this isolated bioactive compound from Streptomyces SUK10 exhibits very low toxicity and is a good candidate for potential use as an antimalarial agent in an animal model.
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Affiliation(s)
- Noraziah Mohamad Zin
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur
| | - Mohd Shukri Baba
- Department of Biomedical Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan
| | | | - Jalifah Latip
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi
| | - Noor Wini Mazlan
- Analytical and Environmental Chemistry, School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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57
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Anderson TJC, Nair S, McDew-White M, Cheeseman IH, Nkhoma S, Bilgic F, McGready R, Ashley E, Pyae Phyo A, White NJ, Nosten F. Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites. Mol Biol Evol 2016; 34:131-144. [PMID: 28025270 PMCID: PMC5216669 DOI: 10.1093/molbev/msw228] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population genetic parameters for Plasmodium. We sequenced kelch13 (n = 1,876), genotyped 75 flanking SNPs, and measured clearance rate (n = 3,552) in parasite infections from Western Thailand (2001–2014). We describe 32 independent coding mutations including common mutations outside the kelch13 propeller associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ∼0.079. ART-R allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The frequency with which adaptive alleles arise is determined by the rate of mutation and the population size. Two factors drive this soft sweep: (1) multiple kelch13 amino-acid mutations confer resistance providing a large mutational target—we estimate the target is 87–163 bp. (2) The population mutation parameter (Θ = 2Neμ) can be estimated from the frequency distribution of ART-R alleles and is ∼5.69, suggesting that short term effective population size is 88 thousand to 1.2 million. This is 52–705 times greater than Ne estimated from fluctuation in allele frequencies, suggesting that we have previously underestimated the capacity for adaptive evolution in Plasmodium. Our central conclusions are that retrospective studies may underestimate the complexity of selective events and the Ne relevant for adaptation for malaria is considerably higher than previously estimated.
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Affiliation(s)
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Marina McDew-White
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell Nkhoma
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Fatma Bilgic
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Elizabeth Ashley
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicholas J White
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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58
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Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet 2016; 50:447-465. [PMID: 27732796 DOI: 10.1146/annurev-genet-120215-035211] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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59
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Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain. Proc Natl Acad Sci U S A 2016; 113:11495-11500. [PMID: 27671660 DOI: 10.1073/pnas.1611017113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe-where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.
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60
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Mapua MI, Petrželková KJ, Burgunder J, Dadáková E, Brožová K, Hrazdilová K, Stewart FA, Piel AK, Vallo P, Fuehrer HP, Hashimoto C, Modrý D, Qablan MA. A comparative molecular survey of malaria prevalence among Eastern chimpanzee populations in Issa Valley (Tanzania) and Kalinzu (Uganda). Malar J 2016; 15:423. [PMID: 27543045 PMCID: PMC4992209 DOI: 10.1186/s12936-016-1476-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 08/10/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Habitat types can affect vector and pathogen distribution and transmission dynamics. The prevalence and genetic diversity of Plasmodium spp. in two eastern chimpanzee populations-Kalinzu Forest Reserve, Uganda and Issa Valley, Tanzania-inhabiting different habitat types was investigated. As a follow up study the effect of host sex and age on infections patterns in Kalinzu Forest Reserve chimpanzees was determined. METHODS Molecular methods were employed to detect Plasmodium DNA from faecal samples collected from savanna-woodland (Issa Valley) and forest (Kalinzu Forest Reserve) chimpanzee populations. RESULTS Based on a Cytochrome-b PCR assay, 32 out of 160 Kalinzu chimpanzee faecal samples were positive for Plasmodium DNA, whilst no positive sample was detected in 171 Issa Valley chimpanzee faecal samples. Sequence analysis revealed that previously known Laverania species (Plasmodium reichenowi, Plasmodium billbrayi and Plasmodium billcollinsi) are circulating in the Kalinzu chimpanzees. A significantly higher proportion of young individuals were tested positive for infections, and switching of Plasmodium spp. was reported in one individual. Amongst the positive individuals sampled more than once, the success of amplification of Plasmodium DNA from faeces varied over sampling time. CONCLUSION The study showed marked differences in the prevalence of malaria parasites among free ranging chimpanzee populations living in different habitats. In addition, a clear pattern of Plasmodium infections with respect to host age was found. The results presented in this study contribute to understanding the ecological aspects underlying the malaria infections in the wild. Nevertheless, integrative long-term studies on vector abundance, Plasmodium diversity during different seasons between sites would provide more insight on the occurrence, distribution and ecology of these pathogens.
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Affiliation(s)
- Mwanahamisi I Mapua
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00, Brno, Czech Republic.,Liberec Zoo, 460 01, Liberec, Czech Republic.,Institute of Parasitology, Biology Centre, Czech of the Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Jade Burgunder
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.,Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Eva Dadáková
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic
| | - Kristýna Brožová
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic
| | - Kristýna Hrazdilová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.,Department of Virology, Veterinary Research Institute, 621 00, Brno, Czech Republic.,CEITEC-Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic
| | - Fiona A Stewart
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L33AF, UK
| | - Peter Vallo
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00, Brno, Czech Republic.,Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Albert-Einstein Allee 11, 89069, Ulm, Germany
| | - Hans-Peter Fuehrer
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Chie Hashimoto
- Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi, 484-8506, Japan
| | - David Modrý
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech of the Academy of Sciences, 370 05, České Budějovice, Czech Republic.,CEITEC-Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic
| | - Moneeb A Qablan
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.,CEITEC-Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, 612 42, Brno, Czech Republic.,Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
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Yusof R, Ahmed MA, Jelip J, Ngian HU, Mustakim S, Hussin HM, Fong MY, Mahmud R, Sitam FAT, Japning JRR, Snounou G, Escalante AA, Lau YL. Phylogeographic Evidence for 2 Genetically Distinct Zoonotic Plasmodium knowlesi Parasites, Malaysia. Emerg Infect Dis 2016; 22:1371-80. [PMID: 27433965 PMCID: PMC4982179 DOI: 10.3201/eid2208.151885] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections of humans with the zoonotic simian malaria parasite Plasmodium knowlesi occur throughout Southeast Asia, although most cases have occurred in Malaysia, where P. knowlesi is now the dominant malaria species. This apparently skewed distribution prompted an investigation of the phylogeography of this parasite in 2 geographically separated regions of Malaysia, Peninsular Malaysia and Malaysian Borneo. We investigated samples collected from humans and macaques in these regions. Haplotype network analyses of sequences from 2 P. knowlesi genes, type A small subunit ribosomal 18S RNA and cytochrome c oxidase subunit I, showed 2 genetically distinct divergent clusters, 1 from each of the 2 regions of Malaysia. We propose that these parasites represent 2 distinct P. knowlesi types that independently became zoonotic. These types would have evolved after the sea-level rise at the end of the last ice age, which separated Malaysian Borneo from Peninsular Malaysia.
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Abstract
The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. DOI:http://dx.doi.org/10.7554/eLife.08714.001 Malaria is an infectious disease caused by a microscopic parasite called Plasmodium, which is transferred between humans by mosquitos. One species of malaria parasite called Plasmodium falciparum can cause particularly severe and life-threatening forms of the disease. Currently, the most widely used treatment for P. falciparum infections is artemisinin combination therapy, a treatment that combines the drug artemisinin (or a closely related molecule) with another antimalarial drug. However, resistance to artemisinin has started to spread throughout Southeast Asia. Artemisinin resistance is caused by mutations in a parasite gene called kelch13, and researchers have identified over 20 different mutations in P. falciparum that confer artemisinin resistance. The diversity of mutations involved, and the fact that the same mutation can arise independently in different locations, make it difficult to track the spread of resistance using conventional molecular marker approaches. Here, Amato, Miotto et al. sequenced the entire genomes of more than 3,000 clinical samples of P. falciparum from Southeast Asia and Africa, collected as part of a global network of research groups called the MalariaGEN Plasmodium falciparum Community Project. Amato, Miotto et al. found that African parasites had independently acquired many of the same kelch13 mutations that are known to cause resistance to artemisinin in Southeast Asia. However the kelch13 mutations seen in Africa remained at low levels in the parasite population, and appeared to be under much less pressure for evolutionary selection than those found in Southeast Asia. These findings demonstrate that the emergence and spread of resistance to antimalarial drugs does not depend solely on the mutational process, but also on other factors that influence whether the mutations will spread in the population. Understanding how this is affected by different patterns of drug treatments and other environmental conditions will be important in developing more effective strategies for combating malaria. DOI:http://dx.doi.org/10.7554/eLife.08714.002
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Huang B, Deng C, Yang T, Xue L, Wang Q, Huang S, Su XZ, Liu Y, Zheng S, Guan Y, Xu Q, Zhou J, Yuan J, Bacar A, Abdallah KS, Attoumane R, Mliva AMSA, Zhong Y, Lu F, Song J. Polymorphisms of the artemisinin resistant marker (K13) in Plasmodium falciparum parasite populations of Grande Comore Island 10 years after artemisinin combination therapy. Parasit Vectors 2015; 8:634. [PMID: 26667053 PMCID: PMC4678476 DOI: 10.1186/s13071-015-1253-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/10/2015] [Indexed: 12/03/2022] Open
Abstract
Background Plasmodium falciparum malaria is a significant public health problem in Comoros, and artemisinin combination therapy (ACT) remains the first choice for treating acute uncomplicated P. falciparum. The emergence and spread of artemisinin-resistant P. falciparum in Southeast Asia, associated with mutations in K13-propeller gene, poses a potential threat to ACT efficacy. Detection of mutations in the P. falciparum K13-propeller gene may provide the first-hand information on changes in parasite susceptibility to artemisinin. The objective of this study is to determinate the prevalence of mutant K13-propeller gene among the P. falciparum isolates collected from Grande Comore Island, Union of Comoros, where ACT has been in use since 2004. Methods A total of 207 P. falciparum clinical isolates were collected from the island during March 2006 and October 2007 (n = 118) and March 2013 and December 2014 (n = 89). All isolates were analysed for single nucleotide polymorphisms (SNPs) and haplotypes in the K13-propeller gene using nested PCR and DNA sequencing. Results Only three 2006–2007 samples carried SNPs in the K13-propeller gene, one having a synonymous (G538G) and the other having two non-synonymous (S477Y and D584E) substitutions leading to two mutated haplotypes (2.2 %, 2/95). Three synonymous mutations (R471R, Y500Y, and G538G) (5.9 %, 5/85) and 7 non-synonymous substitutions (21.2 %, 18/85) with nine mutated haplotypes (18.8 %, 16/85) were found in isolates from 2013 to 2014. However, none of the polymorphisms associated with artemisinin-resistance in Southeast Asia was detected from any of the parasites examined. Conclusion This study showed increased K13-propeller gene diversity among P. falciparum populations on the Island over the course of 8 years (2006–2014). Nevertheless, none of the polymorphisms known to be associated with artemisinin resistance in Asia was detected in the parasite populations examined. Our data suggest that P. falciparum populations in Grande Comore are still effectively susceptible to artemisinin. Our results provide insights into P. falciparum populations regarding mutations in the gene associated with artemisinin resistance and will be useful for developing and updating anti-malarial guidance in Comoros.
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Affiliation(s)
- Bo Huang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Changsheng Deng
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Tao Yang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Linlu Xue
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Qi Wang
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Shiguang Huang
- School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, PR China.
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. .,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, PR China.
| | - Yajun Liu
- The first affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Shaoqin Zheng
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Yezhi Guan
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Qin Xu
- Research Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Jiuyao Zhou
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Jie Yuan
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Afane Bacar
- National Malaria Control Programme, Moroni, Union of Comoros.
| | | | | | | | - Yanchun Zhong
- Traditional Chinese Medicine Collage, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
| | - Fangli Lu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, Guangdong, PR China.
| | - Jianping Song
- Science and Technology Park, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, PR China.
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Differential Spleen Remodeling Associated with Different Levels of Parasite Virulence Controls Disease Outcome in Malaria Parasite Infections. mSphere 2015; 1:mSphere00018-15. [PMID: 27303680 PMCID: PMC4863626 DOI: 10.1128/msphere.00018-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/11/2015] [Indexed: 11/20/2022] Open
Abstract
Infections by malaria parasites can lead to very different clinical outcomes, ranging from mild symptoms to death. Differences in the ability of the spleen to deal with the infected red blood cells (iRBCs) are linked to differences in virulence. Using virulent and avirulent strains of the rodent malaria parasite Plasmodium yoelii, we investigated how parasite virulence modulates overall spleen function. Following parasite invasion, a difference in parasite virulence was observed in association with different levels of spleen morphology and iRBC rigidity, both of which contributed to enhanced parasite clearance. Moreover, iRBC rigidity as modulated by the spleen was demonstrated to correlate with disease outcome and thus can be used as a robust indicator of virulence. The data indicate that alterations in the biomechanical properties of iRBCs are the result of the complex interaction between host and parasite. Furthermore, we confirmed that early spleen responses are a key factor in directing the clinical outcome of an infection. IMPORTANCE The spleen and its response to parasite infection are important in eliminating parasites in malaria. By comparing P. yoelii parasite lines with different disease outcomes in mice that had either intact spleens or had had their spleens removed, we showed that upon parasite infection, the spleen exhibits dramatic changes that can affect parasite clearance. The spleen itself directly impacts RBC deformability independently of parasite genetics. The data indicated that the changes in the biomechanical properties of malaria parasite-infected RBCs are the result of the complex interaction between host and parasite, and RBC deformability itself can serve as a novel predictor of clinical outcome. The results also suggest that early responses in the spleen are a key factor directing the clinical outcome of an infection.
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Baba MS, Zin NM, Hassan ZAA, Latip J, Pethick F, Hunter IS, Edrada-Ebel R, Herron PR. In vivo antimalarial activity of the endophytic actinobacteria, Streptomyces SUK 10. J Microbiol 2015; 53:847-55. [PMID: 26626355 DOI: 10.1007/s12275-015-5076-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 10/30/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022]
Abstract
Endophytic bacteria, such as Streptomyces, have the potential to act as a source for novel bioactive molecules with medicinal properties. The present study was aimed at assessing the antimalarial activity of crude extract isolated from various strains of actinobacteria living endophytically in some Malaysian medicinal plants. Using the four day suppression test method on male ICR strain mice, compounds produced from three strains of Streptomyces (SUK8, SUK10, and SUK27) were tested in vivo against Plasmodium berghei PZZ1/100 in an antimalarial screen using crude extracts at four different concentrations. One of these extracts, isolated from Streptomyces SUK10 obtained from the bark of Shorea ovalis tree, showed inhibition of the test organism and was further tested against P. berghei-infected mice for antimalarial activity at different concentrations. There was a positive relationship between the survival of the infected mouse group treated with 50 µg/kg body weight (bw) of ethyl acetate-SUK10 crude extract and the ability to inhibit the parasites growth. The parasite inhibition percentage for this group showed that 50% of the mice survived for more than 90 days after infection with the parasite. The nucleotide sequence and phylogenetic tree suggested that Streptomyces SUK10 may constitute a new species within the Streptomyces genus. As part of the drug discovery process, these promising finding may contribute to the medicinal and pharmaceutical field for malarial treatment.
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Affiliation(s)
- Mohd Shukri Baba
- School of Diagnostic Sciences and Applied Health, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
| | - Noraziah Mohamad Zin
- School of Diagnostic Sciences and Applied Health, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia.
| | - Zainal Abidin Abu Hassan
- Department of Parasitology, Medical Faculty, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | - Jalifah Latip
- School of Chemistry Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Florence Pethick
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, United Kingdom
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, United Kingdom
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, United Kingdom
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, United Kingdom
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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Lawal B, Shittu OK, Kabiru AY, Jigam AA, Umar MB, Berinyuy EB, Alozieuwa BU. Potential antimalarials from African natural products: A reviw. JOURNAL OF COMPLEMENTARY MEDICINE RESEARCH 2015; 4:318-43. [PMID: 26649238 PMCID: PMC4665028 DOI: 10.5455/jice.20150928102856] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/14/2015] [Indexed: 12/22/2022]
Abstract
Malaria remains an overwhelming infectious disease with significant health challenges in African and other endemic countries globally. Resistance to antimalarial drugs has become one of the most momentous challenges to human health, and thus has necessitated the hunt for new and effective drugs. Consequently, few decades have witnessed a surfeit of research geared to validate the effectiveness of commonly used traditionally medicines against malaria fever. The present review work focuses on documenting natural products from African whose activity has been reported in vivo or in vitro against malaria parasite. Literature was collected using electronic search of published articles (Google Scholar, PubMed, Medline, Sciencedirect, and Science domain) that report on antiplasmodial activity of natural products from differernts Africa region. A total of 652 plant taxa from 146 families, 134 isolated antimalarial compounds from 39 plants species, 2 herbal formulations and 4 insect/products were found to be reported in literature from 1996 to 2015. Plants species from family Asteraceae (11.04%), Fababceae (8.128%), Euphorbiaceae (5.52%), Rubiaceas (5.52%), and Apocyanaceae (5.214%), have received more scientific validation than others. African natural products possess remarkable healing properties as revealed in the various citations as promising antimalarial agents. Some of these natural products from Africa demonstrate high, promising or low activities against Plasmodium parasite. This study also shows that natural products from Africa have a huge amount of novel antimalarial compounds that could serve as a leads for the development of new and effective antiplasmodial drugs. However, in a view of bridging the gap in knowledge, clinical validation of these natural products are of paramount importance.
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Affiliation(s)
- Bashir Lawal
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
| | - Oluwatosin Kudirat Shittu
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
| | - Adamu Yusuf Kabiru
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
| | - Ali Audu Jigam
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
| | - Maimuna Bello Umar
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
| | | | - Blessing Uchenna Alozieuwa
- Department of Biochemistry, Tropical Disease Research Unit, Federal University of Technology, P.M.B. 65, Minna, Nigeria
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Ingasia LA, Cheruiyot J, Okoth SA, Andagalu B, Kamau E. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya. INFECTION GENETICS AND EVOLUTION 2015; 39:372-380. [PMID: 26472129 DOI: 10.1016/j.meegid.2015.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
Abstract
Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p<0.0001) whereas Kisii had the least significant index of association values (0.03; p<0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.
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Affiliation(s)
- Luicer A Ingasia
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Jelagat Cheruiyot
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Sheila Akinyi Okoth
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States; Atlanta Research and Education Foundation/VA Medical Center, Decatur, GA, United States
| | - Ben Andagalu
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Edwin Kamau
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya.
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Band G, Rockett KA, Spencer CCA, Kwiatkowski DP. A novel locus of resistance to severe malaria in a region of ancient balancing selection. Nature 2015; 526:253-7. [PMID: 26416757 PMCID: PMC4629224 DOI: 10.1038/nature15390] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 08/10/2015] [Indexed: 12/13/2022]
Abstract
The high prevalence of sickle haemoglobin in Africa shows that malaria has been a major force for human evolutionary selection, but surprisingly few other polymorphisms have been proven to confer resistance to malaria in large epidemiological studies. To address this problem, we conducted a multi-centre genome-wide association study (GWAS) of life-threatening Plasmodium falciparum infection (severe malaria) in over 11,000 African children, with replication data in a further 14,000 individuals. Here we report a novel malaria resistance locus close to a cluster of genes encoding glycophorins that are receptors for erythrocyte invasion by P. falciparum. We identify a haplotype at this locus that provides 33% protection against severe malaria (odds ratio = 0.67, 95% confidence interval = 0.60-0.76, P value = 9.5 × 10(-11)) and is linked to polymorphisms that have previously been shown to have features of ancient balancing selection, on the basis of haplotype sharing between humans and chimpanzees. Taken together with previous observations on the malaria-protective role of blood group O, these data reveal that two of the strongest GWAS signals for severe malaria lie in or close to genes encoding the glycosylated surface coat of the erythrocyte cell membrane, both within regions of the genome where it appears that evolution has maintained diversity for millions of years. These findings provide new insights into the host-parasite interactions that are critical in determining the outcome of malaria infection.
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Molina-Cruz A, Barillas-Mury C. The remarkable journey of adaptation of the Plasmodium falciparum malaria parasite to New World anopheline mosquitoes. Mem Inst Oswaldo Cruz 2015; 109:662-7. [PMID: 25185006 PMCID: PMC4156459 DOI: 10.1590/0074-0276130553] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/25/2014] [Indexed: 12/22/2022] Open
Abstract
Plasmodium falciparum originated in Africa, dispersed around the
world as a result of human migration and had to adapt to several different indigenous
anopheline mosquitoes. Anophelines from the New World are evolutionary distant form
African ones and this probably resulted in a more stringent selection of
Plasmodium as it adapted to these vectors. It is thought that
Plasmodium has been genetically selected by some anopheline species
through unknown mechanisms. The mosquito immune system can greatly limit infection
and P. falciparum evolved a strategy to evade these responses, at
least in part mediated by Pfs47, a highly polymorphic gene. We
propose that adaptation of P. falciparum to new vectors may require
evasion of their immune system. Parasites with a Pfs47 haplotype
compatible with the indigenous mosquito vector would be able to survive and be
transmitted. The mosquito antiplasmodial response could be an important determinant
of P. falciparum population structure and could affect malaria
transmission in the Americas.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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Tyagi S, Pande V, Das A. Mitochondrial genome sequence diversity of Indian Plasmodium falciparum isolates. Mem Inst Oswaldo Cruz 2015; 109:494-8. [PMID: 25075789 PMCID: PMC4155855 DOI: 10.1590/0074-0276130531] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 03/11/2014] [Indexed: 11/22/2022] Open
Abstract
We have analysed the whole mitochondrial (mt) genome sequences (each
~6 kilo nucleotide base pairs in length) of four field isolates of the malaria
parasite Plasmodium falciparum collected from different locations
in India. Comparative genomic analyses of mt genome sequences
revealed three novel India-specific single nucleotide polymorphisms. In general, high
mt genome diversity was found in Indian P.
falciparum, at a level comparable to African isolates. A population
phylogenetic tree placed the presently sequenced Indian P. falciparum
with the global isolates, while a previously sequenced Indian isolate was an
outlier. Although this preliminary study is limited to a few numbers of isolates, the
data have provided fundamental evidence of the mt genome diversity
and evolutionary relationships of Indian P. falciparum with that of
global isolates.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, India
| | - Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India
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Tyagi S, Das A. Mitochondrial population genomic analyses reveal population structure and demography of Indian Plasmodium falciparum. Mitochondrion 2015; 24:9-21. [PMID: 26149324 DOI: 10.1016/j.mito.2015.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/29/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
Inference on the genetic diversity of Plasmodium falciparum populations could help in better management of malaria. A very recent study with mitochondrial (mt) genomes in global P. falciparum had revealed interesting evolutionary genetic patterns of Indian isolates in comparison to global ones. However, no population genetic study using the whole mt genome sequences of P. falciparum isolates collected in the entire distribution range in India has yet been performed. We herewith have analyzed 85 whole mt genomes (48 already published and 37 entirely new) sampled from eight differentially endemic Indian locations to estimate genetic diversity and infer population structure and historical demography of Indian P. falciparum. We found 19 novel Indian-specific Single Nucleotide Polymorphisms (SNPs) and 22 novel haplotypes segregating in Indian P. falciparum. Accordingly, high haplotype and nucleotide diversities were detected in Indian P. falciparum in comparison to many other global isolates. Indian P. falciparum populations were found to be moderately sub-structured with four different genetic clusters. Interestingly, group of local populations aggregate to form each cluster; while samples from Jharkhand and Odisha formed a single cluster, P. falciparum isolates from Asom formed an independent one. Similarly, Surat, Bilaspur and Betul formed a single cluster and Goa and Mangalore formed another. Interestingly, P. falciparum isolates from the two later populations were significantly genetically differentiated from isolates collected in other six Indian locations. Signature of historical population expansion was evident in five population samples, and the onset of expansion event was found to be very similar to African P. falciparum. In agreement with the previous finding, the estimated Time to Most Recent Common Ancestor (TMRCA) and the effective population size were high in Indian P. falciparum. All these genetic features of Indian P. falciparum with high mt genome diversity are somehow similar to Africa, but quite different from other Asian population samples.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India
| | - Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India.
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74
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Paquette AM, Harahap A, Laosombat V, Patnode JM, Satyagraha A, Sudoyo H, Thompson MK, Yusoff NM, Wilder JA. The evolutionary origins of Southeast Asian Ovalocytosis. INFECTION GENETICS AND EVOLUTION 2015; 34:153-9. [PMID: 26047685 DOI: 10.1016/j.meegid.2015.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Southeast Asian Ovalocytosis (SAO) is a common red blood cell disorder that is maintained as a balanced polymorphism in human populations. In individuals heterozygous for the SAO-causing mutation there are minimal detrimental effects and well-documented protection from severe malaria caused by Plasmodium vivax and Plasmodium falciparum; however, the SAO-causing mutation is fully lethal in utero when homozygous. The present-day high frequency of SAO in Island Southeast Asia indicates the trait is maintained by strong heterozygote advantage. Our study elucidates the evolutionary origin of SAO by characterizing DNA sequence variation in a 9.5 kilobase region surrounding the causal mutation in the SLC4A1 gene. We find substantial haplotype diversity among SAO chromosomes and estimate the age of the trait to be approximately 10,005 years (95% CI: 4930-23,200 years). This date is far older than any other human malaria-resistance trait examined previously in Southeast Asia, and considerably pre-dates the widespread adoption of agriculture associated with the spread of speakers of Austronesian languages some 4000 years ago. Using a genealogy-based method we find no evidence of historical positive selection acting on SAO (s=0.0, 95% CI: 0.0-0.03), in sharp contrast to the strong present-day selection coefficient (e.g., 0.09) estimated from the frequency of this recessively lethal trait. This discrepancy may be due to a recent increase in malaria-driven selection pressure following the spread of agriculture, with SAO targeted as a standing variant by positive selection in malarial populations.
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Affiliation(s)
- A M Paquette
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Harahap
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - V Laosombat
- Division of Pediatric Hematology & Oncology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkla 90110, Thailand
| | - J M Patnode
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Satyagraha
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - H Sudoyo
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - M K Thompson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - N M Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - J A Wilder
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.
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Plasmodium vivax populations are more genetically diverse and less structured than sympatric Plasmodium falciparum populations. PLoS Negl Trop Dis 2015; 9:e0003634. [PMID: 25874894 PMCID: PMC4398418 DOI: 10.1371/journal.pntd.0003634] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/20/2015] [Indexed: 11/20/2022] Open
Abstract
Introduction The human malaria parasite, Plasmodium vivax, is proving more difficult to control and eliminate than Plasmodium falciparum in areas of co-transmission. Comparisons of the genetic structure of sympatric parasite populations may provide insight into the mechanisms underlying the resilience of P. vivax and can help guide malaria control programs. Methodology/Principle findings P. vivax isolates representing the parasite populations of four areas on the north coast of Papua New Guinea (PNG) were genotyped using microsatellite markers and compared with previously published microsatellite data from sympatric P. falciparum isolates. The genetic diversity of P. vivax (He = 0.83–0.85) was higher than that of P. falciparum (He = 0.64–0.77) in all four populations. Moderate levels of genetic differentiation were found between P. falciparum populations, even over relatively short distances (less than 50 km), with 21–28% private alleles and clear geospatial genetic clustering. Conversely, very low population differentiation was found between P. vivax catchments, with less than 5% private alleles and no genetic clustering observed. In addition, the effective population size of P. vivax (30353; 13043–69142) was larger than that of P. falciparum (18871; 8109–42986). Conclusions/Significance Despite comparably high prevalence, P. vivax had higher diversity and a panmictic population structure compared to sympatric P. falciparum populations, which were fragmented into subpopulations. The results suggest that in comparison to P. falciparum, P. vivax has had a long-term large effective population size, consistent with more intense and stable transmission, and limited impact of past control and elimination efforts. This underlines suggestions that more intensive and sustained interventions will be needed to control and eventually eliminate P. vivax. This research clearly demonstrates how population genetic analyses can reveal deeper insight into transmission patterns than traditional surveillance methods. The neglected human malaria parasite Plasmodium vivax is responsible for a large proportion of the global malaria burden. Efforts to control malaria have revealed that P. vivax is more resilient than the other major human malaria parasite, Plasmodium falciparum. This study utilised population genetics to compare patterns of P. vivax and P. falciparum transmission in Papua New Guinea, a region where infection rates of the two species are similar. The results demonstrated that P. vivax populations are more genetically diverse than those of P. falciparum suggestive of a parasite population that is more resilient to environmental challenges, undergoing higher levels of interbreeding locally and between distant parasite populations. Unique characteristics of P. vivax such as relapse, which allows different strains from past infections to produce subsequent infections, may provide more opportunities for the exchange and dissemination of genetic material. The contrasting patterns observed for the two species may be the result of a differential impact of past elimination attempts and indicate that more rigorous interventions will be needed in efforts to control and eventually eliminate P. vivax.
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Samad H, Coll F, Preston MD, Ocholla H, Fairhurst RM, Clark TG. Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. PLoS Genet 2015; 11:e1005131. [PMID: 25928499 PMCID: PMC4415759 DOI: 10.1371/journal.pgen.1005131] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 03/06/2015] [Indexed: 11/19/2022] Open
Abstract
Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r2 for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86 k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r2, 0.87-0.96), but the performance of IMPUTE was mixed (allelic r2, 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima's D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and association analyses, and supporting global surveillance for drug resistance markers and candidate vaccine antigens.
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Affiliation(s)
- Hanif Samad
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mark D. Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi and Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - 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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Guerra M, Machado P, Manco L, Fernandes N, Miranda J, Arez AP. Triosephosphate isomerase gene promoter variation: -5G/A and -8G/A polymorphisms in clinical malaria groups in two African populations. INFECTION GENETICS AND EVOLUTION 2015; 32:271-9. [PMID: 25801609 DOI: 10.1016/j.meegid.2015.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/25/2015] [Accepted: 03/15/2015] [Indexed: 11/17/2022]
Abstract
TPI1 promoter polymorphisms occur in high prevalence in individuals from African origin. Malaria-patients from Angola and Mozambique were screened for the TPI1 gene promoter variants rs1800200A>G, (-5G>A), rs1800201G>A, (-8G>A), rs1800202T>G, (-24T>G), and for the intron 5 polymorphism rs2071069G>A, (2262G>A). -5G>A and -8G>A variants occur in 47% and 53% in Angola and Mozambique, respectively while -24T>G was monomorphic for the wild-type T allele. Six haplotypes were identified and -8A occurred in 45% of the individuals, especially associated with the GAG haplotype and more frequent in non-severe malaria groups, although not significantly. The arising and dispersion of -5G>A and -8G>A polymorphisms is controversial. Their age was estimated by analyses of two microsatellite loci, CD4 and ATN1, adjacent to TPI1 gene. The -5G>A is older than -8G>A, with an average estimate of approximately 35,000 years. The -8A variant arose in two different backgrounds, suggesting independent mutational events. The first, on the -5G background, may have occurred in East Africa around 20,800 years ago; the second, on the -5A background, may have occurred in West Africa some 7500 years ago. These estimates are within the period of spread of agriculture and the malaria mosquito vector in Africa, which could has been a possible reason for the selection of -8A polymorphism in malaria endemic countries.
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Affiliation(s)
- Mónica Guerra
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Patrícia Machado
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Licínio Manco
- Centro de Investigação em Antropologia e Saúde (CIAS), Universidade de Coimbra, Portugal
| | - Natércia Fernandes
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | | | - Ana Paula Arez
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal.
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78
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Shanks GD. Hypothesis: dynamics of classical malaria epidemics show Plasmodium falciparum's survival strategy. Am J Trop Med Hyg 2015; 92:561-4. [PMID: 25624407 PMCID: PMC4350549 DOI: 10.4269/ajtmh.14-0541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/07/2014] [Indexed: 11/07/2022] Open
Abstract
Areas of marginal transmission can generate enormous lethal falciparum malaria epidemics when factors favoring the parasite shift only slightly. Although usually described in terms of vectorial capacity, medical scientists working in India in the early 20th century came to the conclusion that "an epidemic of relapses" was the key triggering event of malaria epidemics. This explanation has been largely discarded, because the biology of Plasmodium falciparum recrudescence has since been differentiated from P. vivax relapse. Using data from the Punjab in 1908 and Ceylon in 1934-1935, the genesis of malaria epidemics has been re-examined to inform current control efforts. The epidemics were focused geographically depending on recent rainfall or drought. Epidemics arose very suddenly and simultaneously in several places. Malaria spleen surveys indicated very little recent malaria transmission, and blood smears showed very few gametocytes just before the epidemic. Population stress as indicated by high grain prices because of a poor harvest caused by drought the previous year was a risk factor for malaria epidemics. Although increased female Anopheline survival because of increased humidity played an important part in the magnification of the epidemic, it does not explain its genesis. Human population stress triggering a shift toward gametocytogenesis is hypothesized as the key initiation factor for malaria epidemics. Its evolutionary significance may be that it allows the parasite to match the tropical agricultural cycle.
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Affiliation(s)
- G Dennis Shanks
- Australian Army Malaria Institute, Enoggera, Australia; School of Population Health, University of Queensland, Brisbane, Australia; Department of Zoology, University of Oxford, Oxford, United Kingdom
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79
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Silva JC, Egan A, Arze C, Spouge JL, Harris DG. A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts. Mol Biol Evol 2015; 32:1354-64. [PMID: 25589738 PMCID: PMC4408405 DOI: 10.1093/molbev/msv005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Species in the genus Plasmodium cause malaria in humans and infect a variety of mammals and other vertebrates. Currently, estimated ages for several mammalian Plasmodium parasites differ by as much as one order of magnitude, an inaccuracy that frustrates reliable estimation of evolutionary rates of disease-related traits. We developed a novel statistical approach to dating the relative age of evolutionary lineages, based on Total Least Squares regression. We validated this lineage dating approach by applying it to the genus Drosophila. Using data from the Drosophila 12 Genomes project, our approach accurately reconstructs the age of well-established Drosophila clades, including the speciation event that led to the subgenera Drosophila and Sophophora, and age of the melanogaster species subgroup. We applied this approach to hundreds of loci from seven mammalian Plasmodium species. We demonstrate the existence of a molecular clock specific to individual Plasmodium proteins, and estimate the relative age of mammalian-infecting Plasmodium. These analyses indicate that: 1) the split between the human parasite Plasmodium vivax and P. knowlesi, from Old World monkeys, occurred 6.1 times earlier than that between P. falciparum and P. reichenowi, parasites of humans and chimpanzees, respectively; and 2) mammalian Plasmodium parasites originated 22 times earlier than the split between P. falciparum and P. reichenowi. Calibrating the absolute divergence times for Plasmodium with eukaryotic substitution rates, we show that the split between P. falciparum and P. reichenowi occurred 3.0-5.5 Ma, and that mammalian Plasmodium parasites originated over 64 Ma. Our results indicate that mammalian-infecting Plasmodium evolved contemporaneously with their hosts, with little evidence for parasite host-switching on an evolutionary scale, and provide a solid timeframe within which to place the evolution of new Plasmodium species.
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Affiliation(s)
- Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine Department of Microbiology and Immunology, University of Maryland School of Medicine
| | - Amy Egan
- Institute for Genome Sciences, University of Maryland School of Medicine
| | - Cesar Arze
- Institute for Genome Sciences, University of Maryland School of Medicine
| | - John L Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - David G Harris
- Department of Applied Mathematics and Statistics, University of Maryland, College Park
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80
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Basumallick S, Row TNG. Binding Study of Cis-Atovaquone with Cytochrome bc1 of Yeast. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/cmb.2015.54007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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81
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Tadmouri GO, Sastry KS, Chouchane L. Arab gene geography: From population diversities to personalized medical genomics. Glob Cardiol Sci Pract 2014; 2014:394-408. [PMID: 25780794 PMCID: PMC4355514 DOI: 10.5339/gcsp.2014.54] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/11/2014] [Indexed: 12/20/2022] Open
Abstract
Genetic disorders are not equally distributed over the geography of the Arab region. While a number of disorders have a wide geographical presence encompassing 10 or more Arab countries, almost half of these disorders occur in a single Arab country or population. Nearly, one-third of the genetic disorders in Arabs result from congenital malformations and chromosomal abnormalities, which are also responsible for a significant proportion of neonatal and perinatal deaths in Arab populations. Strikingly, about two-thirds of these diseases in Arab patients follow an autosomal recessive mode of inheritance. High fertility rates together with increased consanguineous marriages, generally noticed in Arab populations, tend to increase the rates of genetic and congenital abnormalities. Many of the nearly 500 genes studied in Arab people revealed striking spectra of heterogeneity with many novel and rare mutations causing large arrays of clinical outcomes. In this review we provided an overview of Arab gene geography, and various genetic abnormalities in Arab populations, including disorders of blood, metabolic, circulatory and neoplasm, and also discussed their associated molecules or genes responsible for the cause of these disorders. Although studying Arab-specific genetic disorders resulted in a high value knowledge base, approximately 35% of genetic diseases in Arabs do not have a defined molecular etiology. This is a clear indication that comprehensive research is required in this area to understand the molecular pathologies causing diseases in Arab populations.
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Affiliation(s)
| | - Konduru S Sastry
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
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82
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Cheeseman IH, McDew-White M, Phyo AP, Sriprawat K, Nosten F, Anderson TJC. Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. Mol Biol Evol 2014; 32:1080-90. [PMID: 25534029 PMCID: PMC4379400 DOI: 10.1093/molbev/msu397] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging artemisinin (ART) resistance in a South-East Asian malaria parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated patients and mutations in the kelch gene (chr. 13) have been strongly implicated to play a role. We constructed triplicate pools of 70 slow-clearing (resistant) and 70 fast-clearing (sensitive) infections collected from the Thai–Myanmar border and sequenced these to high (∼150-fold) read depth. Allele frequency estimates from pools showed almost perfect correlation (Lin’s concordance = 0.98) with allele frequencies at 93 single nucleotide polymorphisms measured directly from individual infections, giving us confidence in the accuracy of this approach. By mapping genome-wide divergence (FST) between pools of drug-resistant and drug-sensitive parasites, we identified two large (>150 kb) regions (on chrs. 13 and 14) and 17 smaller candidate genome regions. To identify individual genes within these genome regions, we resequenced an additional 38 parasite genomes (16 slow and 22 fast-clearing) and performed rare variant association tests. These confirmed kelch as a major molecular marker for ART resistance (P = 6.03 × 10−6). This two-tier approach is powerful because pooled sequencing rapidly narrows down genome regions of interest, while targeted rare variant association testing within these regions can pinpoint the genetic basis of resistance. We show that our approach is robust to recurrent mutation and the generation of soft selective sweeps, which are predicted to be common in pathogen populations with large effective population sizes, and may confound more traditional gene mapping approaches.
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Affiliation(s)
| | | | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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83
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Oyebola MK, Idowu ET, Nyang H, Olukosi YA, Otubanjo OA, Nwakanma DC, Awolola ST, Amambua-Ngwa A. Microsatellite markers reveal low levels of population sub-structuring of Plasmodium falciparum in southwestern Nigeria. Malar J 2014; 13:493. [PMID: 25496185 PMCID: PMC4300683 DOI: 10.1186/1475-2875-13-493] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic diversity studies provide evidence of Plasmodium falciparum differentiation that could affect fitness and adaptation to drugs and target antigens for vaccine development. This study describes the genetic structure of P. falciparum populations in urban and rural sites from southwestern Nigeria. METHODOLOGY Ten neutral microsatellite loci were genotyped in 196 P. falciparum infections from three localities: Aramoko-Ekiti, a rural community; Lekki, an urban location and Badagry, a peri-urban border settlement. Analysis was performed on the genetic diversity, linkage disequilibrium, population structure and inter-population differentiation. RESULTS Allelic diversity values were similar across all populations, with mean expected heterozygosity (HE) values between 0.65 and 0.79. No matching multilocus haplotypes were found and analysis of multilocus LD showed no significant index of association. Genetic differentiation between populations was low (ΦPT = 0.017). CONCLUSION The absence of detectable population structure of P. falciparum in southwestern Nigeria is evident in the lack of significant differentiation between populations separated by about 200 km. This implies that a fairly uniform malaria control strategy may be effective over a wide geographic range in this highly endemic region. However, more wide-scale survey across the country will be required to inform malaria control in this large and densely populated endemic region.
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84
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Akala HM, Achieng AO, Eyase FL, Juma DW, Ingasia L, Cheruiyot AC, Okello C, Omariba D, Owiti EA, Muriuki C, Yeda R, Andagalu B, Johnson JD, Kamau E. Five-year tracking of Plasmodium falciparum allele frequencies in a holoendemic area with indistinct seasonal transitions. J Multidiscip Healthc 2014; 7:515-23. [PMID: 25395861 PMCID: PMC4227620 DOI: 10.2147/jmdh.s67252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The renewed malaria eradication efforts require an understanding of the seasonal patterns of frequency of polymorphic variants in order to focus limited funds productively. Although cross-sectional studies in holoendemic areas spanning a single year could be useful in describing parasite genotype status at a given point, such information is inadequate in describing temporal trends in genotype polymorphisms. For Plasmodium falciparum isolates from Kisumu District Hospital, Plasmodium falciparum chloroquine-resistance transporter gene (Pfcrt-K76T) and P. falciparum multidrug resistance gene 1 (PfMDR1-N86Y), were analyzed for polymorphisms and parasitemia changes in the 53 months from March 2008 to August 2012. Observations were compared with prevailing climatic factors, including humidity, rainfall, and temperature. METHODS Parasitemia (the percentage of infected red blood cells per total red blood cells) was established by microscopy for P. falciparum malaria-positive samples. P. falciparum DNA was extracted from whole blood using a Qiagen DNA Blood Mini Kit. Single nucleotide polymorphism identification at positions Pfcrt-K76T and PfMDR1-N86Y was performed using real-time polymerase chain reaction and/or sequencing. Data on climatic variables were obtained from http://www.tutiempo.net/en/. RESULTS A total of 895 field isolates from 2008 (n=169), 2009 (n=161), 2010 (n=216), 2011 (n=223), and 2012 (n=126) showed large variations in monthly frequency of PfMDR1-N86Y and Pfcrt-K76T as the mutant genotypes decreased from 68.4%±15% and 38.1%±13% to 29.8%±18% and 13.3%±9%, respectively. The mean percentage of parasitemia was 2.61%±1.01% (coefficient of variation 115.86%; n=895). There was no correlation between genotype or parasitemia and climatic factors. CONCLUSION This study shows variability in the frequency of Pfcrt-K76T and PfMDR1-N86Y polymorphisms during the study period, bringing into focus the role of cross-sectional studies in describing temporal genotype trends. The lack of correlation between genotypes and climatic changes, especially precipitation, emphasizes the cost of investment in genotype change.
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Affiliation(s)
- Hoseah M Akala
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Angela O Achieng
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Fredrick L Eyase
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Dennis W Juma
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Luiser Ingasia
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Agnes C Cheruiyot
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Charles Okello
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Duke Omariba
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Eunice A Owiti
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Catherine Muriuki
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Redemptah Yeda
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Ben Andagalu
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Jacob D Johnson
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Edwin Kamau
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
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85
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Lü J, Hu SJ, Ma XY, Chen JM, Li QQ, Ye H. Origin and expansion of the Yunnan Shoot Borer, Tomicus yunnanensis (coleoptera: scolytinae): a mixture of historical natural expansion and contemporary human-mediated relocation. PLoS One 2014; 9:e111940. [PMID: 25372458 PMCID: PMC4221261 DOI: 10.1371/journal.pone.0111940] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/02/2014] [Indexed: 11/21/2022] Open
Abstract
The Yunnan shoot borer, Tomicus yunnanensis, is a recently-discovered, aggressive pest of the Yunnan pine stands in southwestern China. Despite many bionomics studies and massive controlling efforts, research on its population genetics is extremely limited. The present study, aimed at investigating the origin and dispersal of this important forestry pest, analyzed the population genetic structure and demographic history using a mitochondrial cox1 gene fragment. Our results showed that T. yunnanensis most likely originated from the Central-Yunnan Altiplano, and the divergence time analysis placed the origin approximately 0.72 million-years ago. Host separation and specialization might have caused the speciation of T. yunnanensis. Genetic structure analyses identified two population groups, with six populations near the origin area forming one group and the remaining six populations from western and eastern Yunnan and southwestern Sichuan comprising the other. Divergence time analysis placed the split of the two groups at approximately 0.60 million-years ago, and haplotype phylogenetic tree, network, as well as migration rate suggested that populations of the latter group were established via a small number of individuals from the former one. Migration analysis also showed a certain degree of recent expansion from southwestern Sichuan to eastern Yunnan. Our findings implied that T. yunnanensis underwent both historical expansion and recent dispersal. The historical expansion may relate to the oscillation of regional climate due to glacial and interglacial periods in the Pleistocene, while human-mediated transportation of pine-wood material might have assisted the relocation and establishment of this pest in novel habitats.
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Affiliation(s)
- Jun Lü
- Laboratory of Biological Invasion and Ecosecurity, Yunnan University, Kunming, 650091, China
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-security, Yunnan University, Kunming, 650091, China
| | - Shao-ji Hu
- Laboratory of Biological Invasion and Ecosecurity, Yunnan University, Kunming, 650091, China
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-security, Yunnan University, Kunming, 650091, China
| | - Xue-yu Ma
- Laboratory of Biological Invasion and Ecosecurity, Yunnan University, Kunming, 650091, China
- School of Mathematics and Computer Science, Yunnan University of Nationalities, Kunming, 650031, China
| | - Jin-min Chen
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China
| | - Qing-qing Li
- Life Science College, Yunnan Normal University, Kunming, 650092, China
| | - Hui Ye
- Laboratory of Biological Invasion and Ecosecurity, Yunnan University, Kunming, 650091, China
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-security, Yunnan University, Kunming, 650091, China
- * E-mail:
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86
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A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nat Commun 2014; 5:4052. [PMID: 24923250 PMCID: PMC4082634 DOI: 10.1038/ncomms5052] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/06/2014] [Indexed: 11/21/2022] Open
Abstract
Malaria is a major public health problem that is actively being addressed in a global eradication campaign. Increased population mobility through international air travel has elevated the risk of re-introducing parasites to elimination areas and dispersing drug-resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable public health tool for locating the source of imported outbreaks. Here we analyse the mitochondrion and apicoplast genomes of 711 Plasmodium falciparum isolates from 14 countries, and find evidence that they are non-recombining and co-inherited. The high degree of linkage produces a panel of relatively few single-nucleotide polymorphisms (SNPs) that is geographically informative. We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide. Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions.
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87
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Tyagi S, Pande V, Das A. New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates. Mol Ecol 2014; 23:2975-87. [PMID: 24845521 DOI: 10.1111/mec.12800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 05/16/2014] [Accepted: 05/16/2014] [Indexed: 12/31/2022]
Abstract
Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug-resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum-like isolates (infecting non-human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector - 8 Dwarka, New Delhi, 110077, India
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88
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Karanth SS, Marupudi KC, Gupta A. Intracerebral bleed, right haemiparesis and seizures: an atypical presentation of vivax malaria. BMJ Case Rep 2014; 2014:bcr-2014-204833. [PMID: 24920515 DOI: 10.1136/bcr-2014-204833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Falciparum malaria is notoriously known to produce life-threatening complications. Despite growing reports of chloroquine resistance and severe disease, vivax malaria continues to be viewed as a benign disease. We report a rare case of a 47-year-old healthy man from a malaria-endemic region, presenting with intracerebral bleed, right haemiparesis, aphasia and seizures following vivax malaria. This was successfully managed conservatively, without any neurosurgical intervention, with combination therapy of intravenous artesunate, oral hydroxychloquine and primaquine. In a country where Plasmodium vivax is responsible for majority of cases of malaria, it is high time the national malaria control programmes focus on the elimination of P. vivax in addition to its more dangerous counterpart, P. falciparum.
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Affiliation(s)
- Suman S Karanth
- Department of Internal Medicine, Kasturba Medical College, Manipal, Karnataka, India
| | | | - Anurag Gupta
- Department of Neurosurgery, Fortis Memorial Hospital, Manipal, Karnataka, India
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89
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Preston MD, Assefa SA, Ocholla H, Sutherland CJ, Borrmann S, Nzila A, Michon P, Hien TT, Bousema T, Drakeley CJ, Zongo I, Ouédraogo JB, Djimde AA, Doumbo OK, Nosten F, Fairhurst RM, Conway DJ, Roper C, Clark TG. PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. J Infect Dis 2014; 209:1808-15. [PMID: 24338354 PMCID: PMC4017360 DOI: 10.1093/infdis/jit812] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/21/2013] [Indexed: 11/17/2022] Open
Abstract
Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600,000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).
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Affiliation(s)
- Mark D. Preston
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Samuel A. Assefa
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre 3, Malawi
- Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Colin J. Sutherland
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Steffen Borrmann
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases, Heidelberg University School of Medicine, Heidelberg 69120, Germany
| | - Alexis Nzila
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- King Fahd University of Petroleum and Minerals, PO Box 468, Dhahran 31262, Kingdom of Saudi Arabia
| | - Pascal Michon
- Papua New Guinea Institute of Medical Research, PO Box 483, Madang, Papua New Guinea
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Teun Bousema
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Christopher J. Drakeley
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Issaka Zongo
- Institut de Recherche en Sciences de la Sant, Bobo–Dioulasso, Burkina Faso
| | - Jean-Bosco Ouédraogo
- Institut de Recherche en Sciences de la Sant, BP 545, Bobo-Dioulasso 01, Burkina Faso
| | - Abdoulaye A. Djimde
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako, Mali
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako, Mali
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok 10400, Thailand
- Centre for Tropical Medicine, University of Oxford, Oxford OX3 7LJ, United Kingdom
- Shoklo Malaria Research Unit, Mae Sot TAK 63110, Thailand
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David J. Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Cally Roper
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Taane G. Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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90
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Hall AJ, Chappell MJ, Aston JAD, Ward SA. Reprint of "Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin". COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 114:e14-e28. [PMID: 24457047 DOI: 10.1016/j.cmpb.2013.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 04/15/2013] [Accepted: 05/15/2013] [Indexed: 06/03/2023]
Abstract
A four compartment mechanistic mathematical model is developed for the pharmacokinetics of the commonly used anti-malarial drug artesunate and its principle metabolite dihydroartemisinin following oral administration of artesunate. The model is structurally unidentifiable unless additional constraints are imposed. Combinations of mechanistically derived constraints are considered to assess their effects on structural identifiability and on model fits. Certain combinations of the constraints give rise to locally or globally identifiable model structures. Initial validation of the model under various combinations of the constraints leading to identifiable model structures was performed against a dataset of artesunate and dihydroartemisinin concentration-time profiles of 19 malaria patients. When all the discussed constraints were imposed on the model, the resulting globally identifiable model structure was found to fit reasonably well to those patients with normal drug absorption profiles. However, there is wide variability in the fitted parameters and further investigation is warranted.
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Affiliation(s)
- Adam J Hall
- Departments of Mathematics and Statistics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Michael J Chappell
- School of Engineering, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - John A D Aston
- Department of Statistics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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91
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Yalcindag E, Rougeron V, Elguero E, Arnathau C, Durand P, Brisse S, Diancourt L, Aubouy A, Becquart P, D'Alessandro U, Fontenille D, Gamboa D, Maestre A, Ménard D, Musset L, Noya O, Veron V, Wide A, Carme B, Legrand E, Chevillon C, Ayala FJ, Renaud F, Prugnolle F. Patterns of selection onPlasmodium falciparumerythrocyte-binding antigens after the colonization of the New World. Mol Ecol 2014; 23:1979-93. [DOI: 10.1111/mec.12696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erhan Yalcindag
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Kotlářská 2 611 37 Brno Czech Republic
| | - Virginie Rougeron
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
- Centre International de Recherches Médicales de Franceville (CIRMF); BP 769 Franceville Gabon
| | - Eric Elguero
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Céline Arnathau
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Patrick Durand
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Sylvain Brisse
- Institut Pasteur; Plate-forme Génotypage des Pathogènes et Santé Publique; 28 Rue du docteur Roux 75724 Paris France
| | - Laure Diancourt
- Institut Pasteur; Plate-forme Génotypage des Pathogènes et Santé Publique; 28 Rue du docteur Roux 75724 Paris France
| | - Agnes Aubouy
- Institut de Recherche pour le Développement (IRD); UMR152; Université Paul Sabatier; 35 Chemin des Maraîchers 31062 Toulouse France
| | - Pierre Becquart
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | | | - Didier Fontenille
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt; Universidad Peruana Cayetano Heredia; AP 4314 Lima 100 Peru
| | - Amanda Maestre
- Grupo Salud y Comunidad; Facultad de Medicina; Universidad de Antioquía; Medellín Colombia
| | - Didier Ménard
- Molecular Epidemiology Unit; Pasteur Institute of Cambodia; 5 Boulevard Monivong - PO Box 983 Phnom Penh Cambodia
| | - Lise Musset
- Parasitology laboratory; Institut Pasteur de Guyane; BP6010 97306 Cayenne Cedex French Guiana
| | - Oscar Noya
- Centro para Estudios Sobre Malaria; Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”-INH; Ministerio del Poder Popular para la Salud; Instituto de Medicina Tropical; Universidad Central de Venezuela; Caracas Venezuela
| | | | - Albina Wide
- Centro para Estudios Sobre Malaria; Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”-INH; Ministerio del Poder Popular para la Salud; Instituto de Medicina Tropical; Universidad Central de Venezuela; Caracas Venezuela
| | - Bernard Carme
- Centre d'Investigation Clinique Epidémiologie Clinique Antilles; Guyane CIC-EC 802; Cayenne General Hospital; Cayenne French Guiana
| | - Eric Legrand
- Parasitology laboratory; Institut Pasteur de Guyane; BP6010 97306 Cayenne Cedex French Guiana
| | - Christine Chevillon
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology; University of California; Irvine CA 92697 USA
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle); UMR CNRS 5290/IRD 224; Université Montpellier 1; Université Montpellier 2; CHRU de Montpellier; 39 Avenue Charles Flahault 34295 Montpellier France
- Centre International de Recherches Médicales de Franceville (CIRMF); BP 769 Franceville Gabon
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Mobegi VA, Duffy CW, Amambua-Ngwa A, Loua KM, Laman E, Nwakanma DC, MacInnis B, Aspeling-Jones H, Murray L, Clark TG, Kwiatkowski DP, Conway DJ. Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity. Mol Biol Evol 2014; 31:1490-9. [PMID: 24644299 PMCID: PMC4032133 DOI: 10.1093/molbev/msu106] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Locally varying selection on pathogens may be due to differences in drug pressure, host immunity, transmission opportunities between hosts, or the intensity of between-genotype competition within hosts. Highly recombining populations of the human malaria parasite Plasmodium falciparum throughout West Africa are closely related, as gene flow is relatively unrestricted in this endemic region, but markedly varying ecology and transmission intensity should cause distinct local selective pressures. Genome-wide analysis of sequence variation was undertaken on a sample of 100 P. falciparum clinical isolates from a highly endemic region of the Republic of Guinea where transmission occurs for most of each year and compared with data from 52 clinical isolates from a previously sampled population from The Gambia, where there is relatively limited seasonal malaria transmission. Paired-end short-read sequences were mapped against the 3D7 P. falciparum reference genome sequence, and data on 136,144 single nucleotide polymorphisms (SNPs) were obtained. Within-population analyses identifying loci showing evidence of recent positive directional selection and balancing selection confirm that antimalarial drugs and host immunity have been major selective agents. Many of the signatures of recent directional selection reflected by standardized integrated haplotype scores were population specific, including differences at drug resistance loci due to historically different antimalarial use between the countries. In contrast, both populations showed a similar set of loci likely to be under balancing selection as indicated by very high Tajima’s D values, including a significant overrepresentation of genes expressed at the merozoite stage that invades erythrocytes and several previously validated targets of acquired immunity. Between-population FST analysis identified exceptional differentiation of allele frequencies at a small number of loci, most markedly for five SNPs covering a 15-kb region within and flanking the gdv1 gene that regulates the early stages of gametocyte development, which is likely related to the extreme differences in mosquito vector abundance and seasonality that determine the transmission opportunities for the sexual stage of the parasite.
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Affiliation(s)
- Victor A Mobegi
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United KingdomMedical Research Council Unit, Fajara, Banjul, The Gambia
| | - Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Kovana M Loua
- National Institute of Public Health, Conakry, Republic of Guinea
| | - Eugene Laman
- National Institute of Public Health, Conakry, Republic of Guinea
| | | | - Bronwyn MacInnis
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Harvey Aspeling-Jones
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lee Murray
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G Clark
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dominic P Kwiatkowski
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United KingdomWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United KingdomMedical Research Council Unit, Fajara, Banjul, The Gambia
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93
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Rodrigues PT, Alves JMP, Santamaria AM, Calzada JE, Xayavong M, Parise M, da Silva AJ, Ferreira MU. Using mitochondrial genome sequences to track the origin of imported Plasmodium vivax infections diagnosed in the United States. Am J Trop Med Hyg 2014; 90:1102-8. [PMID: 24639297 DOI: 10.4269/ajtmh.13-0588] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Although the geographic origin of malaria cases imported into the United States can often be inferred from travel histories, these histories may be lacking or incomplete. We hypothesized that mitochondrial haplotypes could provide region-specific molecular barcodes for tracing the origin of imported Plasmodium vivax infections. An analysis of 348 mitochondrial genomes from worldwide parasites and new sequences from 69 imported malaria cases diagnosed across the United States allowed for a geographic assignment of most infections originating from the Americas, southeast Asia, east Asia, and Melanesia. However, mitochondrial lineages from Africa, south Asia, central Asia, and the Middle East, which altogether contribute the vast majority of imported malaria cases in the United States, were closely related to each other and could not be reliably assigned to their geographic origins. More mitochondrial genomes are required to characterize molecular barcodes of P. vivax from these regions.
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Affiliation(s)
- Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - João Marcelo P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ana María Santamaria
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - José E Calzada
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maniphet Xayavong
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Monica Parise
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alexandre J da Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama; Center for Global Health, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
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94
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Abstract
Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright–Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study demonstrates the importance of considering the life cycle in genetic analysis, especially in parasites with complex life cycles.
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95
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Tyagi S, Pande V, Das A. Whole mitochondrial genome sequence of an Indian Plasmodium falciparum field isolate. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:99-103. [PMID: 24623891 PMCID: PMC3949004 DOI: 10.3347/kjp.2014.52.1.99] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/25/2013] [Accepted: 12/09/2013] [Indexed: 12/04/2022]
Abstract
Mitochondrial genome sequence of malaria parasites has served as a potential marker for inferring evolutionary history of the Plasmodium genus. In Plasmodium falciparum, the mitochondrial genome sequences from around the globe have provided important evolutionary understanding, but no Indian sequence has yet been utilized. We have sequenced the whole mitochondrial genome of a single P. falciparum field isolate from India using novel primers and compared with the 3D7 reference sequence and 1 previously reported Indian sequence. While the 2 Indian sequences were highly divergent from each other, the presently sequenced isolate was highly similar to the reference 3D7 strain.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand 263001, India
| | - Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India
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96
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Cerritos R, González-Cerón L, Nettel JA, Wegier A. Genetic structure of Plasmodium vivax using the merozoite surface protein 1 icb5-6 fragment reveals new hybrid haplotypes in southern Mexico. Malar J 2014; 13:35. [PMID: 24472213 PMCID: PMC3923247 DOI: 10.1186/1475-2875-13-35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium vivax is a protozoan parasite with an extensive worldwide distribution, being highly prevalent in Asia as well as in Mesoamerica and South America. In southern Mexico, P. vivax transmission has been endemic and recent studies suggest that these parasites have unique biological and genetic features. The msp1 gene has shown high rate of nucleotide substitutions, deletions, insertions, and its mosaic structure reveals frequent events of recombination, maybe between highly divergent parasite isolates. METHODS The nucleotide sequence variation in the polymorphic icb5-6 fragment of the msp1 gene of Mexican and worldwide isolates was analysed. To understand how genotype diversity arises, disperses and persists in Mexico, the genetic structure and genealogical relationships of local isolates were examined. To identify new sequence hybrids and their evolutionary relationships with other P. vivax isolates circulating worldwide two haplotype networks were constructed questioning that two portions of the icb5-6 have different evolutionary history. RESULTS Twelve new msp1 icb5-6 haplotypes of P. vivax from Mexico were identified. These nucleotide sequences show mosaic structure comprising three partially conserved and two variable subfragments and resulted into five different sequence types. The variable subfragment sV1 has undergone recombination events and resulted in hybrid sequences and the haplotype network allocated the Mexican haplotypes to three lineages, corresponding to the Sal I and Belem types, and other more divergent group. In contrast, the network from icb5-6 fragment but not sV1 revealed that the Mexican haplotypes belong to two separate lineages, none of which are closely related to Sal I or Belem sequences. CONCLUSIONS These results suggest that the new hybrid haplotypes from southern Mexico were the result of at least three different recombination events. These rearrangements likely resulted from the recombination between haplotypes of highly divergent lineages that are frequently distributed in South America and Asia and diversified rapidly.
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Affiliation(s)
| | - Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, México.
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97
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Chemical Cues for Malaria Vectors Oviposition Site Selection: Challenges and Opportunities. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/685182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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98
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Hall AJ, Chappell MJ, Aston JAD, Ward SA. Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 112:1-15. [PMID: 23871681 DOI: 10.1016/j.cmpb.2013.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 04/15/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
A four compartment mechanistic mathematical model is developed for the pharmacokinetics of the commonly used anti-malarial drug artesunate and its principle metabolite dihydroartemisinin following oral administration of artesunate. The model is structurally unidentifiable unless additional constraints are imposed. Combinations of mechanistically derived constraints are considered to assess their effects on structural identifiability and on model fits. Certain combinations of the constraints give rise to locally or globally identifiable model structures. Initial validation of the model under various combinations of the constraints leading to identifiable model structures was performed against a dataset of artesunate and dihydroartemisinin concentration-time profiles of 19 malaria patients. When all the discussed constraints were imposed on the model, the resulting globally identifiable model structure was found to fit reasonably well to those patients with normal drug absorption profiles. However, there is wide variability in the fitted parameters and further investigation is warranted.
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Affiliation(s)
- Adam J Hall
- Departments of Mathematics and Statistics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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99
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Tanabe K, Zollner G, Vaughan JA, Sattabongkot J, Khuntirat B, Honma H, Mita T, Tsuboi T, Coleman R. Plasmodium falciparum: genetic diversity and complexity of infections in an isolated village in western Thailand. Parasitol Int 2013; 64:260-6. [PMID: 24060540 DOI: 10.1016/j.parint.2013.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 01/11/2023]
Abstract
Genetic diversity of Plasmodium falciparum is intimately associated with morbidity, mortality and malaria control strategies. It is therefore imperative to study genetic makeup and population structure of this parasite in endemic areas. In Kong Mong Tha, an isolated village in western Thailand, the majority of P. falciparum infections are asymptomatic. In this study we investigated complexity of infections and single nucleotide polymorphisms (SNPs) in the P. falciparum population of Kong Mong Tha, and compared results with those previously obtained from Mae Sod, in northwestern Thailand, where the majority of infections were symptomatic. Using PCR-based determination of the 5' merozoite surface protein 1 gene (msp1) recombinant types, we found that 39% of 59 P. falciparum isolates from Kong Mong Tha had multiple 5' recombinant types with a mean number of 1.54. These values were much lower than those obtained from Mae Sod: 96% for multiple infections and with a mean number of 3.61. Analysis of full-length sequences of two housekeeping genes, the P-type Ca(2+)-transporting ATPase gene (n=33) plus adenylosuccinate lyase gene (n=33), and three vaccine candidate antigen genes, msp1 (n=26), the circumsporozoite protein gene, csp (n=30) and the apical membrane antigen 1 gene, ama 1 (n=32), revealed that in all of these genes within-population SNP diversity was at similar levels between Kong Mong Tha and Mae Sod, suggesting that the extent of MOI and clinical manifestations of malaria are not strongly associated with genetic diversity. Additionally, we did not detect significant genetic differentiation between the two parasite populations, as estimated by the Wright's fixation index of inter-population variance in allele frequencies, suggesting that gene flow prevented the formation of population structuring. Thus, this study highlights unique features of P. falciparum populations in Thailand. The implications of these finding are discussed.
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Affiliation(s)
- Kazuyuki Tanabe
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
| | - Gabriela Zollner
- Department of Entomology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Jefferson A Vaughan
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Jetsumon Sattabongkot
- Department of Entomology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Benjawan Khuntirat
- Department of Entomology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Hajime Honma
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshihiro Mita
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, Tokyo, Japan; Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
| | - Russell Coleman
- Department of Entomology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
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100
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Pacheco MA, Cranfield M, Cameron K, Escalante AA. Malarial parasite diversity in chimpanzees: the value of comparative approaches to ascertain the evolution of Plasmodium falciparum antigens. Malar J 2013; 12:328. [PMID: 24044371 PMCID: PMC3848613 DOI: 10.1186/1475-2875-12-328] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 09/13/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Plasmodium falciparum shares its most recent common ancestor with parasites found in African apes; these species constitute the so-called Laverania clade. In this investigation, the evolutionary history of Plasmodium lineages found in chimpanzees (Pan troglodytes) was explored. METHODS Here, the remainders of 74 blood samples collected as part of the chimpanzees' routine health examinations were studied. For all positive samples with parasite lineages belonging to the Laverania clade, the complete mitochondrial genome (mtDNA), the gene encoding dihydrofolate reductase-thymidylate synthase (dhfr-ts), the chloroquine resistance transporter (Pfcrt), the circumsporozoite protein (csp), merozoite surface protein 2 (msp2), and the DBL-1 domain from var2CSA were amplified, cloned, and sequenced. Other Plasmodium species were included in the mtDNA, dhfr-ts, and csp analyses. Phylogenetic and evolutionary genetic analyses were performed, including molecular clock analyses on the mtDNA. RESULTS/CONCLUSIONS Nine chimpanzees were malaria positive (12.2%); four of those infections were identified as P. falciparum, two as a Plasmodium reichenowi-like parasite or Plasmodium sp., one as Plasmodium gaboni, and two as Plasmodium malariae. All P. falciparum isolates were resistant to chloroquine indicating that the chimpanzees acquired such infections from humans in recent times. Such findings, however, are not sufficient for implicating chimpanzees as an animal reservoir for P. falciparum.Timing estimates support that the Laverania clade has co-existed with hominids for a long-period of time. The proposed species P. gaboni, Plasmodium billbrayi, and Plasmodium billcollinsi are monophyletic groups supporting that they are indeed different species.An expanded CSP phylogeny is presented, including all the Laverania species and other malarial parasites. Contrasting with other Plasmodium, the Laverania csp exhibits great conservation at the central tandem repeat region. Msp2 and var2CSA, however, show extended recent polymorphism in P. falciparum that likely originated after the P. reichenowi-P. falciparum split. The accumulation of such diversity may indicate adaptation to the human host. These examples support the notion that comparative approaches among P. falciparum and its related species will be of great value in understanding the evolution of proteins that are important in parasite invasion of the human red blood cell, as well as those involved in malaria pathogenesis.
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Affiliation(s)
- M Andreína Pacheco
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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