101
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Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W, Cowman AF, Yu Z, Tham WH. Cryo-EM structure of an essential Plasmodium vivax invasion complex. Nature 2018; 559:135-139. [PMID: 29950717 DOI: 10.1038/s41586-018-0249-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/01/2018] [Indexed: 12/21/2022]
Abstract
Plasmodium vivax is the most widely distributed malaria parasite that infects humans1. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1)2. TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates2. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.
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Affiliation(s)
- Jakub Gruszczyk
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Rick K Huang
- CryoEM Shared Resource, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Menant
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Chuan Hong
- CryoEM Shared Resource, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Richard D Pearson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Wilson Wong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zhiheng Yu
- CryoEM Shared Resource, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.
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102
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Kittichai V, Nguitragool W, Ngassa Mbenda HG, Sattabongkot J, Cui L. Genetic diversity of the Plasmodium vivax multidrug resistance 1 gene in Thai parasite populations. INFECTION GENETICS AND EVOLUTION 2018; 64:168-177. [PMID: 29936038 DOI: 10.1016/j.meegid.2018.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022]
Abstract
Plasmodium vivax resistance to chloroquine (CQ) was first reported over 60 years ago. Here we analyzed sequence variations in the multidrug resistance 1 gene (Pvmdr1), a putative molecular marker for P. vivax CQ resistance, in field isolates collected from three sites in Thailand during 2013-2016. Several single nucleotide polymorphisms previously implicated in reduced CQ sensitivity were found. These genetic variations encode amino acids in the two nucleotide-binding domains as well as the transmembrane domains of the protein. The high level of genetic diversity of Pvmdr1 provides insights into the evolutionary history of this gene. Specifically, there was little evidence of positive selection at amino acid F1076L in global isolates to be promoted as a possible marker for CQ resistance. Population genetic analysis clearly divided the parasites into eastern and western populations, which is consistent with their geographical separation by the central malaria-free area of Thailand. With CQ-primaquine remaining as the frontline treatment for vivax malaria in all regions of Thailand, such a population subdivision could be shaped and affected by the current drugs for P. falciparum since mixed P. falciparum/P. vivax infections often occur in this region.
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Affiliation(s)
- Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Liwang Cui
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA.
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103
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Tantiamornkul K, Pumpaibool T, Piriyapongsa J, Culleton R, Lek-Uthai U. The prevalence of molecular markers of drug resistance in Plasmodium vivax from the border regions of Thailand in 2008 and 2014. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:229-237. [PMID: 29677637 PMCID: PMC6039358 DOI: 10.1016/j.ijpddr.2018.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 02/08/2023]
Abstract
The prevalence of Plasmodium vivax is increasing in the border regions of Thailand; one potential problem confounding the control of malaria in these regions is the emergence and spread of drug resistance. The aim of this study was to determine the genetic diversity in genes potentially linked to drug resistance in P. vivax parasites isolated from four different border regions of Thailand; Thai-Myanmar (Tak, Mae Hong Son and Prachuap Khiri Khan Provinces), and Thai-Cambodian borders (Chanthaburi Province). Isolates were collected from 345 P. vivax patients in 2008 and 2014, and parasite DNA extracted and subjected to nucleotide sequencing at five putative drug-resistance loci (Pvdhfr, Pvdhps, Pvmdr1, Pvcrt-o and Pvk12). The prevalence of mutations in Pvdhfr, Pvdhps and Pvmdr1 were markedly different between the Thai-Myanmar and Thai-Cambodian border areas and also varied between sampling times. All isolates carried the Pvdhfr (58R and 117N/T) mutation, however, whereas the quadruple mutant allele (I57R58M61T117) was the most prevalent (69.6%) in the Thai-Myanmar border region, the double mutant allele (F57R58T61N117) was at fixation on the Thai-Cambodian border (100%). The most prevalent genotypes of Pvdhps and Pvmdr1 were the double mutant (S382G383K512G553) (65.1%) and single mutant (M958Y976F1076) (46.5%) alleles, respectively on the Thai-Myanmar border while the single Pvdhps mutant (S382G383K512A553) (52.7%) and the triple Pvmdr1 mutant (M958F976L1076) (81%) alleles were dominant on the Thai-Cambodian border. No mutations were observed in the Pvcrt-o gene in either region. Novel mutations in the Pvk12 gene, the P. vivax orthologue of PfK13, linked to artemisinin resistance in Plasmodium falciparum, were observed with three nonsynonymous and three synonymous mutations in six isolates (3.3%).
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Affiliation(s)
- Kritpaphat Tantiamornkul
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Rajvithi Rd, Rajthewee District, Bangkok 10400, Thailand; Faculty of Graduate Studies, Mahidol University, Phuttamonthon 4 Rd, Nakorn Pathom 73170, Thailand
| | - Tepanata Pumpaibool
- College of Public Health Science, Chulalongkorn University, Phyathai Rd, Bangkok 10330, Thailand
| | - Jittima Piriyapongsa
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki 8528523, Japan.
| | - Usa Lek-Uthai
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Rajvithi Rd, Rajthewee District, Bangkok 10400, Thailand.
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104
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Gunalan K, Niangaly A, Thera MA, Doumbo OK, Miller LH. Plasmodium vivax Infections of Duffy-Negative Erythrocytes: Historically Undetected or a Recent Adaptation? Trends Parasitol 2018. [PMID: 29530446 DOI: 10.1016/j.pt.2018.02.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Plasmodium vivax is the main cause of malarial disease in Asia and South America. Plasmodium vivax infection was thought to be absent in African populations who are Duffy blood group antigen negative (Duffy-negative). However, many cases of P. vivax infection have recently been observed in Duffy-negative Africans. This raises the question: were P. vivax infections in Duffy-negative populations previously missed or has P. vivax adapted to infect Duffy-negative populations? This review focuses on recent P. vivax findings in Africa and reports views on the parasite ligands that may play a role in Duffy-negative P. vivax infections. In addition, clues gained from studying P. vivax infection of reticulocytes are presented, which may provide possible avenues for establishing P. vivax culture in vitro.
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Affiliation(s)
- Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; These authors contributed equally.
| | - Amadou Niangaly
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali; These authors contributed equally
| | - Mahamadou A Thera
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Ogobara K Doumbo
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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105
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Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
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Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
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106
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Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific. PLoS Negl Trop Dis 2018; 12:e0006146. [PMID: 29373596 PMCID: PMC5802943 DOI: 10.1371/journal.pntd.0006146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 02/07/2018] [Accepted: 12/01/2017] [Indexed: 01/17/2023] Open
Abstract
The human malaria parasite Plasmodium vivax is more resistant to malaria control strategies than Plasmodium falciparum, and maintains high genetic diversity even when transmission is low. To investigate whether declining P. vivax transmission leads to increasing population structure that would facilitate elimination, we genotyped samples from across the Southwest Pacific region, which experiences an eastward decline in malaria transmission, as well as samples from two time points at one site (Tetere, Solomon Islands) during intensified malaria control. Analysis of 887 P. vivax microsatellite haplotypes from hyperendemic Papua New Guinea (PNG, n = 443), meso-hyperendemic Solomon Islands (n = 420), and hypoendemic Vanuatu (n = 24) revealed increasing population structure and multilocus linkage disequilibrium yet a modest decline in diversity as transmission decreases over space and time. In Solomon Islands, which has had sustained control efforts for 20 years, and Vanuatu, which has experienced sustained low transmission for many years, significant population structure was observed at different spatial scales. We conclude that control efforts will eventually impact P. vivax population structure and with sustained pressure, populations may eventually fragment into a limited number of clustered foci that could be targeted for elimination. Plasmodium vivax is a major human malaria parasite, common in endemic areas outside sub-Saharan Africa, and more difficult to control than other malaria parasite species. The distinct lifecycle biology of P. vivax is thought to contribute to its more stable and efficient transmission allowing the maintenance of high diversity and potentially, gene flow. Independent studies are therefore needed to understand how P. vivax populations respond to changing transmission levels, in order to inform malaria control and elimination efforts. Here we have determined parasite population genetic structure in three countries of the Southwest Pacific, an island chain with a natural west to east decline in transmission intensity (Papua New Guinea > Solomon Islands > Vanuatu). With declining transmission, P. vivax populations experience only a modest decline in diversity but a significant increase in multilocus linkage disequilibrium and population structure, indicating that parasite populations become more inbred and begin to fragment into clustered foci. Analysis of two time points in one study area (Tetere, Solomon Islands) also show similar changes in association with intensifying malaria control. The results indicate that with long term sustained malaria control P. vivax populations will eventually fracture into population clusters that could be targeted for elimination.
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107
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Gruszczyk J, Kanjee U, Chan LJ, Menant S, Malleret B, Lim NT, Schmidt CQ, Mok YF, Lin KM, Pearson RD, Rangel G, Smith BJ, Call MJ, Weekes MP, Griffin MDW, Murphy JM, Abraham J, Sriprawat K, Menezes MJ, Ferreira MU, Russell B, Renia L, Duraisingh MT, Tham WH. Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax. Science 2018; 359:48-55. [PMID: 29302006 PMCID: PMC5788258 DOI: 10.1126/science.aan1078] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/29/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
Abstract
Plasmodium vivax shows a strict host tropism for reticulocytes. We identified transferrin receptor 1 (TfR1) as the receptor for P. vivax reticulocyte-binding protein 2b (PvRBP2b). We determined the structure of the N-terminal domain of PvRBP2b involved in red blood cell binding, elucidating the molecular basis for TfR1 recognition. We validated TfR1 as the biological target of PvRBP2b engagement by means of TfR1 expression knockdown analysis. TfR1 mutant cells deficient in PvRBP2b binding were refractory to invasion of P. vivax but not to invasion of P. falciparum Using Brazilian and Thai clinical isolates, we show that PvRBP2b monoclonal antibodies that inhibit reticulocyte binding also block P. vivax entry into reticulocytes. These data show that TfR1-PvRBP2b invasion pathway is critical for the recognition of reticulocytes during P. vivax invasion.
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Affiliation(s)
- Jakub Gruszczyk
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, USA
| | - Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Sébastien Menant
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Benoit Malleret
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
- Singapore Immunology Network, A*STAR, 138648 Singapore
| | - Nicholas T.Y. Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Christoph Q. Schmidt
- Institute of Pharmacology of Natural Products and Clinical Pharmacology, Ulm University, Germany
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kai-Min Lin
- Cambridge Institute for Medical Research, Cambridge, CB2 OXY, United Kingdom
| | - Richard D. Pearson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Gabriel Rangel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, USA
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne Victoria 3086, Australia
| | - Melissa J. Call
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, Cambridge, CB2 OXY, United Kingdom
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - James M. Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan Abraham
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Maria J. Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Laurent Renia
- Singapore Immunology Network, A*STAR, 138648 Singapore
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, USA
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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108
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Zhu SJ, Almagro-Garcia J, McVean G. Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. Bioinformatics 2018; 34:9-15. [PMID: 28961721 PMCID: PMC5870807 DOI: 10.1093/bioinformatics/btx530] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/14/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022] Open
Abstract
Motivation The presence of multiple infecting strains of the malarial parasite Plasmodium falciparum affects key phenotypic traits, including drug resistance and risk of severe disease. Advances in protocols and sequencing technology have made it possible to obtain high-coverage genome-wide sequencing data from blood samples and blood spots taken in the field. However, analyzing and interpreting such data is challenging because of the high rate of multiple infections present. Results We have developed a statistical method and implementation for deconvolving multiple genome sequences present in an individual with mixed infections. The software package DEploid uses haplotype structure within a reference panel of clonal isolates as a prior for haplotypes present in a given sample. It estimates the number of strains, their relative proportions and the haplotypes presented in a sample, allowing researchers to study multiple infection in malaria with an unprecedented level of detail. Availability and implementation The open source implementation DEploid is freely available at https://github.com/mcveanlab/DEploid under the conditions of the GPLv3 license. An R version is available at https://github.com/mcveanlab/DEploid-r. Contact joe.zhu@bdi.ox.ac.uk or gil.mcvean@bdi.ox.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sha Joe Zhu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Jacob Almagro-Garcia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
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109
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Parker DM, Landier J, Thu AM, Lwin KM, Delmas G, Nosten FH. Scale up of a Plasmodium falciparum elimination program and surveillance system in Kayin State, Myanmar. Wellcome Open Res 2017; 2:98. [PMID: 29384151 PMCID: PMC5701446 DOI: 10.12688/wellcomeopenres.12741.2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
Background: Myanmar has one of the largest malaria burdens in the Greater Mekong Subregion (GMS). Throughout the GMS,
Plasmodium falciparum parasites are increasingly resistant to artemisinin combination therapies. Given that there are no current alternative treatment therapies, one proposed solution to the threat of untreatable
P. falciparum malaria is to eliminate the parasite from the region. Several small-scale elimination projects have been piloted in the GMS, including along the Myanmar-Thailand border. Following the success of the pilot elimination project along the Myanmar-Thailand border, there was a scale up to a broad area of Eastern Kayin State, Myanmar. Here we describe the establishment of the scale up elimination project in Easter Kayin State. Methods: The scale up relied on geographic reconnaissance and a geographic information system, community engagement, generalized access to community-based early diagnosis and treatment, near real-time epidemiological surveillance, cross sectional malaria prevalence surveys and targeted mass drug administration in villages with high prevalence of
P. falciparum malaria. Molecular markers of drug resistance were also monitored in individuals with symptomatic and asymptomatic infections. Discussion: This protocol illustrates the establishment of an elimination project and operational research in a remote, rural area encompassing several armed groups, multiple political organizations and a near-absent health care infrastructure. The establishment of the project relied on a strong rapport with the target community, on-the-ground knowledge (through geographic surveys and community engagement), rapid decision making and an approach that was flexible enough to quickly adapt to a complex landscape. The elimination project is ongoing, now over three years in operation, and assessment of the impact of this operational research will follow. This project has relevance not only for other malaria elimination projects but also for operational research aimed at eliminating other diseases.
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Affiliation(s)
- Daniel M Parker
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Jordi Landier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Khin Maung Lwin
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Gilles Delmas
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François H Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
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110
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Parker DM, Landier J, Thu AM, Lwin KM, Delmas G, Nosten FH. Scale up of a Plasmodium falciparum elimination program and surveillance system in Kayin State, Myanmar. Wellcome Open Res 2017. [PMID: 29384151 DOI: 10.12688/wellcomeopenres.12741.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Myanmar has one of the largest malaria burdens in the Greater Mekong Subregion (GMS). Throughout the GMS, Plasmodium falciparum parasites are increasingly resistant to artemisinin combination therapies. Given that there are no current alternative treatment therapies, one proposed solution to the threat of untreatable P. falciparum malaria is to eliminate the parasite from the region. Several small-scale elimination projects have been piloted in the GMS, including along the Myanmar-Thailand border. Following the success of the pilot elimination project along the Myanmar-Thailand border, there was a scale up to a broad area of Eastern Kayin State, Myanmar. Here we describe the establishment of the scale up elimination project in Easter Kayin State. Methods: The scale up relied on geographic reconnaissance and a geographic information system, community engagement, generalized access to community-based early diagnosis and treatment, near real-time epidemiological surveillance, cross sectional malaria prevalence surveys and targeted mass drug administration in villages with high prevalence of P. falciparum malaria. Molecular markers of drug resistance were also monitored in individuals with symptomatic and asymptomatic infections. Discussion: This protocol illustrates the establishment of an elimination project and operational research in a remote, rural area encompassing several armed groups, multiple political organizations and a near-absent health care infrastructure. The establishment of the project relied on a strong rapport with the target community, on-the-ground knowledge (through geographic surveys and community engagement), rapid decision making and an approach that was flexible enough to quickly adapt to a complex landscape. The elimination project is ongoing, now over three years in operation, and assessment of the impact of this operational research will follow. This project has relevance not only for other malaria elimination projects but also for operational research aimed at eliminating other diseases.
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Affiliation(s)
- Daniel M Parker
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Jordi Landier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Khin Maung Lwin
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Gilles Delmas
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François H Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
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Lo E, Lam N, Hemming-Schroeder E, Nguyen J, Zhou G, Lee MC, Yang Z, Cui L, Yan G. Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers. J Infect Dis 2017; 216:1254-1263. [PMID: 28329141 DOI: 10.1093/infdis/jix106] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/02/2017] [Indexed: 11/13/2022] Open
Abstract
Background In Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission. Methods Microsatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission. Results P. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow. Conclusions The admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas.
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Affiliation(s)
- Eugenia Lo
- Program in Public Health, University of California-Irvine
| | - Nancy Lam
- Program in Public Health, University of California-Irvine
| | | | | | - Guofa Zhou
- Program in Public Health, University of California-Irvine
| | - Ming-Chieh Lee
- Program in Public Health, University of California-Irvine
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, China
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park
| | - Guiyun Yan
- Program in Public Health, University of California-Irvine
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Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission. PLoS Negl Trop Dis 2017; 11:e0005930. [PMID: 29036178 PMCID: PMC5658191 DOI: 10.1371/journal.pntd.0005930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 09/04/2017] [Indexed: 11/23/2022] Open
Abstract
Background Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. Methodology/Results A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins. Conclusion/Significance Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination. This study presents an updated view of the P. vivax populations along the Thai-Myanmar and the Thai-Cambodian borders. Genotyping of parasite samples collected after intensified malaria control demonstrated that despite the decline in overall transmission intensity, the genetic diversity of the P. vivax parasites remained high. Parasite populations from three border provinces showed clear genetic separation. This indicates successful interruption of parasite gene flow within Thailand, but suggests frequent parasite migration across international borders. From the analysis of 10 microsatellite markers, we further refined a set of four that are sufficient for distinguishing the provincial origins of these parasites, which should allow tracking of parasite introduction among these provinces.
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113
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Zhou X, Tambo E, Su J, Fang Q, Ruan W, Chen JH, Yin MB, Zhou XN. Genetic Diversity and Natural Selection in 42 kDa Region of Plasmodium vivax Merozoite Surface Protein-1 from China-Myanmar Endemic Border. THE KOREAN JOURNAL OF PARASITOLOGY 2017; 55:473-480. [PMID: 29103262 PMCID: PMC5678462 DOI: 10.3347/kjp.2017.55.5.473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Plasmodium vivax merozoite surface protein-1 (PvMSP1) gene codes for a major malaria vaccine candidate antigen. However, its polymorphic nature represents an obstacle to the design of a protective vaccine. In this study, we analyzed the genetic polymorphism and natural selection of the C-terminal 42 kDa fragment within PvMSP1 gene (Pv MSP142) from 77 P. vivax isolates, collected from imported cases of China-Myanmar border (CMB) areas in Yunnan province and the inland cases from Anhui, Yunnan, and Zhejiang province in China during 2009-2012. Totally, 41 haplotypes were identified and 30 of them were new haplotypes. The differences between the rates of non-synonymous and synonymous mutations suggest that PvMSP142 has evolved under natural selection, and a high selective pressure preferentially acted on regions identified of PvMSP133. Our results also demonstrated that PvMSP142 of P. vivax isolates collected on China-Myanmar border areas display higher genetic polymorphisms than those collected from inland of China. Such results have significant implications for understanding the dynamic of the P. vivax population and may be useful information towards China malaria elimination campaign strategies.
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Affiliation(s)
- Xia Zhou
- Medical College of Soochow University, Suzhou 215123, P. R. China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, P. R. China
| | - Ernest Tambo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, P. R. China
- Department of Biochemistry, Higher Institute of Health Sciences, Université des Montagnes, Bangangté BP208, Cameroon
| | - Jing Su
- School of Life Science, Fudan University, Shanghai 200438, P. R. China
| | - Qiang Fang
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu 233030, P. R. China
| | - Wei Ruan
- Department of Parasitic Disease Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, P. R. China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, P. R. China
| | - Ming-Bo Yin
- School of Life Science, Fudan University, Shanghai 200438, P. R. China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, P. R. China
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114
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Malaria Epidemiology at the Clone Level. Trends Parasitol 2017; 33:974-985. [PMID: 28966050 DOI: 10.1016/j.pt.2017.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
Abstract
Genotyping to distinguish between parasite clones is nowadays a standard in many molecular epidemiological studies of malaria. It has become crucial in drug trials and to follow individual clones in epidemiological studies, and to understand how drug resistance emerges and spreads. Here, we review the applications of the increasingly available genotyping tools and whole-genome sequencing data, and argue for a better integration of population genetics findings into malaria-control strategies.
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115
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Soontarawirat I, Andolina C, Paul R, Day NPJ, Nosten F, Woodrow CJ, Imwong M. Plasmodium vivax genetic diversity and heterozygosity in blood samples and resulting oocysts at the Thai-Myanmar border. Malar J 2017; 16:355. [PMID: 28870214 PMCID: PMC5584506 DOI: 10.1186/s12936-017-2002-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/29/2017] [Indexed: 11/30/2022] Open
Abstract
Background Polyclonal blood-stage infections of Plasmodium vivax are frequent even in low transmission settings, allowing meiotic recombination between heterologous parasites. Empirical data on meiotic products are however lacking. This study examined microsatellites in oocysts derived by membrane feeding of mosquitoes from blood-stage P. vivax infections at the Thai–Myanmar border. Methods Blood samples from patients presenting with vivax malaria were fed to Anopheles cracens by membrane feeding and individual oocysts from midguts were obtained by dissection after 7 days. DNA was extracted from oocysts and parental blood samples and tested by microsatellite analysis. Results A focused study of eight microsatellite markers was undertaken for nine blood stage infections from 2013, for which derived oocysts were studied in six cases. One or more alleles were successfully amplified for 131 oocysts, revealing high levels of allelic diversity in both blood and oocyst stages. Based on standard criteria for defining minor alleles, there was evidence of clear deviation from random mating (inbreeding) with relatively few heterozygous oocysts compared to variance across the entire oocyst population (FIT = 0.89). The main explanation appeared to be natural compartmentalisation at mosquito (FSC = 0.27) and human stages (FCT = 0.68). One single human case produced a total of 431 successfully amplified loci (across 70 oocysts) that were homozygous and identical to parental alleles at all markers, indicating clonal infection and transmission. Heterozygous oocyst alleles were found at 15/176 (8.5%) successfully amplified loci in the other five cases. There was apparently reduced oocyst heterozygosity in individual oocysts compared to diversity within individual mosquitoes (FIS = 0.55), but this may simply reflect the difficulty of detecting minor alleles in oocysts, given the high rate of amplification failure. Inclusion of minor allele peaks (irrespective of height) when matching peaks were found in related blood or oocyst samples, added 11 minor alleles for 9 oocysts, increasing the number of heterozygous loci to 26/176 (14.8%; p = 0.096). Conclusion There was an apparently low level of heterozygous oocysts but this can be explained by a combination of factors: relatively low complexity of parental infection, natural compartmentalisation in humans and mosquitoes, and the methodological challenge of detecting minor alleles. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2002-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ingfar Soontarawirat
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chiara Andolina
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Richard Paul
- Unité de Génétique Fonctionnelle Des Maladies Infectieuses, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris, France.,Centre National de la Recherche Scientifique, URA3012, 28 rue du Docteur Roux, 75724, Paris, France
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Charles J Woodrow
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mallika Imwong
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Abstract
Plasmodium vivax is the second most prevalent cause of malaria worldwide and the leading cause of malaria outside of Africa. Although infections are seldom fatal clinical disease can be debilitating and imposes significant health and economic impacts on affected populations. Estimates of transmission and prevalence intensity can be problematic because many episodes of vivax originate from hypnozoite stages in the liver that have remained dormant from previous infections by an unknown mechanism. Lack of treatment options to clear hypnozoites and the ability to infect mosquitoes before disease symptoms present represent major challenges for control and eradication of vivax malaria. Compounding these challenges is the unique biology of P. vivax and limited progress in development of experimental research tools, thereby hindering development of new drugs and vaccines. Renewed emphasis on vivax malaria research is beginning to make progress in overcoming some of these challenges.
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Affiliation(s)
- John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Victoria 3052, Australia
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117
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de Oliveira TC, Rodrigues PT, Menezes MJ, Gonçalves-Lopes RM, Bastos MS, Lima NF, Barbosa S, Gerber AL, Loss de Morais G, Berná L, Phelan J, Robello C, de Vasconcelos ATR, Alves JMP, Ferreira MU. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS Negl Trop Dis 2017; 11:e0005824. [PMID: 28759591 PMCID: PMC5552344 DOI: 10.1371/journal.pntd.0005824] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/10/2017] [Accepted: 07/20/2017] [Indexed: 01/15/2023] Open
Abstract
Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. Plasmodium vivax is the most common human malaria parasite in the Americas, but how and when this species arrived in the New World remains unclear. Here we describe high-quality whole-genome sequence data for nine P. vivax isolates from Brazil, a country that accounts for 37% of the malaria burden in this continent, and compare these data with additional publicly available P. vivax genomes from Brazil, Peru, Colombia, and Mexico. P. vivax populations from the New World were found to be as diverse as their counterparts from areas with substantially higher malaria transmission, such as Southeast Asia, and to carry several non-synonymous substitutions in candidate drug-resistance genes. Moreover, genome-wide patterns of linkage disequilibrium between pairs of polymorphic sites are consistent with very frequent outcrossing in these populations. Interestingly, local P. vivax is more polymorphic, with less between-population differentiation, than sympatric populations of P. falciparum, possibly as a result of different demographic histories of these two species in the Americas. We hypothesize that local P. vivax lineages originated from successive migratory waves and subsequent admixture between parasites from geographically diverse sites.
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Affiliation(s)
- Thais C. de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria José Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Raquel M. Gonçalves-Lopes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S. Bastos
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandra L. Gerber
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Luisa Berná
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Robello
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Ana Tereza R. de Vasconcelos
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Niangaly A, Karthigayan Gunalan, Amed Ouattara, Coulibaly D, Sá JM, Adams M, Travassos MA, Ferrero J, Laurens MB, Kone AK, Thera MA, Plowe CV, Miller LH, Doumbo OK. Plasmodium vivax Infections over 3 Years in Duffy Blood Group Negative Malians in Bandiagara, Mali. Am J Trop Med Hyg 2017; 97:744-752. [PMID: 28749772 DOI: 10.4269/ajtmh.17-0254] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Plasmodium vivax was thought to infect only the erythrocytes of Duffy blood group positive people. In the last decade, P. vivax has appeared throughout Africa, both in areas where Duffy positive and negative people live side by side as in Madagascar and Ethiopia and in areas where people are primarily Duffy negative, such as in western Kenya. We performed quantitative polymerase chain reaction on blood samples dried onto filter paper to determine the prevalence of P. vivax and Plasmodium falciparum in a cohort of 300 children (newborn to 6 years of age) in Bandiagara, a Sahelian area of Mali, west Africa, where the people are Duffy negative. We report 1-3 occurrences of P. vivax in each of 25 Duffy-negative children at six time points over two rainy seasons and the beginning of the third season. The prevalence of P. vivax infection was 2.0-2.5% at every time point (June 2009 to June 2010). All children with P. vivax infections were asymptomatic and afebrile, and parasite densities were extremely low. Anemia, however, was the main burden of infection. Plasmodium vivax could become a burden to sub-Saharan Africa, and the evidence of P. vivax existence needs to be taken into consideration in designing malaria control and elimination strategies in Africa.
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Affiliation(s)
- Amadou Niangaly
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Amed Ouattara
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland.,Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Juliana M Sá
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Matthew Adams
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Mark A Travassos
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Jennifer Ferrero
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Matthew B Laurens
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Abdoulaye K Kone
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Mahamadou A Thera
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Christopher V Plowe
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Ogobara K Doumbo
- Malaria Research and Training Center, International Center for Excellence in Research, University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
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Plasmodium falciparum and Plasmodium vivax Demonstrate Contrasting Chloroquine Resistance Reversal Phenotypes. Antimicrob Agents Chemother 2017; 61:AAC.00355-17. [PMID: 28533239 PMCID: PMC5527611 DOI: 10.1128/aac.00355-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/08/2017] [Indexed: 01/12/2023] Open
Abstract
High-grade chloroquine (CQ) resistance has emerged in both Plasmodium falciparum and P. vivax The aim of the present study was to investigate the phenotypic differences of CQ resistance in both of these species and the ability of known CQ resistance reversal agents (CQRRAs) to alter CQ susceptibility. Between April 2015 and April 2016, the potential of verapamil (VP), mibefradil (MF), L703,606 (L7), and primaquine (PQ) to reverse CQ resistance was assessed in 46 P. falciparum and 34 P. vivax clinical isolates in Papua, Indonesia, where CQ resistance is present in both species, using a modified schizont maturation assay. In P. falciparum, CQ 50% inhibitory concentrations (IC50s) were reduced when CQ was combined with VP (1.4-fold), MF (1.2-fold), L7 (4.2-fold), or PQ (1.8-fold). The degree of CQ resistance reversal in P. falciparum was highly correlated with CQ susceptibility for all CQRRAs (R2 = 0.951, 0.852, 0.962, and 0.901 for VP, MF, L7, and PQ, respectively), in line with observations in P. falciparum laboratory strains. In contrast, no reduction in the CQ IC50s was observed with any of the CQRRAs in P. vivax, even in those isolates with high chloroquine IC50s. The differential effect of CQRRAs in P. falciparum and P. vivax suggests significant differences in CQ kinetics and, potentially, the likely mechanism of CQ resistance between these two species.
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120
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Htun MW, Mon NCN, Aye KM, Hlaing CM, Kyaw MP, Handayuni I, Trimarsanto H, Bustos D, Ringwald P, Price RN, Auburn S, Thriemer K. Chloroquine efficacy for Plasmodium vivax in Myanmar in populations with high genetic diversity and moderate parasite gene flow. Malar J 2017; 16:281. [PMID: 28693552 PMCID: PMC5504659 DOI: 10.1186/s12936-017-1912-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/26/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax malaria remains a major public health burden in Myanmar. Resistance to chloroquine (CQ), the first-line treatment for P. vivax, has been reported in the country and has potential to undermine local control efforts. METHODS Patients over 6 years of age with uncomplicated P. vivax mono-infection were enrolled into clinical efficacy studies in Myawaddy in 2014 and Kawthoung in 2012. Study participants received a standard dose of CQ (25 mg/kg over 3 days) followed by weekly review until day 28. Pvmdr1 copy number (CN) and microsatellite diversity were assessed on samples from the patients enrolled in the clinical study and additional cross-sectional surveys undertaken in Myawaddy and Shwegyin in 2012. RESULTS A total of 85 patients were enrolled in the CQ clinical studies, 25 in Myawaddy and 60 in Kawthoung. One patient in Myawaddy (1.2%) had an early treatment failure and two patients (2.3%) in Kawthoung presented with late treatment failures on day 28. The day 28 efficacy was 92.0% (95% CI 71.6-97.9) in Myawaddy and 98.3% (95% CI 88.7-99.8) in Kawthoung. By day 2, 92.2% (23/25) in Myawaddy and 85.0% (51/60) in Kawthoung were aparasitaemic. Genotyping and pvmdr1 CN assessment was undertaken on 43, 52 and 46 clinical isolates from Myawaddy, Kawthoung and Shwegyin respectively. Pvmdr1 amplification was observed in 3.2% (1/31) of isolates in Myawaddy, 0% (0/49) in Kawthoung and 2.5% (1/40) in Shwegyin. Diversity was high in all sites (H E 0.855-0.876), with low inter-population differentiation (F ST 0.016-0.026, P < 0.05). CONCLUSIONS Treatment failures after chloroquine were observed following chloroquine monotherapy, with pvmdr1 amplification present in both Myawaddy and Shwegyin. The results emphasize the importance of ongoing P. vivax drug resistance surveillance in Myanmar, particularly given the potential connectivity between parasite population at different sites.
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Affiliation(s)
- Myo Win Htun
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Nan Cho Nwe Mon
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Khin Myo Aye
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Chan Myae Hlaing
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Myat Phone Kyaw
- grid.415741.2Department of Medical Research, Yangon, 11191 Myanmar
| | - Irene Handayuni
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
| | - Hidayat Trimarsanto
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jl. Diponegoro 69, Central Jakarta, 10430 Indonesia ,grid.466915.9The Ministry of Research and Technology (RISTEK), Jakarta, Indonesia ,0000 0001 0746 0534grid.432292.cAgency for Assessment and Application of Technology, Jl. MH Thamrin 8, Jakarta, 10340 Indonesia
| | - Dorina Bustos
- 0000 0004 0576 2573grid.415836.dWorld Health Organization, Country Office for Thailand, Ministry of Public Health, Nonthaburi, Thailand
| | - Pascal Ringwald
- 0000000121633745grid.3575.4Global Malaria Programme, World Health Organization, 20 Avenue Appia, 1211 Geneva, 27, Switzerland
| | - Ric N. Price
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia ,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Sarah Auburn
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
| | - Kamala Thriemer
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810 Australia
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González-Cerón L, Montoya A, Corzo-Gómez JC, Cerritos R, Santillán F, Sandoval MA. Genetic diversity and natural selection of Plasmodium vivax multi-drug resistant gene (pvmdr1) in Mesoamerica. Malar J 2017; 16:261. [PMID: 28666481 PMCID: PMC5493867 DOI: 10.1186/s12936-017-1905-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/23/2017] [Indexed: 01/09/2023] Open
Abstract
Background The Plasmodium vivax multidrug resistant 1 gene (pvmdr1) codes for a transmembrane protein of the parasite’s digestive vacuole. It is likely that the pvmdr1 gene mutations occur at different sites by convergent evolution. In here, the genetic variation of pvmdr1 at three sites of the Mesoamerican region was studied. Since 1950s, malarious patients of those areas have been treated only with chloroquine and primaquine. Methods Blood samples from patients infected with P. vivax were obtained in southern Mexico (SMX), in the Northwest (NIC-NW) and in the northeast (NIC-NE) of Nicaragua. Genomic DNA was obtained and fragments of pvmdr1 were amplified and sequenced. The nucleotide and amino acid changes as well as the haplotype frequency in pvmdr1 were determined per strain and per geographic site. The sequences of pvmdr1 obtained from the studied regions were compared with homologous sequences from the GenBank database to explore the P. vivax genetic structure. Results In 141 parasites, eight nucleotide changes (two changes were synonymous and other six were nonsynonymous) were detected in 1536 bp. The PvMDR1 amino acid changes Y976F, F1076FL were predominant in endemic parasites from NIC-NE and outbreak parasites in NIC-NW but absent in SMX. Thirteen haplotypes were resolved, and found to be closely related, but their frequency at each geographic site was different (P = 0.0001). The pvmdr1codons 925–1083 gene fragment showed higher genetic and haplotype diversity in parasites from NIC-NE than the other areas outside Latin America. The haplotype networks suggested local diversification of pvmdr1 and no significant departure from neutrality. The FST values were low to moderate regionally, but high between NIC-NE or NIC-NW and other regions inside and outside Latin America. Conclusions The pvmdr1 gene might have diversified recently at regional level. In the absence of significant natural, genetic drift might have caused differential pvmdr1 haplotype frequencies at different geographic sites in Mesoamerica. A very recent expansion of divergent pvmdr1 haplotypes in NIC-NE/NIC-NW produced high differentiation between these and parasites from other sites including SMX. These data are useful to set a baseline for epidemiological surveillance.
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Affiliation(s)
- Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico.
| | - Alberto Montoya
- Departamento de Parasitología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Josselin C Corzo-Gómez
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
| | - Rene Cerritos
- Division de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Frida Santillán
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
| | - Marco A Sandoval
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
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Shen HM, Chen SB, Wang Y, Xu B, Abe EM, Chen JH. Genome-wide scans for the identification of Plasmodium vivax genes under positive selection. Malar J 2017; 16:238. [PMID: 28587615 PMCID: PMC5461743 DOI: 10.1186/s12936-017-1882-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current trend of Plasmodium vivax cases imported from Southeast Asia into China has sharply increased recently, especially from the China-Myanmar border (CMB) area. High recombination rates of P. vivax populations associated with varied transmission intensity might cause distinct local selective pressures. The information on the genetic variability of P. vivax in this area is scant. Hence, this study assessed the genetic diversity of P. vivax genome sequence in CMB area and aimed to provide information on the positive selection of new gene loci. RESULTS This study reports a genome-wide survey of P. vivax in CMB area, using blood samples from local patients to identify population-specific selective processes. The result showed that considerable genetic diversity and mean pair-wise divergence among the sequenced P. vivax isolates were higher in some important gene families. Using the standardized integrated haplotype score (|iHS|) for all SNPs in chromosomal regions with SNPs above the top 1% distribution, it was observed that the top score locus involved 356 genes and most of them are associated with red blood cell invasion and immune evasion. The XP-EHH test was also applied and some important genes associated with anti-malarial drug resistance were observed in high positive scores list. This result suggests that P. vivax in CMB area is facing more pressure to survive than any other region and this has led to the strong positive selection of genes that are associated with host-parasite interactions. CONCLUSIONS This study suggests that greater genetic diversity in P. vivax from CMB area and positive selection signals in invasion and drug resistance genes are consistent with the history of drug use during malaria elimination programme in CMB area. Furthermore, this result also demonstrates that haplotype-based detecting selection can assist the genome-wide methods to identify the determinants of P. vivax diversity.
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Affiliation(s)
- Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Yue Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.,Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, People's Republic of China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Eniola Michael Abe
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, 207 Rui Jin Er Road, Shanghai, 200025, People's Republic of China.
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Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Roper C, Campino S, Clark TG. Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PLoS One 2017; 12:e0177134. [PMID: 28493919 PMCID: PMC5426636 DOI: 10.1371/journal.pone.0177134] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/21/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors. RESULTS We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents. Using population genetic methods we identified hotspots of selection pressure, including the previously reported MRP1 and DHPS genes, both putative drug resistance loci. Extra copies and deletions in the promoter region of another drug resistance candidate, MDR1 gene, and duplications in the Duffy binding protein gene (PvDBP) potentially involved in erythrocyte invasion, were also identified. For surveillance applications, continental-informative markers were found in putative drug resistance loci, and we show that organellar polymorphisms could classify P. vivax populations across continents and differentiate between Plasmodia spp. CONCLUSIONS This study has shown that genomic diversity that lies within and between P. vivax populations can be used to elucidate potential drug resistance and invasion mechanisms, as well as facilitate the molecular barcoding of the parasite for surveillance applications.
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Affiliation(s)
- Ernest Diez Benavente
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Zoe Ward
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- The Bioinformatics Group, School of Water Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Wilson Chan
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Fady R. Mohareb
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colin J. Sutherland
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Cally Roper
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Susana Campino
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Taane G. Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
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Folegatti PM, Siqueira AM, Monteiro WM, Lacerda MVG, Drakeley CJ, Braga ÉM. A systematic review on malaria sero-epidemiology studies in the Brazilian Amazon: insights into immunological markers for exposure and protection. Malar J 2017; 16:107. [PMID: 28270152 PMCID: PMC5341168 DOI: 10.1186/s12936-017-1762-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/28/2017] [Indexed: 01/11/2023] Open
Abstract
Background Considerable success in reducing malaria incidence and mortality has been achieved in Brazil, leading to discussions over the possibility of moving towards elimination. However, more than reporting and counting clinical cases, elimination will require the use of efficient tools and strategies for measuring transmission dynamics and detecting the infectious reservoir as the primary indicators of interest for surveillance and evaluation. Because acquisition and maintenance of anti-malarial antibodies depend on parasite exposure, seroprevalence rates could be used as a reliable tool for assessing malaria endemicity and an adjunct measure for monitoring transmission in a rapid and cost-effective manner. Methods This systematic review synthesizes the existing literature on seroprevalence of malaria in the Brazilian Amazon Basin. Different study designs (cross-sectional surveys and longitudinal studies) with reported serological results in well-defined Brazilian populations were considered. Medline (via PubMed), EMBASE and LILACS databases were screened and the articles were included per established selection criteria. Data extraction was performed by two authors and a modified critical appraisal tool was applied to assess the quality and completeness of cross-sectional studies regarding defined variables of interest. Results From 220 single records identified, 23 studies were included in this systematic review for the qualitative synthesis. Five studies reported serology results on Plasmodium falciparum, 14 papers assessed Plasmodium vivax and four articles reported results on both Plasmodium species. Considerable heterogeneity among the evaluated malarial antigens, including sporozoite and blood stage antigens, was observed. The majority of recent studies analysed IgG responses against P. vivax antigens reflecting the species distribution pattern in Brazil over the last decades. Most of the published papers were cross-sectional surveys (73.9%) and only six cohort studies were included in this review. Three studies pointed to an association between antibodies against circumsporozoite protein of both P. falciparum and P. vivax and malaria exposure. Furthermore, five out 13 cross-sectional studies evidenced a positive association between IgG antibodies to the conserved 19-kDa C-terminal region of the merozoite surface protein 1 of P. vivax (PvMSP119) and malaria exposure. Conclusions This systematic review identifies potential biomarkers of P. falciparum and P. vivax exposure in areas with variable and unstable malaria transmission in Brazil. However, this study highlights the need for standardization of further studies to provide an ideal monitoring tool to evaluate trends in malaria transmission and the effectiveness of malaria intervention programmes in Brazil. Moreover, the score-based weighted tool developed and used in this study still requires further validation.
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Affiliation(s)
- Pedro M Folegatti
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - André M Siqueira
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Wuelton M Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil.,Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Marcus Vinícius G Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil.,Instituto de Pesquisas Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - Chris J Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Érika M Braga
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. .,Departamento de Parasitologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
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Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. mBio 2017; 8:mBio.02257-16. [PMID: 28174312 PMCID: PMC5296604 DOI: 10.1128/mbio.02257-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system. Current techniques used to enrich P. vivax DNA from clinical samples require significant resources or are not consistently effective. Here, we demonstrate that selective whole-genome amplification (SWGA) can enrich P. vivax gDNA from unprocessed human blood samples and dried blood spots for high-quality WGS, allowing genetic characterization of isolates that would otherwise have been prohibitively expensive or impossible to sequence. We achieved an average genome coverage of 24×, with up to 95% of the P. vivax core genome covered by ≥5 reads. The single-nucleotide polymorphism (SNP) characteristics and drug resistance mutations seen were consistent with those of other P. vivax sequences from a similar region in Peru, demonstrating that SWGA produces high-quality sequences for downstream analysis. SWGA is a robust tool that will enable efficient, cost-effective WGS of P. vivax isolates from clinical samples that can be applied to other neglected microbial pathogens. Malaria is a disease caused by Plasmodium parasites that caused 214 million symptomatic cases and 438,000 deaths in 2015. Plasmodium vivax is the most widely distributed species, causing the majority of malaria infections outside sub-Saharan Africa. Whole-genome sequencing (WGS) of Plasmodium parasites from clinical samples has revealed important insights into the epidemiology and mechanisms of drug resistance of malaria. However, WGS of P. vivax is challenging due to low parasite levels in humans and the lack of a routine system to culture the parasites. Selective whole-genome amplification (SWGA) preferentially amplifies the genomes of pathogens from mixtures of target and host gDNA. Here, we demonstrate that SWGA is a simple, robust method that can be used to enrich P. vivax genomic DNA (gDNA) from unprocessed human blood samples and dried blood spots for cost-effective, high-quality WGS.
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126
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Chen SB, Wang Y, Kassegne K, Xu B, Shen HM, Chen JH. Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area. BMC Genomics 2017; 18:131. [PMID: 28166727 PMCID: PMC5294834 DOI: 10.1186/s12864-017-3523-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/27/2017] [Indexed: 11/29/2022] Open
Abstract
Background Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. Results The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area. Conclusion Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3523-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Yue Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.,Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, People's Republic of China
| | - Kokouvi Kassegne
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.
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Amato R, Lim P, Miotto O, Amaratunga C, Dek D, Pearson RD, Almagro-Garcia J, Neal AT, Sreng S, Suon S, Drury E, Jyothi D, Stalker J, Kwiatkowski DP, Fairhurst RM. Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study. THE LANCET. INFECTIOUS DISEASES 2017; 17:164-173. [PMID: 27818095 PMCID: PMC5564489 DOI: 10.1016/s1473-3099(16)30409-1] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND As the prevalence of artemisinin-resistant Plasmodium falciparum malaria increases in the Greater Mekong subregion, emerging resistance to partner drugs in artemisinin combination therapies seriously threatens global efforts to treat and eliminate this disease. Molecular markers that predict failure of artemisinin combination therapy are urgently needed to monitor the spread of partner drug resistance, and to recommend alternative treatments in southeast Asia and beyond. METHODS We did a genome-wide association study of 297 P falciparum isolates from Cambodia to investigate the relationship of 11 630 exonic single-nucleotide polymorphisms (SNPs) and 43 copy number variations (CNVs) with in-vitro piperaquine 50% inhibitory concentrations (IC50s), and tested whether these genetic variants are markers of treatment failure with dihydroartemisinin-piperaquine. We then did a survival analysis of 133 patients to determine whether candidate molecular markers predicted parasite recrudescence following dihydroartemisinin-piperaquine treatment. FINDINGS Piperaquine IC50s increased significantly from 2011 to 2013 in three Cambodian provinces (2011 vs 2013 median IC50s: 20·0 nmol/L [IQR 13·7-29·0] vs 39·2 nmol/L [32·8-48·1] for Ratanakiri, 19·3 nmol/L [15·1-26·2] vs 66·2 nmol/L [49·9-83·0] for Preah Vihear, and 19·6 nmol/L [11·9-33·9] vs 81·1 nmol/L [61·3-113·1] for Pursat; all p≤10-3; Kruskal-Wallis test). Genome-wide analysis of SNPs identified a chromosome 13 region that associates with raised piperaquine IC50s. A non-synonymous SNP (encoding a Glu415Gly substitution) in this region, within a gene encoding an exonuclease, associates with parasite recrudescence following dihydroartemisinin-piperaquine treatment. Genome-wide analysis of CNVs revealed that a single copy of the mdr1 gene on chromosome 5 and a novel amplification of the plasmepsin 2 and plasmepsin 3 genes on chromosome 14 also associate with raised piperaquine IC50s. After adjusting for covariates, both exo-E415G and plasmepsin 2-3 markers significantly associate (p=3·0 × 10-8 and p=1·7 × 10-7, respectively) with decreased treatment efficacy (survival rates 0·38 [95% CI 0·25-0·51] and 0·41 [0·28-0·53], respectively). INTERPRETATION The exo-E415G SNP and plasmepsin 2-3 amplification are markers of piperaquine resistance and dihydroartemisinin-piperaquine failures in Cambodia, and can help monitor the spread of these phenotypes into other countries of the Greater Mekong subregion, and elucidate the mechanism of piperaquine resistance. Since plasmepsins are involved in the parasite's haemoglobin-to-haemozoin conversion pathway, targeted by related antimalarials, plasmepsin 2-3 amplification probably mediates piperaquine resistance. FUNDING Intramural Research Program of the US National Institute of Allergy and Infectious Diseases, National Institutes of Health, Wellcome Trust, Bill & Melinda Gates Foundation, Medical Research Council, and UK Department for International Development.
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Affiliation(s)
- Roberto Amato
- Wellcome Trust Sanger Institute, Hinxton, UK; Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK.
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA; National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Olivo Miotto
- Wellcome Trust Sanger Institute, Hinxton, UK; Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Dalin Dek
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Richard D Pearson
- Wellcome Trust Sanger Institute, Hinxton, UK; Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Jacob Almagro-Garcia
- Wellcome Trust Sanger Institute, Hinxton, UK; Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Aaron T Neal
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Sokunthea Sreng
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | | | | | - Jim Stalker
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, UK; Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Rick M Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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Tham WH, Beeson JG, Rayner JC. Plasmodium vivax vaccine research - we've only just begun. Int J Parasitol 2016; 47:111-118. [PMID: 27899329 DOI: 10.1016/j.ijpara.2016.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/24/2016] [Accepted: 09/29/2016] [Indexed: 10/25/2022]
Abstract
Plasmodium vivax parasites cause the majority of malaria cases outside Africa, and are increasingly being acknowledged as a cause of severe disease. The unique attributes of P. vivax biology, particularly the capacity of the dormant liver stage, the hypnozoite, to maintain blood-stage infections even in the absence of active transmission, make blood-stage vaccines particularly attractive for this species. However, P. vivax vaccine development remains resolutely in first gear, with only a single blood-stage candidate having been evaluated in any depth. Experience with Plasmodium falciparum suggests that a much broader search for new candidates and a deeper understanding of high priority targets will be required to make significant advances. This review discusses some of the particular challenges of P. vivax blood-stage vaccine development, highlighting both recent advances and key remaining barriers to overcome in order to move development forward.
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Affiliation(s)
- Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - James G Beeson
- Macfarlane Burnet Institute of Medical Research, 85 Commercial Road, Melbourne, Victoria 3004, Australia; Central Clinical School and Department of Microbiology, Monash University, Victoria, Australia
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
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129
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Abstract
The two main species causing malaria in humans, Plasmodium falciparum and P. vivax, differ significantly from each other in their evolutionary response to common drugs, but the reasons for this are not clear. Here we utilized the recently available large-scale genome sequencing data from these parasites and compared the pattern of single nucleotide polymorphisms, which may be related to these differences. We found that there was a five-fold higher preference for AT nucleotides compared to GC nucleotides at synonymous single nucleotide polymorphism sites in P. vivax. The preference for AT nucleotides was also present at non-synonymous sites, which lead to amino acid changes favouring those with codons of higher AT content. The substitution bias was also present at low and moderately conserved amino acid positions, but not at highly conserved positions. No marked bias was found at synonymous and non-synonymous sites in P. falciparum. The difference in the substitution bias between P. falciparum and P. vivax found in the present study may possibly contribute to their divergent evolutionary response to similar drug pressures.
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130
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Auburn S, Böhme U, Steinbiss S, Trimarsanto H, Hostetler J, Sanders M, Gao Q, Nosten F, Newbold CI, Berriman M, Price RN, Otto TD. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Res 2016; 1:4. [PMID: 28008421 PMCID: PMC5172418 DOI: 10.12688/wellcomeopenres.9876.1] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous
ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of
P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200
Plasmodium interspersed repeat (
pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ulrike Böhme
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Jessica Hostetler
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Mandy Sanders
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Qi Gao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Jiangsu, China
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Chris I Newbold
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
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131
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Faway E, Musset L, Pelleau S, Volney B, Casteras J, Caro V, Menard D, Briolant S, Legrand E. Plasmodium vivax multidrug resistance-1 gene polymorphism in French Guiana. Malar J 2016; 15:540. [PMID: 27825387 PMCID: PMC5101641 DOI: 10.1186/s12936-016-1595-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/31/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Plasmodium vivax malaria is a major public health problem in French Guiana. Some cases of resistance to chloroquine, the first-line treatment used against P. vivax malaria, have been described in the Brazilian Amazon region. The aim of this study is to investigate a possible dispersion of chloroquine-resistant P. vivax isolates in French Guiana. The genotype, polymorphism and copy number variation, of the P. vivax multidrug resistance gene-1 (pvmdr1) have been previously associated with modification of the susceptibility to chloroquine. METHODS The pvmdr1 gene polymorphism was evaluated by sequencing and copy number variation was assessed by real-time PCR, in P. vivax isolates obtained from 591 symptomatic patients from 1997 to 2013. RESULTS The results reveal that 1.0% [95% CI 0.4-2.2] of French Guiana isolates carry the mutations Y976F and F1076L, and that the proportion of isolates with multiple copies of pvmdr1 has significantly decreased over time, from 71.3% (OR = 6.2 [95% CI 62.9-78.7], p < 0.0001) in 1997-2004 to 12.8% (OR = 0.03 [95% CI 9.4-16.9], p < 0.0001) in 2009-2013. A statistically significant relationship was found between Guf-A (harboring the single mutation T958M) and Sal-1 (wild type) alleles and pvmdr1 copy number. CONCLUSIONS Few P. vivax isolates harboring chloroquine-resistant mutations in the pvmdr1 gene are circulating in French Guiana. However, the decrease in the prevalence of isolates carrying multiple copies of pvmdr1 might indicate that the P. vivax population in French Guiana is evolving towards a decreased susceptibility to chloroquine.
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Affiliation(s)
- Emilie Faway
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,URPhyM-NARILIS, University of Namur, Namur, Belgium
| | - Lise Musset
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,National Reference Center for Malaria, Institut Pasteur de la Guyane, Cayenne, French Guiana.,World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Stéphane Pelleau
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,National Reference Center for Malaria, Institut Pasteur de la Guyane, Cayenne, French Guiana.,World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Béatrice Volney
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,National Reference Center for Malaria, Institut Pasteur de la Guyane, Cayenne, French Guiana.,World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Jessica Casteras
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,National Reference Center for Malaria, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Valérie Caro
- Environment and Infectious Risks unit, Genotyping of Pathogens Pole, Institut Pasteur, Paris, France
| | - Didier Menard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia.,Malaria Translational Research Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Sébastien Briolant
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana.,Direction Interarmées du Service de Santé, Cayenne, French Guiana.,Institut de Recherche Biomédicale des Armées, Brétigny sur Orge, France
| | - Eric Legrand
- Laboratoire de Parasitologie, Institut Pasteur de la Guyane, Cayenne, French Guiana. .,National Reference Center for Malaria, Institut Pasteur de la Guyane, Cayenne, French Guiana. .,World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana. .,Malaria Translational Research Unit, Institut Pasteur, Paris, France. .,Genetics and Genomics of Insect Vectors Unit, Institut Pasteur, Paris, France.
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132
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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133
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Deng S, Ruan Y, Bai Y, Hu Y, Deng Z, He Y, Ruan R, Wu Y, Yang Z, Cui L. Genetic diversity of the Pvk12 gene in Plasmodium vivax from the China-Myanmar border area. Malar J 2016; 15:528. [PMID: 27809837 PMCID: PMC5096284 DOI: 10.1186/s12936-016-1592-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/28/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Plasmodium falciparum resistance to artemisinin emerged in the Greater Mekong Sub-region has been associated with mutations in the propeller domain of the kelch gene Pfk13. METHODS Here the polymorphisms in Pvk12 gene, the orthologue of Pfk13 in Plasmodium vivax, were determined by PCR and sequencing in 262 clinical isolates collected in recent years (2012-2015) from the China-Myanmar border area. RESULTS Sequencing of full-length Pvk12 genes from these isolates identified three synonymous mutations (N172N, S360S, S697S) and one non-synonymous mutation M124I, all of which were at very low prevalence (2.0-3.1%). Moreover, these mutations were non-overlapping between the two study sites on both sides of the border. Molecular evolutionary analysis detected signature of purifying selection on Pvk12. CONCLUSIONS There is no direct evidence that Pvk12 is involved in artemisinin resistance in P. vivax, but it remains a potential candidate requiring further investigation. Continuous monitoring of potential drug resistance in this parasite is needed in order to facilitate the regional malaria elimination campaign.
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Affiliation(s)
- Shuang Deng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500, Yunnan Province, China.,Department of Pathology, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Yonghua Ruan
- Department of Pathology, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Yao Bai
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500, Yunnan Province, China.,Department of Pharmacology, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Yue Hu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500, Yunnan Province, China.,Department of Pathology, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Zeshuai Deng
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Yongshu He
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Rui Ruan
- Department of Orthopedics, The First Affiliated Hospital, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Yanrui Wu
- Department of Cell Biology and Medical Genetics, Kunming Medical University, Kunming, 650500, Yunnan Province, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500, Yunnan Province, China.
| | - Liwang Cui
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500, Yunnan Province, China.
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134
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Rosas-Aguirre A, Gamboa D, Manrique P, Conn JE, Moreno M, Lescano AG, Sanchez JF, Rodriguez H, Silva H, Llanos-Cuentas A, Vinetz JM. Epidemiology of Plasmodium vivax Malaria in Peru. Am J Trop Med Hyg 2016; 95:133-144. [PMID: 27799639 PMCID: PMC5201219 DOI: 10.4269/ajtmh.16-0268] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/29/2016] [Indexed: 01/01/2023] Open
Abstract
Malaria in Peru, dominated by Plasmodium vivax, remains a public health problem. The 1990s saw newly epidemic malaria emerge, primarily in the Loreto Department in the Amazon region, including areas near to Iquitos, the capital city, but sporadic malaria transmission also occurred in the 1990s–2000s in both north-coastal Peru and the gold mining regions of southeastern Peru. Although a Global Fund-supported intervention (PAMAFRO, 2005–2010) was temporally associated with a decrease of malaria transmission, from 2012 to the present, both P. vivax and Plasmodium falciparum malaria cases have rapidly increased. The Peruvian Ministry of Health continues to provide artemesinin-based combination therapy for microscopy-confirmed cases of P. falciparum and chloroquine–primaquine for P. vivax. Malaria transmission continues in remote areas nonetheless, where the mobility of humans and parasites facilitates continued reintroduction outside of ongoing surveillance activities, which is critical to address for future malaria control and elimination efforts. Ongoing P. vivax research gaps in Peru include the following: identification of asymptomatic parasitemics, quantification of the contribution of patent and subpatent parasitemics to mosquito transmission, diagnosis of nonparasitemic hypnozoite carriers, and implementation of surveillance for potential emergence of chloroquine- and 8-aminoquinoline-resistant P. vivax. Clinical trials of tafenoquine in Peru have been promising, and glucose-6-phosphate dehydrogenase deficiency in the region has not been observed to be a limitation to its use. Larger-scale challenges for P. vivax (and malaria in general) in Peru include logistical difficulties in accessing remote riverine populations, consequences of government policy and poverty trends, and obtaining international funding for malaria control and elimination.
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Affiliation(s)
- Angel Rosas-Aguirre
- Research Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium.,Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Paulo Manrique
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jan E Conn
- Wadsworth Center, New York State Department of Health, Albany, New York.,Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, New York
| | - Marta Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, California
| | - Andres G Lescano
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Juan F Sanchez
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Hugo Rodriguez
- Dirección Regional de Salud Loreto, Ministerio de Salud, Iquitos, Peru
| | - Hermann Silva
- Dirección Regional de Salud Loreto, Ministerio de Salud, Iquitos, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.,Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, California
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135
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Hostetler JB, Lo E, Kanjee U, Amaratunga C, Suon S, Sreng S, Mao S, Yewhalaw D, Mascarenhas A, Kwiatkowski DP, Ferreira MU, Rathod PK, Yan G, Fairhurst RM, Duraisingh MT, Rayner JC. Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications. PLoS Negl Trop Dis 2016; 10:e0005091. [PMID: 27798646 PMCID: PMC5087946 DOI: 10.1371/journal.pntd.0005091] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/03/2016] [Indexed: 11/23/2022] Open
Abstract
Background Plasmodium vivax causes the majority of malaria episodes outside Africa, but remains a relatively understudied pathogen. The pathology of P. vivax infection depends critically on the parasite’s ability to recognize and invade human erythrocytes. This invasion process involves an interaction between P. vivax Duffy Binding Protein (PvDBP) in merozoites and the Duffy antigen receptor for chemokines (DARC) on the erythrocyte surface. Whole-genome sequencing of clinical isolates recently established that some P. vivax genomes contain two copies of the PvDBP gene. The frequency of this duplication is particularly high in Madagascar, where there is also evidence for P. vivax infection in DARC-negative individuals. The functional significance and global prevalence of this duplication, and whether there are other copy number variations at the PvDBP locus, is unknown. Methodology/Principal Findings Using whole-genome sequencing and PCR to study the PvDBP locus in P. vivax clinical isolates, we found that PvDBP duplication is widespread in Cambodia. The boundaries of the Cambodian PvDBP duplication differ from those previously identified in Madagascar, meaning that current molecular assays were unable to detect it. The Cambodian PvDBP duplication did not associate with parasite density or DARC genotype, and ranged in prevalence from 20% to 38% over four annual transmission seasons in Cambodia. This duplication was also present in P. vivax isolates from Brazil and Ethiopia, but not India. Conclusions/Significance PvDBP duplications are much more widespread and complex than previously thought, and at least two distinct duplications are circulating globally. The same duplication boundaries were identified in parasites from three continents, and were found at high prevalence in human populations where DARC-negativity is essentially absent. It is therefore unlikely that PvDBP duplication is associated with infection of DARC-negative individuals, but functional tests will be required to confirm this hypothesis. Malaria parasites must be adaptable to evade the human immune system and successfully transmit themselves to different individuals. Key to this adaptability is the fact that malaria parasite genomes are highly variable, containing mutations ranging from simple small changes in DNA sequence to complex large-scale changes in the number of copies of individual genes. Some samples of Plasmodium vivax, the parasite that causes most malaria episodes outside Africa, have recently been found to have duplicated the gene encoding Duffy Binding Protein, which enables P. vivax parasites to recognize and invade human red blood cells. By studying parasites from Cambodian patients with P. vivax malaria, we have discovered that there are actually two different types of gene duplication, with the new duplication type identified in this study present in 20% to 38% of Cambodian P. vivax isolates tested. The same gene duplication was also found in parasites from Brazilian and Ethiopian patients with P. vivax malaria, suggesting that variation in this gene is more complex and common than previously thought. The functional significance and origin of these two gene duplications requires further study.
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Affiliation(s)
- Jessica B. Hostetler
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Eugenia Lo
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Chanaki Amaratunga
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sokunthea Sreng
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sivanna Mao
- Sampov Meas Referral Hospital, Pursat, Cambodia
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Anjali Mascarenhas
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- MESA-ICEMR, Goa Medical College and Hospital, Bambolim, Goa, India
| | | | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- MESA-ICEMR, Goa Medical College and Hospital, Bambolim, Goa, India
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
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Olliaro PL, Barnwell JW, Barry A, Mendis K, Mueller I, Reeder JC, Shanks GD, Snounou G, Wongsrichanalai C. Implications of Plasmodium vivax Biology for Control, Elimination, and Research. Am J Trop Med Hyg 2016; 95:4-14. [PMID: 27799636 PMCID: PMC5201222 DOI: 10.4269/ajtmh.16-0160] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 09/29/2016] [Indexed: 12/03/2022] Open
Abstract
This paper summarizes our current understanding of the biology of Plasmodium vivax, how it differs from Plasmodium falciparum, and how these differences explain the need for P. vivax-tailored interventions. The article further pinpoints knowledge gaps where investments in research are needed to help identify and develop such specific interventions. The principal obstacles to reduce and eventually eliminate P. vivax reside in 1) its higher vectorial capacity compared with P. falciparum due to its ability to develop at lower temperature and over a shorter sporogonic cycle in the vector, allowing transmission in temperate zones and making it less sensitive to vector control measures that are otherwise effective on P. falciparum; 2) the presence of dormant liver forms (hypnozoites), sustaining multiple relapsing episodes from a single infectious bite that cannot be diagnosed and are not susceptible to any available antimalarial except primaquine, with routine deployment restricted by toxicity; 3) low parasite densities, which are difficult to detect with current diagnostics leading to missed diagnoses and delayed treatments (and protracted transmission), coupled with 4) transmission stages (gametocytes) occurring early in acute infections, before infection is diagnosed.
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Affiliation(s)
- Piero L Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - John W Barnwell
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alyssa Barry
- Department of Medical Biology, University of Melbourne, Melbourne, Australia.,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Ivo Mueller
- Institute of Global Health (ISGLOBAL), Barcelona, Spain.,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - John C Reeder
- UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - G Dennis Shanks
- School of Population Health, University of Queensland, Brisbane, Australia
| | - Georges Snounou
- Centre d'Immunologie et de Maladies Infectieuses (CIMI)-Paris, Institut National de la Santé et de la Recherche Médicale (INSERM) U1135-Centre National de la Recherche Scientifique (CNRS) ERL 8255, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UPMC UMRS CR7, Paris, France
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137
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Auburn S, Serre D, Pearson RD, Amato R, Sriprawat K, To S, Handayuni I, Suwanarusk R, Russell B, Drury E, Stalker J, Miotto O, Kwiatkowski DP, Nosten F, Price RN. Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand. J Infect Dis 2016; 214:1235-42. [PMID: 27456706 PMCID: PMC5034950 DOI: 10.1093/infdis/jiw323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/20/2016] [Indexed: 01/13/2023] Open
Abstract
In regions of coendemicity for Plasmodium falciparum and Plasmodium vivax where mefloquine is used to treat P. falciparum infection, drug pressure mediated by increased copy numbers of the multidrug resistance 1 gene (pvmdr1) may select for mefloquine-resistant P. vivax Surveillance is not undertaken routinely owing in part to methodological challenges in detection of gene amplification. Using genomic data on 88 P. vivax samples from western Thailand, we identified pvmdr1 amplification in 17 isolates, all exhibiting tandem copies of a 37.6-kilobase pair region with identical breakpoints. A novel breakpoint-specific polymerase chain reaction assay was designed to detect the amplification. The assay demonstrated high sensitivity, identifying amplifications in 13 additional, polyclonal infections. Application to 132 further samples identified the common breakpoint in all years tested (2003-2015), with a decline in prevalence after 2012 corresponding to local discontinuation of mefloquine regimens. Assessment of the structure of pvmdr1 amplification in other geographic regions will yield information about the population-specificity of the breakpoints and underlying amplification mechanisms.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research institute, Ohio
| | - Richard D. Pearson
- Wellcome Trust Sanger Institute, Hinxton,Wellcome Trust Centre for Human Genetics
| | - Roberto Amato
- Wellcome Trust Sanger Institute, Hinxton,Wellcome Trust Centre for Human Genetics
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Tak
| | - Sheren To
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia
| | - Irene Handayuni
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia
| | - Rossarin Suwanarusk
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | | | - Olivo Miotto
- Wellcome Trust Sanger Institute, Hinxton,Medical Research Council Centre for Genomics and Global Health,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Dominic P. Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton,Wellcome Trust Centre for Human Genetics,Medical Research Council Centre for Genomics and Global Health
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, United Kingdom,Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Tak
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, United Kingdom
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138
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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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139
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O'Brien JD, Amenga-Etego L, Li R. Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data. Malar J 2016; 15:473. [PMID: 27634595 PMCID: PMC5025560 DOI: 10.1186/s12936-016-1531-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/09/2016] [Indexed: 08/30/2023] Open
Abstract
Background The advent of whole-genome sequencing has generated increased interest in modelling the structure of strain mixture within clinical infections of Plasmodium falciparum The life cycle of the parasite implies that the mixture of multiple strains within an infected individual is related to the out-crossing rate across populations, making methods for measuring this process in situ central to understanding the genetic epidemiology of the disease. Results This paper derives a set of new estimators for inferring inbreeding coefficients using whole genome sequence read count data from P. falciparum clinical samples, which provides resources to assess within-sample mixture that connect to extensive literatures in population genetics and conservation ecology. Features of the P. falciparum genome mean that standard methods for inbreeding coefficients and related F-statistics cannot be used directly. After reviewing an initial effort to estimate the inbreeding coefficient within clinical isolates of P. falciparum, several generalizations using both frequentist and Bayesian approaches are provided. A simpler, more intuitive frequentist estimator is shown to have nearly identical properties to the initial estimator both in simulation and in real data sets. The Bayesian approach connects these estimates to the Balding–Nichols model, a mainstay within genetic epidemiology, and a possible framework for more complex modelling. A simulation study shows strong performance for all estimators with as few as ten variants. Application to samples from the PF3K data set indicate significant across-country variation in within-sample mixture. Finally, a comparison with results from a recent mixture model for within-sample strain mixture show that inbreeding coefficients provide a strong proxy for these more complex models. Conclusions This paper provides a set of methods for estimating inbreeding coefficients within P. falciparum samples from whole-genome sequence data, supported by simulation studies and empirical examples. It includes a substantially simple estimator with similar statistical properties to the estimator in current use. These methods will also be applicable to other species with similar life-cycles. Implementations of the methods described are available in an open-source R package pfmix. Estimates for the PF3K public data release are provide as part of this resource.
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Affiliation(s)
- John D O'Brien
- Department of Mathematics, Bowdoin College, 8600 College Station, Brunswick, ME, USA.
| | - Lucas Amenga-Etego
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.,Navrongo Health Research Centre, Upper East Region, Navrongo, Ghana
| | - Ruiqi Li
- Department of Mathematics, Bowdoin College, 8600 College Station, Brunswick, ME, USA
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140
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Abstract
Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.
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Affiliation(s)
- Sebastian Kirchner
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - B Joanne Power
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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141
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Kissinger JC. An unsettling picture emerges from population genomic studies of Plasmodium vivax. Nat Genet 2016; 48:825-6. [PMID: 27463397 DOI: 10.1038/ng.3630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Two new studies confirm that Plasmodium vivax populations are more diverse than Plasmodium falciparum and identify signs of recent selection at many loci, including those for drug resistance. P. vivax shows a trend of regional adaptations that poses challenges to global efforts to control and eliminate this major cause of relapsing malaria.
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Affiliation(s)
- Jessica C Kissinger
- Center for Tropical and Emerging Global Diseases, Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
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142
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Gunalan K, Lo E, Hostetler JB, Yewhalaw D, Mu J, Neafsey DE, Yan G, Miller LH. Role of Plasmodium vivax Duffy-binding protein 1 in invasion of Duffy-null Africans. Proc Natl Acad Sci U S A 2016; 113:6271-6. [PMID: 27190089 PMCID: PMC4896682 DOI: 10.1073/pnas.1606113113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of the malaria parasite Plasmodium vivax to invade erythrocytes is dependent on the expression of the Duffy blood group antigen on erythrocytes. Consequently, Africans who are null for the Duffy antigen are not susceptible to P. vivax infections. Recently, P. vivax infections in Duffy-null Africans have been documented, raising the possibility that P. vivax, a virulent pathogen in other parts of the world, may expand malarial disease in Africa. P. vivax binds the Duffy blood group antigen through its Duffy-binding protein 1 (DBP1). To determine if mutations in DBP1 resulted in the ability of P. vivax to bind Duffy-null erythrocytes, we analyzed P. vivax parasites obtained from two Duffy-null individuals living in Ethiopia where Duffy-null and -positive Africans live side-by-side. We determined that, although the DBP1s from these parasites contained unique sequences, they failed to bind Duffy-null erythrocytes, indicating that mutations in DBP1 did not account for the ability of P. vivax to infect Duffy-null Africans. However, an unusual DNA expansion of DBP1 (three and eight copies) in the two Duffy-null P. vivax infections suggests that an expansion of DBP1 may have been selected to allow low-affinity binding to another receptor on Duffy-null erythrocytes. Indeed, we show that Salvador (Sal) I P. vivax infects Squirrel monkeys independently of DBP1 binding to Squirrel monkey erythrocytes. We conclude that P. vivax Sal I and perhaps P. vivax in Duffy-null patients may have adapted to use new ligand-receptor pairs for invasion.
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Affiliation(s)
- Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Eugenia Lo
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA 92697
| | - Jessica B Hostetler
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; Malaria Programme, Wellcome Trust, Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1RQ, United Kingdom
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, Jimma 5195, Ethiopia; Tropical and Infectious Diseases Research Center, Jimma University, Jimma 5195, Ethiopia
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | | | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA 92697
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;
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