101
|
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.
Collapse
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
| |
Collapse
|
102
|
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.
Collapse
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.
| |
Collapse
|
103
|
Baquero LA, Moreno-Pérez DA, Garzón-Ospina D, Forero-Rodríguez J, Ortiz-Suárez HD, Patarroyo MA. PvGAMA reticulocyte binding activity: predicting conserved functional regions by natural selection analysis. Parasit Vectors 2017; 10:251. [PMID: 28526096 PMCID: PMC5438544 DOI: 10.1186/s13071-017-2183-8] [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: 10/27/2016] [Accepted: 05/10/2017] [Indexed: 12/11/2022] Open
Abstract
Background Adhesin proteins are used by Plasmodium parasites to bind and invade target cells. Hence, characterising molecules that participate in reticulocyte interaction is key to understanding the molecular basis of Plasmodium vivax invasion. This study focused on predicting functionally restricted regions of the P. vivax GPI-anchored micronemal antigen (PvGAMA) and characterising their reticulocyte binding activity. Results The pvgama gene was initially found in P. vivax VCG-I strain schizonts. According to the genetic diversity analysis, PvGAMA displayed a size polymorphism very common for antigenic P. vivax proteins. Two regions along the antigen sequence were highly conserved among species, having a negative natural selection signal. Interestingly, these regions revealed a functional role regarding preferential target cell adhesion. Conclusions To our knowledge, this study describes PvGAMA reticulocyte binding properties for the first time. Conserved functional regions were predicted according to natural selection analysis and their binding ability was confirmed. These findings support the notion that PvGAMA may have an important role in P. vivax merozoite adhesion to its target cells. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2183-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luis A Baquero
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia
| | - Darwin A Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá DC, Colombia
| | - Diego Garzón-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá DC, Colombia
| | - Johanna Forero-Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia
| | - Heidy D Ortiz-Suárez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá DC, Colombia. .,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá DC, Colombia.
| |
Collapse
|
104
|
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.
Collapse
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
| |
Collapse
|
105
|
Flores-Alanis A, González-Cerón L, Santillán F, Ximenez C, Sandoval MA, Cerritos R. Temporal genetic changes in Plasmodium vivax apical membrane antigen 1 over 19 years of transmission in southern Mexico. Parasit Vectors 2017; 10:217. [PMID: 28464959 PMCID: PMC5414334 DOI: 10.1186/s13071-017-2156-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/25/2017] [Indexed: 01/21/2023] Open
Abstract
Background Mexico advanced to the pre-elimination phase in 2009 due to a significant reduction in malaria cases, and since 2000, Plasmodium vivax is the only species transmitted. During the last two decades, malaria transmission has been mostly local and isolated to a few regions. It is important to gain further insights into the impact of control measures on the parasite population structure. Hence, the aim of the current study was to determine detailed changes in P. vivax genetic diversity and population structure based on analysing the gene that encodes the apical membrane antigen 1 (pvama1). This analysis covered from control to pre-elimination (1993–2011) in a hypo-endemic region in southern Mexico. Results The 213 pvama1I-II sequences presently analysed were grouped into six periods of three years each. They showed low genetic diversity, with 15 haplotypes resolved. Among the DNA sequences, there was a gradual decrease in genetic diversity, the number of mixed genotype infections and the intensity of positive selection, in agreement with the parallel decline in malaria cases. At the same time, linkage disequilibrium (R2) increased. The three-dimensional haplotype network revealed that pvama1I-II haplotypes were separated by 1–11 mutational steps, and between one another by 0–3 unsampled haplotypes. In the temporal network, seven haplotypes were detected in at least two of the six-time layers, and only four distinct haplotypes were evidenced in the pre-elimination phase. Structure analysis indicated that three subpopulations fluctuated over time. Only 8.5% of the samples had mixed ancestry. In the pre-elimination phase, subpopulation P1 was drastically reduced, and the admixture was absent. Conclusions The results suggest that P. vivax in southern Mexico evolved based on local adaptation into three “pseudoclonal” subpopulations that diversified at the regional level and persisted over time, although with varying frequency. Control measures and climate events influenced the number of malaria cases and the genetic structure. The sharp decrease in parasite diversity and other related genetic parameters during the pre-elimination phase suggests that malaria elimination is possible in the near future. These results are useful for epidemiological surveillance. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2156-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alejandro Flores-Alanis
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico.
| | - Frida Santillán
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico
| | - Cecilia Ximenez
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 06729, Mexico
| | - Marco A Sandoval
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico
| | - René Cerritos
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| |
Collapse
|
106
|
Fola AA, Harrison GLA, Hazairin MH, Barnadas C, Hetzel MW, Iga J, Siba PM, Mueller I, Barry AE. Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea. Am J Trop Med Hyg 2017; 96:630-641. [PMID: 28070005 DOI: 10.4269/ajtmh.16-0716] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Plasmodium falciparum and Plasmodium vivax have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of P. vivax and P. falciparum throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive P. vivax samples were genotyped at PvMS16 and PvmspF3, and 758 positive P. falciparum samples were genotyped at Pfmsp2. The data were analyzed for multiplicity of infection (MOI) and genetic diversity. Overall, P. vivax had higher polyclonality (71%) and mean MOI (2.32) than P. falciparum (20%, 1.39). These measures were significantly associated with prevalence for P. falciparum but not for P. vivax. The genetic diversity of P. vivax (PvMS16: expected heterozygosity = 0.95, 0.85-0.98; PvMsp1F3: 0.78, 0.66-0.89) was higher and less variable than that of P. falciparum (Pfmsp2: 0.89, 0.65-0.97). Significant associations of MOI with allelic richness (rho = 0.69, P = 0.009) and expected heterozygosity (rho = 0.87, P < 0.001) were observed for P. falciparum. Conversely, genetic diversity was not correlated with polyclonality nor mean MOI for P. vivax. The results demonstrate higher complexity of infection and genetic diversity of P. vivax across the country. Although P. falciparum shows a strong association of these parameters with prevalence, a lack of association was observed for P. vivax and is consistent with higher potential for outcrossing of this species.
Collapse
Affiliation(s)
- Abebe A Fola
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - G L Abby Harrison
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mita Hapsari Hazairin
- Department of Epidemiology and Preventative Medicine, Monash University, Clayton, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Céline Barnadas
- Statens Serum Institut, Copenhagen, Denmark.,European Public Health Microbiology (EUPHEM) Training Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Manuel W Hetzel
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Jonah Iga
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ivo Mueller
- Institut Pasteur, Paris, France.,Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Alyssa E Barry
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| |
Collapse
|
107
|
Chitsanoor S, Somsri S, Panburana P, Mungthin M, Ubalee R, Emyeam M, Jongwutiwes S, Sattabongkot J, Udomsangpetch R. A novel in vitro model reveals distinctive modulatory roles of Plasmodium falciparum and Plasmodium vivax on naïve cell-mediated immunity. Malar J 2017; 16:131. [PMID: 28347310 PMCID: PMC5368906 DOI: 10.1186/s12936-017-1781-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/17/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To date, human peripheral blood mononuclear cells (PBMCs) have been used mainly in immune stimulation assays and the interpretation of data can be influenced by the previous immunological history of donors and cross reactivity with other infectious agents. Resolving these limitations requires an alternative in vitro model to uncover the primary response profiles. METHODS A novel in vitro model of mononuclear cells (MNCs) generated from haematopoietic stem cells (HSCs) was developed and these cells were then co-cultured with various antigens from Plasmodium falciparum and Plasmodium vivax to investigate the response of naïve immune cells to malaria antigens by flow cytometry. RESULTS In vitro stimulation of naïve lymphocytes showed that CD4+ and CD8+ T lymphocytes were significantly reduced (P < 0.01) by exposure to lysates of infected erythrocytes or intact erythrocytes infected with P. falciparum. The depletion was associated with the expression of CD95 (Fas receptor) on the surface of T lymphocytes. Maturation of T lymphocytes was affected differently, showing elevated CD3+CD4+CD8+ and CD3+CD4-CD8- T lymphocytes after stimulation with cell lysates of P. falciparum and P. vivax, respectively. In addition, antigen presenting monocytes and dendritic cells derived from haematopoietic stem cells showed impaired HLA-DR expression as a consequence of exposure to different species of malaria parasites. CONCLUSION These results suggest that naïve mononuclear cells differentiated in vitro from HSCs could provide a valid model for the assessment of immunity. P. falciparum and P. vivax malaria parasites could modulate various populations of immune cells starting from newly differentiated mononuclear cells.
Collapse
Affiliation(s)
- Setthakit Chitsanoor
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sangdao Somsri
- Graduate Programme in Biomedical Science, Faculty of Allied Health Sciences, Thammasart University, Pathumthani, Thailand
| | - Panyu Panburana
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400 Thailand
| | - Ratawan Ubalee
- Department of Entomology, USAMC Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maliwan Emyeam
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rachanee Udomsangpetch
- Centers for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand
- Centers for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| |
Collapse
|
108
|
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.
Collapse
|
109
|
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.
Collapse
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.
| |
Collapse
|
110
|
Signatures of malaria-associated pathology revealed by high-resolution whole-blood transcriptomics in a rodent model of malaria. Sci Rep 2017; 7:41722. [PMID: 28155887 PMCID: PMC5290525 DOI: 10.1038/srep41722] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/28/2016] [Indexed: 11/09/2022] Open
Abstract
The influence of parasite genetic factors on immune responses and development of severe pathology of malaria is largely unknown. In this study, we performed genome-wide transcriptomic profiling of mouse whole blood during blood-stage infections of two strains of the rodent malaria parasite Plasmodium chabaudi that differ in virulence. We identified several transcriptomic signatures associated with the virulent infection, including signatures for platelet aggregation, stronger and prolonged anemia and lung inflammation. The first two signatures were detected prior to pathology. The anemia signature indicated deregulation of host erythropoiesis, and the lung inflammation signature was linked to increased neutrophil infiltration, more cell death and greater parasite sequestration in the lungs. This comparative whole-blood transcriptomics profiling of virulent and avirulent malaria shows the validity of this approach to inform severity of the infection and provide insight into pathogenic mechanisms.
Collapse
|
111
|
Castillo AI, Andreína Pacheco M, Escalante AA. Evolution of the merozoite surface protein 7 (msp7) family in Plasmodium vivax and P. falciparum: A comparative approach. INFECTION GENETICS AND EVOLUTION 2017; 50:7-19. [PMID: 28163236 DOI: 10.1016/j.meegid.2017.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 01/17/2023]
Abstract
Malaria parasites (genus Plasmodium) are a diverse group found in many species of vertebrate hosts. These parasites invade red blood cells in a complex process comprising several proteins, many encoded by multigene families, one of which is merozoite surface protein 7 (msp7). In the case of Plasmodium vivax, the most geographically widespread human-infecting species, differences in the number of paralogs within multigene families have been previously explained, at least in part, as potential adaptations to the human host. To explore this in msp7, we studied its orthologs in closely related nonhuman primate parasites; investigating both paralog evolutionary history and genetic polymorphism. The emerging patterns were then compared with the human parasite Plasmodium falciparum. We found that the evolution of the msp7 family is consistent with a birth-and-death model, where duplications, pseudogenizations, and gene loss events are common. However, all paralogs in P. vivax and P. falciparum had orthologs in their closely related species in non-human primates indicating that the ancestors of those paralogs precede the events leading to their origins as human parasites. Thus, the number of paralogs cannot be explained as an adaptation to human hosts. Although there is no functional information for msp7 in P. vivax, we found evidence for purifying selection in the genetic polymorphism of some of its paralogs as well as their orthologs in closely related non-human primate parasites. We also found evidence indicating that a few of P. vivax's paralogs may have diverged from their orthologs in non-human primates by episodic positive selection. Hence, they may had been under selection when the lineage leading to P. vivax diverged from the Asian non-human primates and switched into Homininae. All these lines of evidence suggest that msp7 is functionally important in P. vivax.
Collapse
Affiliation(s)
| | - M Andreína Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA, USA
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA, USA.
| |
Collapse
|
112
|
Boopathi PA, Subudhi AK, Middha S, Acharya J, Mugasimangalam RC, Kochar SK, Kochar DK, Das A. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates. Acta Trop 2016; 164:438-447. [PMID: 27720625 DOI: 10.1016/j.actatropica.2016.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/05/2016] [Accepted: 10/03/2016] [Indexed: 02/04/2023]
Abstract
High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n=14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n=85) present in the arrays showed perfect correlation (r2=0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r≥0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates.
Collapse
|
113
|
Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia. Proc Natl Acad Sci U S A 2016; 113:E8096-E8105. [PMID: 27911780 DOI: 10.1073/pnas.1608828113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cambodia, in which both Plasmodium vivax and Plasmodium falciparum are endemic, has been the focus of numerous malaria-control interventions, resulting in a marked decline in overall malaria incidence. Despite this decline, the number of P vivax cases has actually increased. To understand better the factors underlying this resilience, we compared the genetic responses of the two species to recent selective pressures. We sequenced and studied the genomes of 70 P vivax and 80 P falciparum isolates collected between 2009 and 2013. We found that although P falciparum has undergone population fracturing, the coendemic P vivax population has grown undisrupted, resulting in a larger effective population size, no discernable population structure, and frequent multiclonal infections. Signatures of selection suggest recent, species-specific evolutionary differences. Particularly, in contrast to P falciparum, P vivax transcription factors, chromatin modifiers, and histone deacetylases have undergone strong directional selection, including a particularly strong selective sweep at an AP2 transcription factor. Together, our findings point to different population-level adaptive mechanisms used by P vivax and P falciparum parasites. Although population substructuring in P falciparum has resulted in clonal outgrowths of resistant parasites, P vivax may use a nuanced transcriptional regulatory approach to population maintenance, enabling it to preserve a larger, more diverse population better suited to facing selective threats. We conclude that transcriptional control may underlie P vivax's resilience to malaria control measures. Novel strategies to target such processes are likely required to eradicate P vivax and achieve malaria elimination.
Collapse
|
114
|
Garzón-Ospina D, Forero-Rodríguez J, Patarroyo MA. Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis. BMC Evol Biol 2016; 16:256. [PMID: 27894257 PMCID: PMC5126858 DOI: 10.1186/s12862-016-0830-x] [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: 09/15/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The merozoite surface protein 7 (MSP7) is a Plasmodium protein which is involved in parasite invasion; the gene encoding it belongs to a multigene family. It has been proposed that MSP7 paralogues seem to be functionally redundant; however, recent experiments have suggested that they could have different roles. Results The msp7 multigene family has been described in newly available Plasmodium genomes; phylogenetic relationships were established in 12 species by using different molecular evolutionary approaches for assessing functional divergence amongst MSP7 members. Gene expansion and contraction rule msp7 family evolution; however, some members could have had concerted evolution. Molecular evolutionary analysis showed that relaxed and/or intensified selection modulated Plasmodium msp7 paralogous evolution. Furthermore, episodic diversifying selection and changes in evolutionary rates suggested that some paralogous proteins have diverged functionally. Conclusions Even though msp7 has mainly evolved in line with a birth-and-death evolutionary model, gene conversion has taken place between some paralogous genes allowing them to maintain their functional redundancy. On the other hand, the evolutionary rate of some MSP7 paralogs has become altered, as well as undergoing relaxed or intensified (positive) selection, suggesting functional divergence. This could mean that some MSP7s can form different parasite protein complexes and/or recognise different host receptors during parasite invasion. These results highlight the importance of this gene family in the Plasmodium genus. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0830-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Diego Garzón-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, DC, Colombia
| | - Johanna Forero-Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia. .,School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, DC, Colombia.
| |
Collapse
|
115
|
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.
Collapse
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.
| |
Collapse
|
116
|
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.
Collapse
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
| |
Collapse
|
117
|
Abstract
Parasites of the genus Plasmodium have a complex life cycle. They alternate between their final mosquito host and their intermediate hosts. The parasite can be either extra- or intracellular, depending on the stage of development. By modifying their shape, motility, and metabolic requirements, the parasite adapts to the different environments in their different hosts. The parasite has evolved to escape the multiple immune mechanisms in the host that try to block parasite development at the different stages of their development. In this article, we describe the mechanisms reported thus far that allow the Plasmodium parasite to evade innate and adaptive immune responses.
Collapse
Affiliation(s)
- Laurent Rénia
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yun Shan Goh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| |
Collapse
|
118
|
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.
Collapse
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.
| |
Collapse
|
119
|
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.
Collapse
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:
| |
Collapse
|
120
|
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.
Collapse
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
| | | |
Collapse
|
121
|
Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Sci Rep 2016; 6:35284. [PMID: 27752055 PMCID: PMC5082761 DOI: 10.1038/srep35284] [Citation(s) in RCA: 62] [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: 07/06/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.
Collapse
Affiliation(s)
- Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle, IBC, Université de Montpellier, 860 rue St Priest, Bat 5 - CC05019, 34095 Montpellier, Cedex 5, France
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Carrie McCracken
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Sahar Usmani-Brown
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Ankit Dwivedi
- Institut de Biologie Computationnelle, IBC, Université de Montpellier, 860 rue St Priest, Bat 5 - CC05019, 34095 Montpellier, Cedex 5, France
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Olukemi O. Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Hanzel T. Gotia
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Azan Z. Virji
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | - Christelle Reynes
- Institut de Genomique Fonctionnelle, IGF - CNRS UMR 5203, 141 rue de la cardonille, 34094 Montpellier, Cedex 05, France
| | - Jacques Colinge
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U896 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d’Aurelle, 34298 Montpellier, Cedex 5 France
| | - Vidya Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | - Lauren Lawres
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| | | | | | - Chris Hung
- Antigen Discovery Inc., Irvine, CA, 92618 USA
| | - Jana Brancato
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Marcus Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Sandy Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Qi Su
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD 21201 USA
| | - Roger Frutos
- Université de Montpellier, IES, UMR 5214, 860 rue de St Priest, Bt5, 34095 Montpellier, France
- CIRAD, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier, France
| | | | - Peter J. Krause
- Yale School of Public Health and Yale School of Medicine, 60 College St., New Haven, Connecticut, CT 06520 USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, 15 York St., New Haven, Connecticut, CT 06520 USA
| |
Collapse
|
122
|
Requena P, Rui E, Padilla N, Martínez-Espinosa FE, Castellanos ME, Bôtto-Menezes C, Malheiro A, Arévalo-Herrera M, Kochar S, Kochar SK, Kochar DK, Umbers AJ, Ome-Kaius M, Wangnapi R, Hans D, Menegon M, Mateo F, Sanz S, Desai M, Mayor A, Chitnis CC, Bardají A, Mueller I, Rogerson S, Severini C, Fernández-Becerra C, Menéndez C, del Portillo H, Dobaño C. Plasmodium vivax VIR Proteins Are Targets of Naturally-Acquired Antibody and T Cell Immune Responses to Malaria in Pregnant Women. PLoS Negl Trop Dis 2016; 10:e0005009. [PMID: 27711158 PMCID: PMC5053494 DOI: 10.1371/journal.pntd.0005009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022] Open
Abstract
P. vivax infection during pregnancy has been associated with poor outcomes such as anemia, low birth weight and congenital malaria, thus representing an important global health problem. However, no vaccine is currently available for its prevention. Vir genes were the first putative virulent factors associated with P. vivax infections, yet very few studies have examined their potential role as targets of immunity. We investigated the immunogenic properties of five VIR proteins and two long synthetic peptides containing conserved VIR sequences (PvLP1 and PvLP2) in the context of the PregVax cohort study including women from five malaria endemic countries: Brazil, Colombia, Guatemala, India and Papua New Guinea (PNG) at different timepoints during and after pregnancy. Antibody responses against all antigens were detected in all populations, with PNG women presenting the highest levels overall. P. vivax infection at sample collection time was positively associated with antibody levels against PvLP1 (fold-increase: 1.60 at recruitment -first antenatal visit-) and PvLP2 (fold-increase: 1.63 at delivery), and P. falciparum co-infection was found to increase those responses (for PvLP1 at recruitment, fold-increase: 2.25). Levels of IgG against two VIR proteins at delivery were associated with higher birth weight (27 g increase per duplicating antibody levels, p<0.05). Peripheral blood mononuclear cells from PNG uninfected pregnant women had significantly higher antigen-specific IFN-γ TH1 responses (p=0.006) and secreted less pro-inflammatory cytokines TNF and IL-6 after PvLP2 stimulation than P. vivax-infected women (p<0.05). These data demonstrate that VIR antigens induce the natural acquisition of antibody and T cell memory responses that might be important in immunity to P. vivax during pregnancy in very diverse geographical settings. Naturally-acquired antibody responses to novel recombinant proteins and synthetic peptides based on sequences from P. vivax VIR antigens were evaluated in women from five distinct geographical regions endemic for malaria, during and after pregnancy. Levels of IgG to VIR antigens were indicative of cumulative malaria exposure and increased with current P. vivax infection and P. falciparum co-infection. Antibody data were consistent with levels of malaria endemicity and current prevalence in the diverse geographical areas studied. In addition, the magnitude of IgG response to two VIR antigens at delivery was associated with higher birth weight. Furthermore, T cell responses to VIR antigens were naturally induced and their magnitude varied according to P. vivax infectious status. Peripheral blood mononuclear cells from uninfected pregnant women from a highly endemic area produced higher TH1 (IFN-γ) and lower pro-inflammatory cytokines (TNF and IL-6) upon stimulation with a long synthetic peptide representing conserved globular domains of VIR antigens than P. vivax-infected women. Data suggest that further investigation on these antigens as potential targets of immunity in naturally-exposed individuals is warranted.
Collapse
Affiliation(s)
- Pilar Requena
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edmilson Rui
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Norma Padilla
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Flor E. Martínez-Espinosa
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Instituto Leônidas e Maria Deane (ILMD/Fiocruz Amazonia), Brazil
| | | | - Camila Bôtto-Menezes
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Adriana Malheiro
- Instituto de Ciências Biológicas. Universidade Federal do Amazonas, Manaus, Brazil
| | | | - Swati Kochar
- Department of Medicine, Medical College, Bikaner, Rajasthan, India
| | - Sanjay K. Kochar
- Department of Medicine, Medical College, Bikaner, Rajasthan, India
| | | | | | - Maria Ome-Kaius
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Regina Wangnapi
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Dhiraj Hans
- International Center for Genetic Engineering and Biotechnology, Delhi, India
| | - Michela Menegon
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Mateo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Sergi Sanz
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Meghna Desai
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Malaria Branch, Atlanta, Georgia, United States of America
| | - Alfredo Mayor
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Chetan C. Chitnis
- International Center for Genetic Engineering and Biotechnology, Delhi, India
| | - Azucena Bardají
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Walter and Eliza Hall Institute, Parkville, Australia
| | - Stephen Rogerson
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Carlo Severini
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Carmen Fernández-Becerra
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Menéndez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Hernando del Portillo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail: (HdP); (CD)
| | - Carlota Dobaño
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- * E-mail: (HdP); (CD)
| |
Collapse
|
123
|
Alnasser Y, Ferradas C, Clark T, Calderon M, Gurbillon A, Gamboa D, McKakpo US, Quakyi IA, Bosompem KM, Sullivan DJ, Vinetz JM, Gilman RH. Colorimetric Detection of Plasmodium vivax in Urine Using MSP10 Oligonucleotides and Gold Nanoparticles. PLoS Negl Trop Dis 2016; 10:e0005029. [PMID: 27706158 PMCID: PMC5051960 DOI: 10.1371/journal.pntd.0005029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 09/09/2016] [Indexed: 11/19/2022] Open
Abstract
Plasmodium vivax is the most prevalent cause of human malaria in the world and can lead to severe disease with high potential for relapse. Its genetic and geographic diversities make it challenging to control. P. vivax is understudied and to achieve control of malaria in endemic areas, a rapid, accurate, and simple diagnostic tool is necessary. In this pilot study, we found that a colorimetric system using AuNPs and MSP10 DNA detection in urine can provide fast, easy, and inexpensive identification of P. vivax. The test exhibited promising sensitivity (84%), high specificity (97%), and only mild cross-reactivity with P. falciparum (21%). It is simple to use, with a visible color change that negates the need for a spectrometer, making it suitable for use in austere conditions. Using urine eliminates the need for finger-prick, increasing both the safety profile and patient acceptance of this model.
Collapse
Affiliation(s)
- Yossef Alnasser
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Universidad Peruana Cayetano Heredia, Lima, Peru
- King Saud University, Riyadh, Saudi Arabia
| | | | - Taryn Clark
- Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Emergency Medicine, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | | | | | | | - Uri S. McKakpo
- School of Public Health and Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Isabella A. Quakyi
- School of Public Health and Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Kwabena M. Bosompem
- School of Public Health and Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - David J. Sullivan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Joseph M. Vinetz
- Universidad Peruana Cayetano Heredia, Lima, Peru
- University of California San Diego, San Diego, California, United States of America
| | - Robert H. Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Universidad Peruana Cayetano Heredia, Lima, Peru
| |
Collapse
|
124
|
Verma A, Joshi H, Singh V, Anvikar A, Valecha N. Plasmodium vivax msp-3α polymorphisms: analysis in the Indian subcontinent. Malar J 2016; 15:492. [PMID: 27663527 PMCID: PMC5035448 DOI: 10.1186/s12936-016-1524-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/06/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plasmodium vivax is the most widely distributed human malaria parasite and accounts for approximately the same number of malaria cases as Plasmodium falciparum in India. Compared with P. falciparum, P. vivax is difficult to eradicate because of its tendency to cause relapses, which impacts treatment and control strategies. The genetic diversity of these parasites, particularly of the merozoite surface protein-3 alpha (msp-3α) gene, can be used to help develop a potential vaccine. The present study aimed to investigate the genetic diversity of P. vivax using the highly polymorphic antigen gene msp-3α and to assess the suitability of using this gene for population genetic studies of P. vivax isolates and was carried out in 2004-06. No recent study has been reported for MSP 3α in the recent decade in India. Limited reports are available on the genetic diversity of the P. vivax population in India; hence, this report aimed to improve the understanding of the molecular epidemiology of the parasite by studying the P. vivax msp-3α (Pvmsp-3α) marker from P. vivax field isolates from India. METHODS Field isolates were collected from different sites distributed across eight states in India. A total of 182 blood samples were analysed by a nested polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique using the HhaI and AluI restriction enzymes to determine genetic msp-3α variation among clinical P. vivax isolates. RESULTS Based on the length variants of the PCR products of Pvmsp-3α gene, three allele sizes, Type A (1.8 kb), Type B (1.5 kb) and Type C (1.2 kb) were detected among the 182 samples. Type A PCR amplicon was more predominant (75.4 %) in the samples compared with the Type B (14.3 %) and Type C (10.0 %) polymorphisms. Among all of the samples analysed, 8.2 % were mixed infections detected by PCR alone. Restriction fragment length polymorphism (RFLP) analysis involving the restriction enzymes AluI and HhaI generated fragment sizes that were highly polymorphic and revealed substantial diversity at the nucleotide level. CONCLUSIONS The present study is the first extensive study in India using the Pvmsp-3α marker. The results indicated that Pvmps-3α, a polymorphic genetic marker of P. vivax, exhibited considerable variability in infection prevalence in field isolates from India. Additionally, the mean multiplicity of infection observed at all of the study sites indicated that P. vivax is highly diverse in nature in India, and Pvmsp-3α is likely an effective and promising epidemiological marker.
Collapse
Affiliation(s)
- Anju Verma
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA.
| | - Hema Joshi
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Vineeta Singh
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Anup Anvikar
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Neena Valecha
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| |
Collapse
|
125
|
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.
Collapse
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.
| |
Collapse
|
126
|
Jackson AP. Gene family phylogeny and the evolution of parasite cell surfaces. Mol Biochem Parasitol 2016; 209:64-75. [DOI: 10.1016/j.molbiopara.2016.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 11/30/2022]
|
127
|
A Novel Erythrocyte Binding Protein of Plasmodium vivax Suggests an Alternate Invasion Pathway into Duffy-Positive Reticulocytes. mBio 2016; 7:mBio.01261-16. [PMID: 27555313 PMCID: PMC4999553 DOI: 10.1128/mbio.01261-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Erythrocyte invasion by malaria parasites is essential for blood-stage development and an important determinant of host range. In Plasmodium vivax, the interaction between the Duffy binding protein (DBP) and its cognate receptor, the Duffy antigen receptor for chemokines (DARC), on human erythrocytes is central to blood-stage infection. Contrary to this established pathway of invasion, there is growing evidence of P. vivax infections occurring in Duffy blood group-negative individuals, suggesting that the parasite might have gained an alternative pathway to infect this group of individuals. Supporting this concept, a second distinct erythrocyte binding protein (EBP2), representing a new member of the DBP family, was discovered in P. vivax and may be the ligand in an alternate invasion pathway. Our study characterizes this novel ligand and determines its potential role in reticulocyte invasion by P. vivax merozoites. EBP2 binds preferentially to young (CD71high) Duffy-positive (Fy+) reticulocytes and has minimal binding capacity for Duffy-negative reticulocytes. Importantly, EBP2 is antigenically distinct from DBP and cannot be functionally inhibited by anti-DBP antibodies. Consequently, our results do not support EBP2 as a ligand for invasion of Duffy-negative blood cells, but instead, EBP2 may represent a novel ligand for an alternate invasion pathway of Duffy-positive reticulocytes. For decades, P. vivax infections in humans have been defined by a unique requirement for the interaction between the Duffy binding protein ligand of the parasite and the Duffy blood group antigen receptor (DARC). Recent reports of P. vivax infections in Duffy-negative individuals challenge this paradigm and suggest an alternate pathway of infection, potentially using the recently discovered EBP2. However, we demonstrate that EBP2 host cell specificity is more restricted than DBP binding and that EBP2 binds preferentially to Duffy-positive, young reticulocytes. This finding indicates that this DBP paralog does mediate a Duffy-independent pathway of infection.
Collapse
|
128
|
Hupalo DN, Luo Z, Melnikov A, Sutton PL, Rogov P, Escalante A, Vallejo AF, Herrera S, Arévalo-Herrera M, Fan Q, Wang Y, Cui L, Lucas CM, Durand S, Sanchez JF, Baldeviano GC, Lescano AG, Laman M, Barnadas C, Barry A, Mueller I, Kazura JW, Eapen A, Kanagaraj D, Valecha N, Ferreira MU, Roobsoong W, Nguitragool W, Sattabonkot J, Gamboa D, Kosek M, Vinetz JM, González-Cerón L, Birren BW, Neafsey DE, Carlton JM. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax. Nat Genet 2016; 48:953-8. [PMID: 27348298 PMCID: PMC5347536 DOI: 10.1038/ng.3588] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/13/2016] [Indexed: 12/13/2022]
Abstract
Plasmodium vivax is a major public health burden, responsible for the majority of malaria infections outside Africa. We explored the impact of demographic history and selective pressures on the P. vivax genome by sequencing 182 clinical isolates sampled from 11 countries across the globe, using hybrid selection to overcome human DNA contamination. We confirmed previous reports of high genomic diversity in P. vivax relative to the more virulent Plasmodium falciparum species; regional populations of P. vivax exhibited greater diversity than the global P. falciparum population, indicating a large and/or stable population. Signals of natural selection suggest that P. vivax is evolving in response to antimalarial drugs and is adapting to regional differences in the human host and the mosquito vector. These findings underline the variable epidemiology of this parasite species and highlight the breadth of approaches that may be required to eliminate P. vivax globally.
Collapse
Affiliation(s)
- Daniel N Hupalo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | - Zunping Luo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | | | - Patrick L Sutton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | - Peter Rogov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ananias Escalante
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | | | | | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Qi Fan
- Dalian Institute of Biotechnology, Dalian, Liaoning, China
| | - Ying Wang
- Third Military Medical University, Shapingba, Chongqing, China
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | | | | | | | - Moses Laman
- Papua New Guinea Institute of Medical Research, Madang, Papua, New Guinea
| | - Celine Barnadas
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Division of Infection and Immunity, Walter &Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Alyssa Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Ivo Mueller
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Global Health (ISGLOBAL), Barcelona, Spain
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alex Eapen
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Chennai, Tamil Nadu, India
| | - Deena Kanagaraj
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Chennai, Tamil Nadu, India
| | - Neena Valecha
- National Institute of Malaria Research, Indian Council of Medical Research, New Delhi, India
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabonkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Dionicia Gamboa
- Instituto de Medicine Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Margaret Kosek
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Joseph M Vinetz
- Instituto de Medicine Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lilia González-Cerón
- Regional Centre for Research in Public Health, National Institute for Public Health, Tapachula, Chiapas, México
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| |
Collapse
|
129
|
Pearson RD, Amato R, Auburn S, Miotto O, Almagro-Garcia J, Amaratunga C, Suon S, Mao S, Noviyanti R, Trimarsanto H, Marfurt J, Anstey NM, William T, Boni MF, Dolecek C, Hien TT, White NJ, Michon P, Siba P, Tavul L, Harrison G, Barry A, Mueller I, Ferreira MU, Karunaweera N, Randrianarivelojosia M, Gao Q, Hubbart C, Hart L, Jeffery B, Drury E, Mead D, Kekre M, Campino S, Manske M, Cornelius VJ, MacInnis B, Rockett KA, Miles A, Rayner JC, Fairhurst RM, Nosten F, Price RN, Kwiatkowski DP. Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nat Genet 2016; 48:959-964. [PMID: 27348299 PMCID: PMC4966634 DOI: 10.1038/ng.3599] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 05/27/2016] [Indexed: 01/12/2023]
Abstract
The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.
Collapse
Affiliation(s)
- Richard D Pearson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Roberto Amato
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Olivo Miotto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Jacob Almagro-Garcia
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Seila Suon
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sivanna Mao
- Sampov Meas Referral Hospital, Pursat, Cambodia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit and Queen Elizabeth Hospital Clinical Research Centre, Kota Kinabalu, Sabah, Malaysia
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tinh Tran Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Pascal Michon
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Faculty of Medicine and Health Sciences, Divine Word University, Madang, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Gabrielle Harrison
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Alyssa Barry
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivo Mueller
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Sri Lanka
| | | | - 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, Wuxi, Jiangsu, People's Republic of China
| | - Christina Hubbart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Lee Hart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria J Cornelius
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Kirk A Rockett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Alistair Miles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rick M Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
- Shoklo Malaria Research Unit, Mae Sot, Tak 63110, Thailand
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7LJ, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| |
Collapse
|
130
|
Shaw-Saliba K, Thomson-Luque R, Obaldía N, Nuñez M, Dutary S, Lim C, Barnes S, Kocken CHM, Duraisingh MT, Adams JH, Pasini EM. Insights into an Optimization of Plasmodium vivax Sal-1 In Vitro Culture: The Aotus Primate Model. PLoS Negl Trop Dis 2016; 10:e0004870. [PMID: 27463518 PMCID: PMC4963040 DOI: 10.1371/journal.pntd.0004870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023] Open
Abstract
Malaria is one of the most significant tropical diseases, and of the Plasmodium species that cause human malaria, P. vivax is the most geographically widespread. However, P. vivax remains a relatively neglected human parasite since research is typically limited to laboratories with direct access to parasite isolates from endemic field settings or from non-human primate models. This restricted research capacity is in large part due to the lack of a continuous P. vivax in vitro culture system, which has hampered the ability for experimental research needed to gain biological knowledge and develop new therapies. Consequently, efforts to establish a long-term P. vivax culture system are confounded by our poor knowledge of the preferred host cell and essential nutrients needed for in vitro propagation. Reliance on very heterogeneous P. vivax field isolates makes it difficult to benchmark parasite characteristics and further complicates development of a robust and reliable culture method. In an effort to eliminate parasite variability as a complication, we used a well-defined Aotus-adapted P. vivax Sal-1 strain to empirically evaluate different short-term in vitro culture conditions and compare them with previous reported attempts at P. vivax in vitro culture Most importantly, we suggest that reticulocyte enrichment methods affect invasion efficiency and we identify stabilized forms of nutrients that appear beneficial for parasite growth, indicating that P. vivax may be extremely sensitive to waste products. Leuko-depletion methods did not significantly affect parasite development. Formatting changes such as shaking and static cultures did not seem to have a major impact while; in contrast, the starting haematocrit affected both parasite invasion and growth. These results support the continued use of Aotus-adapted Sal-1 for development of P. vivax laboratory methods; however, further experiments are needed to optimize culture conditions to support long-term parasite development.
Collapse
Affiliation(s)
- Kathryn Shaw-Saliba
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Richard Thomson-Luque
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Nicanor Obaldía
- Center for the Evaluation of Antimalarial Drugs and Vaccines, Tropical Medicine Research / Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá, Panamá
| | - Marlon Nuñez
- Center for the Evaluation of Antimalarial Drugs and Vaccines, Tropical Medicine Research / Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá, Panamá
| | - Sahir Dutary
- Center for the Evaluation of Antimalarial Drugs and Vaccines, Tropical Medicine Research / Instituto Conmemorativo Gorgas de Estudios de la Salud, Panamá, Panamá
| | - Caeul Lim
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Samantha Barnes
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, 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
- * E-mail: (MTD); (JHA); (EMP)
| | - John H. Adams
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (MTD); (JHA); (EMP)
| | - Erica M. Pasini
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
- * E-mail: (MTD); (JHA); (EMP)
| |
Collapse
|
131
|
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.
Collapse
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
| |
Collapse
|
132
|
Bassat Q, Velarde M, Mueller I, Lin J, Leslie T, Wongsrichanalai C, Baird JK. Key Knowledge Gaps for Plasmodium vivax Control and Elimination. Am J Trop Med Hyg 2016; 95:62-71. [PMID: 27430544 PMCID: PMC5201224 DOI: 10.4269/ajtmh.16-0180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/11/2016] [Indexed: 11/18/2022] Open
Abstract
There is inadequate understanding of the biology, pathology, transmission, and control of Plasmodium vivax, the geographically most widespread cause of human malaria. During the last decades, study of this species was neglected, in part due to the erroneous belief that it is intrinsically benign. In addition, many technical challenges in culturing the parasite also hampered understanding its fundamental biology and molecular and cellular responses to chemotherapeutics. Research on vivax malaria needs to be substantially expanded over the next decade to accelerate its elimination and eradication. This article summarizes key knowledge gaps identified by researchers, national malaria control programs, and other stakeholders assembled by the World Health Organization to develop strategies for controlling and eliminating vivax malaria. The priorities presented in this article emerged in these technical discussions, and were adopted by expert consensus of the authors. All involved understood the priority placed upon pragmatism in this research agenda, that is, focus upon tools delivering better prevention, diagnosis, treatment, and surveillance of P. vivax.
Collapse
Affiliation(s)
- Quique Bassat
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Mar Velarde
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- Population Health and Immunology Division, Walter and Eliza Hall Institute, Victoria, Australia
| | - Jessica Lin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Toby Leslie
- Health Protection and Research Organisation, Kabul, Afghanistan.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - J Kevin Baird
- Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom.,Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
| |
Collapse
|
133
|
Lim C, Pereira L, Saliba KS, Mascarenhas A, Maki JN, Chery L, Gomes E, Rathod PK, Duraisingh MT. Reticulocyte Preference and Stage Development of Plasmodium vivax Isolates. J Infect Dis 2016; 214:1081-4. [PMID: 27432121 DOI: 10.1093/infdis/jiw303] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/11/2016] [Indexed: 11/13/2022] Open
Abstract
Plasmodium vivax, the most widely distributed human malaria parasite, is restricted to reticulocytes, limiting its asexual proliferation. In recent years, cases of severe and high-level P. vivax parasitemia have been reported, challenging the assumption that all isolates are equally restricted. In this article, we analyze the reticulocyte preference of a large number of Indian P. vivax isolates. Our results show that P. vivax isolates significantly vary in their level of reticulocyte preference. In addition, by carefully staging the parasites, we find that P. vivax schizonts are largely missing in peripheral blood, with the presence of schizonts in circulation correlating with a high reticulocyte preference.
Collapse
Affiliation(s)
- Caeul Lim
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Ligia Pereira
- Department of Chemistry, University of Washington, Seattle Department of Medicine, Goa Medical College and Hospital, Bambolim, India
| | - Kathryn Shaw Saliba
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Anjali Mascarenhas
- Department of Chemistry, University of Washington, Seattle Department of Medicine, Goa Medical College and Hospital, Bambolim, India
| | | | - Laura Chery
- Department of Chemistry, University of Washington, Seattle
| | - Edwin Gomes
- Department of Medicine, Goa Medical College and Hospital, Bambolim, India
| | | | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| |
Collapse
|
134
|
Loy DE, Liu W, Li Y, Learn GH, Plenderleith LJ, Sundararaman SA, Sharp PM, Hahn BH. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int J Parasitol 2016; 47:87-97. [PMID: 27381764 DOI: 10.1016/j.ijpara.2016.05.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque. However, the discovery of a multitude of Plasmodium spp. in chimpanzees and gorillas has refuted these theories and instead revealed that both P. falciparum and P. vivax evolved from parasites infecting wild-living African apes. It is now clear that P. falciparum resulted from a recent cross-species transmission of a parasite from a gorilla, whilst P. vivax emerged from an ancestral stock of parasites that infected chimpanzees, gorillas and humans in Africa, until the spread of the protective Duffy-negative mutation eliminated P. vivax from human populations there. Although many questions remain concerning the biology and zoonotic potential of the P. falciparum- and P. vivax-like parasites infecting apes, comparative genomics, coupled with functional parasite and vector studies, are likely to yield new insights into ape Plasmodium transmission and pathogenesis that are relevant to the treatment and prevention of human malaria.
Collapse
Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
135
|
Chen JH, Chen SB, Wang Y, Ju C, Zhang T, Xu B, Shen HM, Mo XJ, Molina DM, Eng M, Liang X, Gardner MJ, Wang R, Hu W. An immunomics approach for the analysis of natural antibody responses to Plasmodium vivax infection. MOLECULAR BIOSYSTEMS 2016; 11:2354-63. [PMID: 26091354 DOI: 10.1039/c5mb00330j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High throughput immunomics is a powerful platform to discover potential targets of host immunity and develop diagnostic tests for infectious diseases. We screened the sera of Plasmodium vivax-exposed individuals to profile the antibody response to blood-stage antigens of P. vivax using a P. vivax protein microarray. A total of 1936 genes encoding the P. vivax proteins were expressed, printed and screened with sera from P. vivax-exposed individuals and normal subjects. Total of 151 (7.8% of the 1936 targets) highly immunoreactive antigens were identified, including five well-characterized antigens of P. vivax (ETRAMP11.2, Pv34, SUB1, RAP2 and MSP4). Among the highly immunoreactive antigens, 5 antigens were predicted as adhesins by MAAP, and 11 antigens were predicted as merozoite invasion-related proteins based on homology with P. falciparum proteins. There are 40 proteins that have serodiagnostic potential for antibody surveillance. These novel Plasmodium antigens identified provide the clues for understanding host immune response to P. vivax infection and the development of antibody surveillance tools.
Collapse
Affiliation(s)
- Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, WHO Collaborating Center for Malaria, Schistosomiasis and Filariasis, Shanghai 200025, People's Republic of China.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
136
|
Friedrich LR, Popovici J, Kim S, Dysoley L, Zimmerman PA, Menard D, Serre D. Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax. PLoS Negl Trop Dis 2016; 10:e0004526. [PMID: 27018585 PMCID: PMC4809505 DOI: 10.1371/journal.pntd.0004526] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plasmodium vivax is the most widely distributed human malaria parasite with 2.9 billion people living in endemic areas. Despite intensive malaria control efforts, the proportion of cases attributed to P. vivax is increasing in many countries. Genetic analyses of the parasite population and its dynamics could provide an assessment of the efficacy of control efforts, but, unfortunately, these studies are limited in P. vivax by the lack of informative markers and high-throughput genotyping methods. METHODOLOGY/PRINCIPAL FINDINGS We developed a sequencing-based assay to simultaneously genotype more than 100 SNPs and applied this approach to ~500 P. vivax-infected individuals recruited across nine locations in Cambodia between 2004 and 2013. Our analyses showed that the vast majority of infections are polyclonal (92%) and that P. vivax displays high genetic diversity in Cambodia without apparent geographic stratification. Interestingly, our analyses also revealed that the proportion of monoclonal infections significantly increased between 2004 and 2013, possibly suggesting that malaria control strategies in Cambodia may be successfully affecting the parasite population. CONCLUSIONS/SIGNIFICANCE Our findings demonstrate that this high-throughput genotyping assay is efficient in characterizing P. vivax diversity and can provide valuable insights to assess the efficacy of malaria elimination programs or to monitor the spread of specific parasites.
Collapse
Affiliation(s)
- Lindsey R. Friedrich
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Jean Popovici
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Saorin Kim
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lek Dysoley
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Peter A. Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Didier Menard
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
137
|
Microsatellite Genotyping of Plasmodium vivax Isolates from Pregnant Women in Four Malaria Endemic Countries. PLoS One 2016; 11:e0152447. [PMID: 27011010 PMCID: PMC4807005 DOI: 10.1371/journal.pone.0152447] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
Plasmodium vivax is the most widely distributed human parasite and the main cause of human malaria outside the African continent. However, the knowledge about the genetic variability of P. vivax is limited when compared to the information available for P. falciparum. We present the results of a study aimed at characterizing the genetic structure of P. vivax populations obtained from pregnant women from different malaria endemic settings. Between June 2008 and October 2011 nearly 2000 pregnant women were recruited during routine antenatal care at each site and followed up until delivery. A capillary blood sample from the study participants was collected for genotyping at different time points. Seven P. vivax microsatellite markers were used for genotypic characterization on a total of 229 P. vivax isolates obtained from Brazil, Colombia, India and Papua New Guinea. In each population, the number of alleles per locus, the expected heterozygosity and the levels of multilocus linkage disequilibrium were assessed. The extent of genetic differentiation among populations was also estimated. Six microsatellite loci on 137 P. falciparum isolates from three countries were screened for comparison. The mean value of expected heterozygosity per country ranged from 0.839 to 0.874 for P. vivax and from 0.578 to 0.758 for P. falciparum. P. vivax populations were more diverse than those of P. falciparum. In some of the studied countries, the diversity of P. vivax population was very high compared to the respective level of endemicity. The level of inter-population differentiation was moderate to high in all P. vivax and P. falciparum populations studied.
Collapse
|
138
|
Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Commun 2016; 7:11078. [PMID: 27002652 PMCID: PMC4804174 DOI: 10.1038/ncomms11078] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
African apes harbour at least six Plasmodium species of the subgenus Laverania, one of which gave rise to human Plasmodium falciparum. Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as Plasmodium reichenowi and Plasmodium gaboni based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both P. reichenowi and P. gaboni are 10-fold more diverse than P. falciparum, indicating a very recent origin of the human parasite. We also find a remarkable Laverania-specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent P. falciparum ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of P. falciparum to colonize humans. African apes harbour six Plasmodium species, one of which gave rise to the human malaria parasite. Here, Sundaraman et al. use selective whole-genome amplification to determine genome sequences from two chimpanzee Plasmodium species, shedding light on the evolutionary origin of the human parasite.
Collapse
|
139
|
Sutton PL, Luo Z, Divis PCS, Friedrich VK, Conway DJ, Singh B, Barnwell JW, Carlton JM, Sullivan SA. Characterizing the genetic diversity of the monkey malaria parasite Plasmodium cynomolgi. INFECTION GENETICS AND EVOLUTION 2016; 40:243-252. [PMID: 26980604 DOI: 10.1016/j.meegid.2016.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 01/05/2023]
Abstract
Plasmodium cynomolgi is a malaria parasite that typically infects Asian macaque monkeys, and humans on rare occasions. P. cynomolgi serves as a model system for the human malaria parasite Plasmodium vivax, with which it shares such important biological characteristics as formation of a dormant liver stage and a preference to invade reticulocytes. While genomes of three P. cynomolgi strains have been sequenced, genetic diversity of P. cynomolgi has not been widely investigated. To address this we developed the first panel of P. cynomolgi microsatellite markers to genotype eleven P. cynomolgi laboratory strains and 18 field isolates from Sarawak, Malaysian Borneo. We found diverse genotypes among most of the laboratory strains, though two nominally different strains were found to be genetically identical. We also investigated sequence polymorphism in two erythrocyte invasion gene families, the reticulocyte binding protein and Duffy binding protein genes, in these strains. We also observed copy number variation in rbp genes.
Collapse
Affiliation(s)
- Patrick L Sutton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States
| | - Zunping Luo
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States
| | - Paul C S Divis
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, United Kingdom; Malaria Research Centre, Faculty of Medicine and Health Sciences, University Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Volney K Friedrich
- Department of Anthropology, New York University, 38 Waverly Place, New York, NY 10003, United States
| | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, United Kingdom; Malaria Research Centre, Faculty of Medicine and Health Sciences, University Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Balbir Singh
- Malaria Research Centre, Faculty of Medicine and Health Sciences, University Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - John W Barnwell
- Laboratory Research and Development Unit, Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States
| | - Steven A Sullivan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States.
| |
Collapse
|
140
|
Shen HM, Chen SB, Wang Y, Chen JH. Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area. Mem Inst Oswaldo Cruz 2016; 110:814-6. [PMID: 26517664 PMCID: PMC4667588 DOI: 10.1590/0074-02760150216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/03/2015] [Indexed: 11/23/2022] Open
Abstract
Currently, there is a trend of an increasing number of Plasmodium
vivaxmalaria cases in China that are imported across its Southeast Asia
border, especially in the China-Myanmar border area (CMB). To date, little is known
about the genetic diversity of P. vivax in this region. In this
paper, we report the first genome sequencing of a P. vivaxisolate
(CMB-1) from a vivax malaria patient in CMB. The sequencing data were aligned onto
96.43% of the P. vivax Salvador I reference strain (Sal I) genome
with 7.84-fold coverage as well as onto 98.32% of 14 Sal I chromosomes. Using
the de novo assembly approach, we generated 8,541 scaffolds and
assembled a total of 27.1 Mb of sequence into CMB-1 scaffolds. Furthermore, we
identified all 295 known virgenes, which is the largest subtelomeric
multigene family in malaria parasites. These results provide an important foundation
for further research onP. vivax population genetics.
Collapse
Affiliation(s)
- Hai-Mo Shen
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, People's Republic of China
| | - Shen-Bo Chen
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, People's Republic of China
| | - Yue Wang
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, People's Republic of China
| | - Jun-Hu Chen
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, People's Republic of China
| |
Collapse
|
141
|
Gunawardena S, Karunaweera ND. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. Pathog Glob Health 2016; 109:123-41. [PMID: 25943157 DOI: 10.1179/2047773215y.0000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals.
Collapse
|
142
|
Ferreira MU, de Oliveira TC. Challenges for Plasmodium vivax malaria elimination in the genomics era. Pathog Glob Health 2016; 109:89-90. [PMID: 25943154 DOI: 10.1179/2047772415z.000000000263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
143
|
Gomes LR, Almeida-de-Oliveira NK, de Lavigne AR, de Lima SRF, de Pina-Costa A, Brasil P, Daniel-Ribeiro CT, Ménard D, Ferreira-da-Cruz MDF. Plasmodium vivax mdr1 genotypes in isolates from successfully cured patients living in endemic and non-endemic Brazilian areas. Malar J 2016; 15:96. [PMID: 26887935 PMCID: PMC4758108 DOI: 10.1186/s12936-016-1141-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/03/2016] [Indexed: 01/10/2023] Open
Abstract
Background Plasmodium vivax is the most widely distributed species causing the highest number of malaria cases in the world. In Brazil, P. vivax is responsible for approximately 84 % of reported cases. In the absence of a vaccine, control strategies are based on the management of cases through rapid diagnosis and adequate treatment, in addition to vector control measures. The approaches used to investigate P. vivax resistance to chloroquine (CQ) were exclusively in vivo studies because of the difficulty in keeping parasites in continuous in vitro culture. In view of the limitations related to follow-up of patients and to assessing the plasma dosage of CQ and its metabolites, an alternative approach to monitor chemo-resistance (QR) is to use molecular markers. Single nucleotide polymorphisms (SNPs) in the multidrug resistance gene pvmdr1 are putative determinants of CQ resistance (CQR), but such SNPs in P. vivax isolates from patients with good response to treatment should be further explored. The aim of this study is to investigate the mutations in the gene, supposedly associated to QR, in P. vivax isolates from successfully cured patients, living in Brazilian endemic and non-endemic areas. Methods Blood samples were collected from 49 vivax malaria patients from endemic (Amazon Basin: 45) and non-endemic (Atlantic Forest: four) Brazilian regions and analysed for SNPs in the CQR-related P. vivax gene (pvmdr1), using PCR-based methods. Results Among the 49 isolates genetically characterized for the gene pvmdr1, 34 (70 %) presented at least one mutation. T958M mutant alleles were the most frequent (73 %) followed Y976F (15 %) and F1076L (12 %). Single mutation was detected in 24 (70.5 %) isolates and double mutations in ten (29.5 %). The most common single mutant genotype was the 958M/Y976/F1076 (79 %), followed by 976F/F1076 (21 %) whereas 958M/Y976/1076L (60 %) and 976F/1076L (40 %) double mutant genotypes were detected. Single mutant profile was observed only in isolates from Amazon Basin, although double mutants were found both in the Amazon and Atlantic Forest regions. Interestingly, the genotype 958M/Y976/1076L was present in all isolates from the Atlantic Forest in the Rio de Janeiro State. Conclusions Considering that primaquine (PQ) efficacy is highly dependent on concurrent administration of a blood schizontocidal agent and that PQ could not circumvent CQR, together with the fact that no pvmdr1 mutation should be expected in successfully cured patients, these findings seem to indicate that the pvmdr1 gene is not a reliable marker of CQR. Further investigations are needed to define a reliable molecular marker for monitoring P. vivax CQR in P. vivax populations.
Collapse
Affiliation(s)
- Larissa Rodrigues Gomes
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| | - Natália Ketrin Almeida-de-Oliveira
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| | - Aline Rosa de Lavigne
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| | - Suelen Rezende Félix de Lima
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| | - Anielle de Pina-Costa
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil. .,Laboratório de Doenças Febris Agudas - Instituto Nacional de Infectologia Evandro Chagas (INI-IPEC) (Fiocruz), Rio de Janeiro, Brazil.
| | - Patrícia Brasil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil. .,Laboratório de Doenças Febris Agudas - Instituto Nacional de Infectologia Evandro Chagas (INI-IPEC) (Fiocruz), Rio de Janeiro, Brazil.
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia.
| | - Maria de Fatima Ferreira-da-Cruz
- Laboratório de Pesquisa em Malária - Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal) Fiocruz, Rio de Janeiro, Brazil.
| |
Collapse
|
144
|
Clinical manifestations and molecular mechanisms in the changing paradigm of vivax malaria in India. INFECTION GENETICS AND EVOLUTION 2016; 39:317-324. [PMID: 26876067 DOI: 10.1016/j.meegid.2016.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/14/2016] [Accepted: 02/09/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Plasmodium vivax once considered benign is now being increasingly associated with complicated malaria where the spectrum of complications is vast and like Plasmodium falciparum. The clinical data is important with respect to the immunopathological status of the patient. Several genes like the vir genes and pvcrt-o are speculated to be attributing to the severity of P. vivax malaria. METHODS In the present study we carried out the transcription analysis of five vir genes (vir 14-related, vir 12, vir 17-like, putative vir 14 and vir 10-related) and pvcrt-o gene in severe (n=12) and non-severe (n=7) P. vivax clinical infections and studied the correlation of these genes with clinical disease severity. RESULTS This study revealed multiorgan involvement in severe vivax cases with severe thrombocytopenia and anemia, the predominantly occurring symptoms. Four out of five vir genes and pvcrt-o showed a significant increase in expression levels of severe infections compared to the non-severe infections indicating their possible role in the changing pathogenesis of P. vivax. CONCLUSIONS The increased virulence in vivax malaria seems to be the result of multifactorial parameters changing it phenotypically as well as genotypically. However more studies are needed to understand the still nascent severity of P. vivax malaria.
Collapse
|
145
|
Zhu L, Mok S, Imwong M, Jaidee A, Russell B, Nosten F, Day NP, White NJ, Preiser PR, Bozdech Z. New insights into the Plasmodium vivax transcriptome using RNA-Seq. Sci Rep 2016; 6:20498. [PMID: 26858037 PMCID: PMC4746618 DOI: 10.1038/srep20498] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
Historically seen as a benign disease, it is now becoming clear that Plasmodium vivax can cause significant morbidity. Effective control strategies targeting P. vivax malaria is hindered by our limited understanding of vivax biology. Here we established the P. vivax transcriptome of the Intraerythrocytic Developmental Cycle (IDC) of two clinical isolates in high resolution by Illumina HiSeq platform. The detailed map of transcriptome generates new insights into regulatory mechanisms of individual genes and reveals their intimate relationship with specific biological functions. A transcriptional hotspot of vir genes observed on chromosome 2 suggests a potential active site modulating immune evasion of the Plasmodium parasite across patients. Compared to other eukaryotes, P. vivax genes tend to have unusually long 5′ untranslated regions and also present multiple transcription start sites. In contrast, alternative splicing is rare in P. vivax but its association with the late schizont stage suggests some of its significance for gene function. The newly identified transcripts, including up to 179 vir like genes and 3018 noncoding RNAs suggest an important role of these gene/transcript classes in strain specific transcriptional regulation.
Collapse
Affiliation(s)
- Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anchalee Jaidee
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Bruce Russell
- Yong Loo Lin School of Medicine, National University Singapore, Singapore
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Nicholas P Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| |
Collapse
|
146
|
Ogbunugafor CB, Hartl D. A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax. Malar J 2016; 15:40. [PMID: 26809718 PMCID: PMC4727274 DOI: 10.1186/s12936-016-1090-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 01/10/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs readily enough that populations of pathogens may revert to their susceptible states. While past studies have suggested limits to reverse evolution, there have been few attempts to properly dissect its mechanistic constraints. METHODS Growth rates were determined from empirical data on the growth and resistance from a set of combinatorially complete set of mutants of a resistance protein (dihydrofolate reductase) in Plasmodium vivax, to construct reverse evolution trajectories. The fitness effects of individual mutations were calculated as a function of drug environment, revealing the magnitude of epistatic interactions between mutations and genetic backgrounds. Evolution across the landscape was simulated in two settings: starting from the population fixed for the quadruple mutant, and from a polymorphic population evenly distributed between double mutants. RESULTS A single mutation of large effect (S117N) serves as a pivot point for evolution to high resistance regions of the landscape. Through epistatic interactions with other mutations, this pivot creates an epistatic ratchet against reverse evolution towards the wild type ancestor, even in environments where the wild type is the most fit of all genotypes. This pivot mutation underlies the directional bias in evolution across the landscape, where evolution towards the ancestor is precluded across all examined drug concentrations from various starting points in the landscape. CONCLUSIONS The presence of pivot mutations can dictate dynamics of evolution across adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.
Collapse
Affiliation(s)
- C Brandon Ogbunugafor
- Department of Biology, University of Vermont, Burlington, VT, USA.
- Vermont Complex Systems Center, The University of Vermont, Burlington, VT, USA.
| | - Daniel Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
147
|
Chen SB, Ai L, Hu W, Xu J, Bergquist R, Qin ZQ, Chen JH. New Anti-Schistosoma Approaches in The People's Republic of China: Development of Diagnostics, Vaccines and Other New Techniques Belonging to the 'Omics' Group. ADVANCES IN PARASITOLOGY 2016; 92:385-408. [PMID: 27137453 DOI: 10.1016/bs.apar.2016.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new national schistosomiasis elimination programme will be implemented for the period 2016-20. To support this approach, we have performed a systematic review to assess anti-schistosome approaches in The People's Republic of China and defined research priorities for the coming years. A systematic search was conducted for articles published from January 2000 to March 2015 in international journals. Totally 410 references were published in English between 2000 and 2015 related to schistosomiasis after unrelated references and reviews or comments were further excluded. A set of research priorities has been identified for the near future that would improve the progress toward schistosomiasis elimination in The People's Republic of China. In particular, there is a lack of sensitive and specific tests for the detection of schistosomiasis cases with low parasite burdens, as well as an effective vaccine against schistosomiasis, and there is a need for surveillance tools that can evaluate the epidemic status for guiding the elimination strategy. Hence, we think that schistosomiasis control and elimination will be improved in The People's Republic of China through development of new tools.
Collapse
Affiliation(s)
- S-B Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China
| | - L Ai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China
| | - W Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China; Fudan University, Shanghai, The People's Republic of China
| | - J Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China
| | - R Bergquist
- Geospatial Health, University of Naples Federico II, Naples, Italy
| | - Z-Q Qin
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China
| | - J-H Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, The People's Republic of China; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai, The People's Republic of China; WHO Collaborating Center for Tropical Diseases, Shanghai, The People's Republic of China
| |
Collapse
|
148
|
Structurally conserved erythrocyte-binding domain in Plasmodium provides a versatile scaffold for alternate receptor engagement. Proc Natl Acad Sci U S A 2015; 113:E191-200. [PMID: 26715754 DOI: 10.1073/pnas.1516512113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Understanding how malaria parasites gain entry into human red blood cells is essential for developing strategies to stop blood stage infection. Plasmodium vivax preferentially invades reticulocytes, which are immature red blood cells. The organism has two erythrocyte-binding protein families: namely, the Duffy-binding protein (PvDBP) and the reticulocyte-binding protein (PvRBP) families. Several members of the PvRBP family bind reticulocytes, specifically suggesting a role in mediating host cell selectivity of P. vivax. Here, we present, to our knowledge, the first high-resolution crystal structure of an erythrocyte-binding domain from PvRBP2a, solved at 2.12 Å resolution. The monomeric molecule consists of 10 α-helices and one short β-hairpin, and, although the structural fold is similar to that of PfRh5--the essential invasion ligand in Plasmodium falciparum--its surface properties are distinct and provide a possible mechanism for recognition of alternate receptors. Sequence alignments of the crystallized fragment of PvRBP2a with other PvRBPs highlight the conserved placement of disulfide bonds. PvRBP2a binds mature red blood cells through recognition of an erythrocyte receptor that is neuraminidase- and chymotrypsin-resistant but trypsin-sensitive. By examining the patterns of sequence diversity within field isolates, we have identified and mapped polymorphic residues to the PvRBP2a structure. Using mutagenesis, we have also defined the critical residues required for erythrocyte binding. Characterization of the structural features that govern functional erythrocyte binding for the PvRBP family provides a framework for generating new tools that block P. vivax blood stage infection.
Collapse
|
149
|
Deroost K, Pham TT, Opdenakker G, Van den Steen PE. The immunological balance between host and parasite in malaria. FEMS Microbiol Rev 2015; 40:208-57. [PMID: 26657789 DOI: 10.1093/femsre/fuv046] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/16/2022] Open
Abstract
Coevolution of humans and malaria parasites has generated an intricate balance between the immune system of the host and virulence factors of the parasite, equilibrating maximal parasite transmission with limited host damage. Focusing on the blood stage of the disease, we discuss how the balance between anti-parasite immunity versus immunomodulatory and evasion mechanisms of the parasite may result in parasite clearance or chronic infection without major symptoms, whereas imbalances characterized by excessive parasite growth, exaggerated immune reactions or a combination of both cause severe pathology and death, which is detrimental for both parasite and host. A thorough understanding of the immunological balance of malaria and its relation to other physiological balances in the body is of crucial importance for developing effective interventions to reduce malaria-related morbidity and to diminish fatal outcomes due to severe complications. Therefore, we discuss in this review the detailed mechanisms of anti-malarial immunity, parasite virulence factors including immune evasion mechanisms and pathogenesis. Furthermore, we propose a comprehensive classification of malaria complications according to the different types of imbalances.
Collapse
Affiliation(s)
- Katrien Deroost
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium The Francis Crick Institute, Mill Hill Laboratory, London, NW71AA, UK
| | - Thao-Thy Pham
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Philippe E Van den Steen
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| |
Collapse
|
150
|
Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis 2015; 9:e0004252. [PMID: 26709695 PMCID: PMC4692395 DOI: 10.1371/journal.pntd.0004252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America.
Collapse
Affiliation(s)
- David J. Winter
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - M. Andreína Pacheco
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Rachel S. Schwartz
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | | | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ananias A. Escalante
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|