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Kattenberg JH, Cabrera-Sosa L, Figueroa-Ildefonso E, Mutsaers M, Monsieurs P, Guetens P, Infante B, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay. PLoS Negl Trop Dis 2024; 18:e0011879. [PMID: 38991038 PMCID: PMC11265702 DOI: 10.1371/journal.pntd.0011879] [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] [Received: 12/21/2023] [Revised: 07/23/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Plasmodium vivax is the most predominant malaria species in Latin America, constituting 71.5% of malaria cases in 2021. With several countries aiming for malaria elimination, it is crucial to prioritize effectiveness of national control programs by optimizing the utilization of available resources and strategically implementing necessary changes. To support this, there is a need for innovative approaches such as genomic surveillance tools that can investigate changes in transmission intensity, imported cases and sources of reintroduction, and can detect molecular markers associated with drug resistance. METHODOLOGY/PRINCIPAL FINDINGS Here, we apply a modified highly-multiplexed deep sequencing assay: Pv AmpliSeq v2 Peru. The tool targets a newly developed 41-SNP Peru barcode for parasite population analysis within Peru, the 33-SNP vivaxGEN-geo panel for country-level classification, and 11 putative drug resistance genes. It was applied to 230 samples from the Peruvian Amazon (2007-2020), generating baseline surveillance data. We observed a heterogenous P. vivax population with high diversity and gene flow in peri-urban areas of Maynas province (Loreto region) with a temporal drift using all SNPs detected by the assay (nSNP = 2909). In comparison, in an indigenous isolated area, the parasite population was genetically differentiated (FST = 0.07-0.09) with moderate diversity and high relatedness between isolates in the community. In a remote border community, a clonal P. vivax cluster was identified, with distinct haplotypes in drug resistant genes and ama1, more similar to Brazilian isolates, likely representing an introduction of P. vivax from Brazil at that time. To test its applicability for Latin America, we evaluated the SNP Peru barcode in P. vivax genomes from the region and demonstrated the capacity to capture local population clustering at within-country level. CONCLUSIONS/SIGNIFICANCE Together this data shows that P. vivax transmission is heterogeneous in different settings within the Peruvian Amazon. Genetic analysis is a key component for regional malaria control, offering valuable insights that should be incorporated into routine surveillance.
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Affiliation(s)
| | - Luis Cabrera-Sosa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Erick Figueroa-Ildefonso
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mathijs Mutsaers
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Guetens
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Berónica Infante
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
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2
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Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
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Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
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3
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De Meulenaere K, Cuypers B, Gamboa D, Laukens K, Rosanas-Urgell A. A new Plasmodium vivax reference genome for South American isolates. BMC Genomics 2023; 24:606. [PMID: 37821878 PMCID: PMC10568799 DOI: 10.1186/s12864-023-09707-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. RESULTS This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. CONCLUSIONS Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
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Rumaseb A, Moraes Barros RR, Sá JM, Juliano JJ, William T, Braima KA, Barber BE, Anstey NM, Price RN, Grigg MJ, Marfurt J, Auburn S. No Association between the Plasmodium vivax crt-o MS334 or In9 pvcrt Polymorphisms and Chloroquine Failure in a Pre-Elimination Clinical Cohort from Malaysia with a Large Clonal Expansion. Antimicrob Agents Chemother 2023; 67:e0161022. [PMID: 37314336 PMCID: PMC10353443 DOI: 10.1128/aac.01610-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 06/15/2023] Open
Abstract
Increasing reports of resistance to a frontline malaria blood-stage treatment, chloroquine (CQ), raises concerns for the elimination of Plasmodium vivax. The absence of an effective molecular marker of CQ resistance in P. vivax greatly constrains surveillance of this emerging threat. A recent genetic cross between CQ sensitive (CQS) and CQ resistant (CQR) NIH-1993 strains of P. vivax linked a moderate CQR phenotype with two candidate markers in P. vivax CQ resistance transporter gene (pvcrt-o): MS334 and In9pvcrt. Longer TGAAGH motif lengths at MS334 were associated with CQ resistance, as were shorter motifs at the In9pvcrt locus. In this study, high-grade CQR clinical isolates of P. vivax from a low endemic setting in Malaysia were used to investigate the association between the MS334 and In9pvcrt variants and treatment efficacy. Among a total of 49 independent monoclonal P. vivax isolates assessed, high-quality MS334 and In9pvcrt sequences could be derived from 30 (61%) and 23 (47%), respectively. Five MS334 and six In9pvcrt alleles were observed, with allele frequencies ranging from 2 to 76% and 3 to 71%, respectively. None of the clinical isolates had the same variant as the NIH-1993 CQR strain, and none of the variants were associated with CQ treatment failure (all P > 0.05). Multi-locus genotypes (MLGs) at 9 neutral microsatellites revealed a predominant P. vivax strain (MLG6) accounting for 52% of Day 0 infections. The MLG6 strain comprised equal proportions of CQS and CQR infections. Our study reveals complexity in the genetic basis of CQ resistance in the Malaysian P. vivax pre-elimination setting and suggests that the proposed pvcrt-o MS334 and In9pvcrt markers are not reliable markers of CQ treatment efficacy in this setting. Further studies are needed in other endemic settings, applying hypothesis-free genome-wide approaches, and functional approaches to understand the biological impact of the TGAAGH repeats linked to CQ response in a cross are warranted to comprehend and track CQR P. vivax.
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Affiliation(s)
- Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Roberto R. Moraes Barros
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy William
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Kamil A. Braima
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bridget E. Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Matthew J. Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- College of Medicine and Public Health, Flinders University, Darwin, Northern Territory, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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5
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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8
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Dia A, Jett C, Trevino SG, Chu CS, Sriprawat K, Anderson TJC, Nosten F, Cheeseman IH. Single-genome sequencing reveals within-host evolution of human malaria parasites. Cell Host Microbe 2021; 29:1496-1506.e3. [PMID: 34492224 DOI: 10.1016/j.chom.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/17/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023]
Abstract
Population genomics of bulk malaria infections is unable to examine intrahost evolution; therefore, most work has focused on the role of recombination in generating genetic variation. We used single-cell sequencing protocol for low-parasitaemia infections to generate 406 near-complete single Plasmodium vivax genomes from 11 patients sampled during sequential febrile episodes. Parasite genomes contain hundreds of de novo mutations, showing strong signatures of selection, which are enriched in the ApiAP2 family of transcription factors, known targets of adaptation. Comparing 315 P. falciparum single-cell genomes from 15 patients with our P. vivax data, we find broad complementary patterns of de novo mutation at the gene and pathway level, revealing the importance of within-host evolution during malaria infections.
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Affiliation(s)
- Aliou Dia
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Catherine Jett
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Simon G Trevino
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Cindy S Chu
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Timothy J C Anderson
- Disease Prevention and Intervention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - François Nosten
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Ian H Cheeseman
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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Tang T, Xu Y, Cao L, Tian P, Shao J, Deng Y, Zhou H, Xiao B. Ten-Year Molecular Surveillance of Drug-Resistant Plasmodium spp. Isolated From the China-Myanmar Border. Front Cell Infect Microbiol 2021; 11:733788. [PMID: 34540721 PMCID: PMC8441003 DOI: 10.3389/fcimb.2021.733788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Antimalarial drug resistance has emerged as a major threat to global malaria control efforts, particularly in the Greater Mekong Subregion (GMS). In this study, we analyzed the polymorphism and prevalence of molecular markers associated with resistance to first-line antimalarial drugs, such as artemisinin, chloroquine, and pyrimethamine, using blood samples collected from malaria patients in the China-Myanmar border region of the GMS from 2008 to 2017, including 225 cases of Plasmodium falciparum and 194 cases of Plasmodium vivax. In artemisinin resistance, only the C580Y mutation with low frequency was detected in pfk13, and no highly frequent stable mutation was found in pvk12. In chloroquine resistance, the frequency of K76T mutation in pfcrt was always high, and the frequency of double mutations in pvmdr1 of P. vivax has been steadily increasing every year. In pyrimidine resistance, pfdhfr and pvdhfr had relatively more complex mutant types associated with drug resistance sites, and the overall mutation rate was still high. Therefore, artemisinin-based combination therapies are still suitable for use as the first choice of antimalarial strategy in the China-Myanmar border region in the future.
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Affiliation(s)
- Tongke Tang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yanchun Xu
- Yunnan Institute of Parasitic Diseases Control, Pu'er, China
| | - Long Cao
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Penghai Tian
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jiang Shao
- Institutional Center for Shared Technologies and Facilities of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yan Deng
- Yunnan Institute of Parasitic Diseases Control, Pu'er, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases Control, Pu'er, China
| | - Bo Xiao
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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Singh A, Kaushik R, Chaurasia DK, Singh M, Jayaram B. PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5857404. [PMID: 32542363 PMCID: PMC7296392 DOI: 10.1093/database/baaa036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/07/2020] [Accepted: 04/29/2020] [Indexed: 01/09/2023]
Abstract
Despite Plasmodium vivax being the main offender in the majority of malarial infections, very little information is available about its adaptation and development in humans. Its capability for activating relapsing infections through its dormant liver stage and resistance to antimalarial drugs makes it as one of the major challenges in eradicating malaria. Noting the immediate necessity for the availability of a comprehensive and reliable structural and functional repository for P. vivax proteome, here we developed a web resource for the new reference genome, PvP01, furnishing information on sequence, structure, functions, active sites and metabolic pathways compiled and predicted using some of the state-of-the-art methods in respective fields. The PvP01 web resource comprises organized data on the soluble proteome consisting of 3664 proteins in blood and liver stages of malarial cycle. The current public resources represent only 163 proteins of soluble proteome of PvP01, with complete information about their molecular function, biological process and cellular components. Also, only 46 proteins of P. vivax have experimentally determined structures. In this milieu of extreme scarcity of structural and functional information, PvP01 web resource offers meticulously validated structures of 3664 soluble proteins. The sequence and structure-based functional characterization led to a quantum leap from 163 proteins available presently to whole soluble proteome offered through PvP01 web resource. We believe PvP01 web resource will serve the researchers in identifying novel protein drug targets and in accelerating the development of structure-based new drug candidates to combat malaria. Database Availability: http://www.scfbio-iitd.res.in/PvP01
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Affiliation(s)
- Ankita Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Centre of Evolution and Medicine, Arizona State University, Life Sciences C, 427 East Tyler Mall, Tempe, AZ 85281, United States
| | - Rahul Kaushik
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - Manpreet Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016.,Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016
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11
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Buyon LE, Elsworth B, Duraisingh MT. The molecular basis of antimalarial drug resistance in Plasmodium vivax. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 16:23-37. [PMID: 33957488 PMCID: PMC8113647 DOI: 10.1016/j.ijpddr.2021.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023]
Abstract
Plasmodium vivax is the most geographically widespread cause of human malaria and is responsible for the majority of cases outside of the African continent. While great progress has been made towards eliminating human malaria, drug resistant parasite strains pose a threat towards continued progress. Resistance has arisen to multiple antimalarials in P. vivax, including to chloroquine, which is currently the first line therapy for P. vivax in most regions. Despite its importance, an understanding of the molecular mechanisms of drug resistance in this species remains elusive, in large part due to the complex biology of P. vivax and the lack of in vitro culture. In this review, we will cover the extent and challenges of measuring clinical and in vitro drug resistance in P. vivax. We will consider the roles of candidate drug resistance genes. We will highlight the development of molecular approaches for studying P. vivax biology that provide the opportunity to validate the role of putative drug resistance mutations as well as identify novel mechanisms of drug resistance in this understudied parasite. Validated molecular determinants and markers of drug resistance are essential for the rapid and cost-effective monitoring of drug resistance in P. vivax, and will be useful for optimizing drug regimens and for informing drug policy in control and elimination settings. Drug resistance is emerging in Plasmodium vivax, an important cause of malaria. The complex biology of P. vivax and the limited range of research tools make it difficult to identify drug resistance. The molecular mechanisms of drug resistance in P. vivax remain elusive. This review highlights the extent of drug resistance, the putative mechanisms of resistance and new technologies for the study of P. vivax drug resistance.
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Affiliation(s)
- Lucas E Buyon
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA.
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12
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Clark MA, Kanjee U, Rangel GW, Chery L, Mascarenhas A, Gomes E, Rathod PK, Brugnara C, Ferreira MU, Duraisingh MT. Plasmodium vivax infection compromises reticulocyte stability. Nat Commun 2021; 12:1629. [PMID: 33712609 PMCID: PMC7955053 DOI: 10.1038/s41467-021-21886-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022] Open
Abstract
The structural integrity of the host red blood cell (RBC) is crucial for propagation of Plasmodium spp. during the disease-causing blood stage of malaria infection. To assess the stability of Plasmodium vivax-infected reticulocytes, we developed a flow cytometry-based assay to measure osmotic stability within characteristically heterogeneous reticulocyte and P. vivax-infected samples. We find that erythroid osmotic stability decreases during erythropoiesis and reticulocyte maturation. Of enucleated RBCs, young reticulocytes which are preferentially infected by P. vivax, are the most osmotically stable. P. vivax infection however decreases reticulocyte stability to levels close to those of RBC disorders that cause hemolytic anemia, and to a significantly greater degree than P. falciparum destabilizes normocytes. Finally, we find that P. vivax new permeability pathways contribute to the decreased osmotic stability of infected-reticulocytes. These results reveal a vulnerability of P. vivax-infected reticulocytes that could be manipulated to allow in vitro culture and develop novel therapeutics. During Plasmodium intra-erythrocytic developmental, parasites compromise the structural integrity of host red-blood cells. Here, Clark et al. develop a flow cytometric osmotic stability assay to show that P. vivax infection destabilizes host reticulocytes, which are less stable than P. falciparum-infected normocytes.
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Affiliation(s)
- Martha A Clark
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gabriel W Rangel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Laura Chery
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Anjali Mascarenhas
- Malaria Evolution in South Asia (MESA)-International Centers of Excellence in Malaria Research (ICEMR), Goa Medical College, Bambolim, Goa, India
| | - Edwin Gomes
- Malaria Evolution in South Asia (MESA)-International Centers of Excellence in Malaria Research (ICEMR), Goa Medical College, Bambolim, Goa, India
| | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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13
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Ford A, Kepple D, Abagero BR, Connors J, Pearson R, Auburn S, Getachew S, Ford C, Gunalan K, Miller LH, Janies DA, Rayner JC, Yan G, Yewhalaw D, Lo E. Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes. PLoS Negl Trop Dis 2020; 14:e0008234. [PMID: 33044985 PMCID: PMC7581005 DOI: 10.1371/journal.pntd.0008234] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 10/22/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale. Plasmodium vivax is the most geographically widespread parasite species that causes malaria in humans. Although it occurs in Africa as a member of a mix of Plasmodium species, P. vivax is dominant in other parts of the world outside of Africa (e.g., Brazil). It was previously thought that most African populations were immune to P. vivax infections due to the absence of Duffy antigen chemokine receptor (DARC) gene expression required for erythrocyte invasion. However, several recent reports have indicated the emergence and potential spread of P. vivax across human populations in Africa. Compared to Southeast Asia and South America where P. vivax is highly endemic, data on polymorphisms in erythrocyte binding gene candidates of P. vivax from Africa is limited. Filling this knowlege gap is critical for identifying functional genes in erythrocyte invasion, biomarkers for tracking the P. vivax isolates from Africa, as well as potential gene targets for vaccine development. This paper examined the level of genetic polymorphisms in a panel of 43 potential erythrocyte binding protein genes based on whole genome sequences and described transmission patterns of P. vivax infections from different study sites in Ethiopia based on the genetic variants. Our analyses showed that chromosomes 9 and 10 of the P. vivax genomes isolated in Ethiopia had the most high-quality genetic polymorphisms. Among all erythrocyte binding protein gene candidates, the merozoite surface proteins 1 and merozoite surface protein 3 showed high levels of polymorphism. MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. The expansion of the Duffy binding protein and merozoite surface protein 3 gene copies was an independent process among the P. vivax lineages in Ethiopia. Various levels of gene flow were observed even at a smaller geographical scale. Our study provided baseline data for future comparison with P. vivax in Duffy negative individuals and help develop a panel of genetic markers that are informative at a micro-geographical scale.
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Affiliation(s)
- Anthony Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
| | - Daniel Kepple
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Ethiopia
| | - Jordan Connors
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Richard Pearson
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United States of America
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Colby Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Louis H. Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Julian C. Rayner
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 OXY, United Kingdom
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, United States of America
- * E-mail: (AF); (GY); (EL)
| | | | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
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14
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Dash M, Pande V, Sinha A. Putative circumsporozoite protein (CSP) of Plasmodium vivax is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway. Gene 2020; 721S:100024. [PMID: 32550551 PMCID: PMC7285988 DOI: 10.1016/j.gene.2019.100024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/29/2022]
Abstract
Amidst technical challenges which limit successful culture and genetic manipulation of P. vivax parasites, we used a computational approach to identify a critical target with evolutionary significance. The putative circumsporozoite protein on chromosome 13 of P. vivax (PvpuCSP)is distinct from the well-known vaccine candidate PfCSP. The aim of this study was to understand the role of PvpuCSP and its relatedness to the well-known CSP. The study revealed PvpuCSP as a membrane bound E3 ubiquitin ligase involved in ubiquitination. It has a species-specific tetra-peptide unit which is differentially repeated in various P. vivax strains. The PvpuCSP is different from CSP in terms of stage-specific expression and function. Since E3 ubiquitin ligases are known antimalarial drug targets targeting the proteasome pathway, PvpuCSP, with evolutionary connotation and a key role in orchestrating protein degradation in P. vivax, can be explored as a potential drug target. PvpuCSP is predicted as E3 ubiquitin ligase, a part of ubiquitination pathway. Tetra-peptide tandem repeat at C terminal of PvpuCSP is exclusive to P. vivax. Moderately expressed during all parasitic stages in host and vector Partially disordered protein with both structured domains and two distinct IDRs A transmembrane protein with highly conserved functional domain across Apicomplexa
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Affiliation(s)
- Manoswini Dash
- Division of Epidemiology and Clinical Research, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Abhinav Sinha
- Division of Epidemiology and Clinical Research, ICMR-National Institute of Malaria Research, New Delhi, India
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15
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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16
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Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. Nat Commun 2019; 10:4300. [PMID: 31541097 PMCID: PMC6754410 DOI: 10.1038/s41467-019-12256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Mainstay treatment for Plasmodium vivax malaria has long relied on chloroquine (CQ) against blood-stage parasites plus primaquine against dormant liver-stage forms (hypnozoites), however drug resistance confronts this regimen and threatens malaria control programs. Understanding the basis of P. vivax chloroquine resistance (CQR) will inform drug discovery and malaria control. Here we investigate the genetics of P. vivax CQR by a cross of parasites differing in drug response. Gametocytogenesis, mosquito infection, and progeny production are performed with mixed parasite populations in nonhuman primates, as methods for P. vivax cloning and in vitro cultivation remain unavailable. Linkage mapping of progeny surviving >15 mg/kg CQ identifies a 76 kb region in chromosome 1 including pvcrt, an ortholog of the Plasmodium falciparum CQR transporter gene. Transcriptional analysis supports upregulated pvcrt expression as a mechanism of CQR.
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Affiliation(s)
- Juliana M Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah R Kaslow
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dingyin Tao
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Rebecca E Salzman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler J Gibson
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Michael A Krause
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Viviana Melendez-Muniz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Whitney A Kite
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul K Han
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adam Kim
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Evan G Kessler
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | | | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa Engels
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marvin L Thomas
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pius S Fasinu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert W Gwadz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Larry Walker
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - Derrick K DeConti
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffrey A Bailey
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | | | | | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Rhoel R Dinglasan
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Emerging Pathogens Institute, Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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ApiAP2 Transcription Factors in Apicomplexan Parasites. Pathogens 2019; 8:pathogens8020047. [PMID: 30959972 PMCID: PMC6631176 DOI: 10.3390/pathogens8020047] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites.
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Kanjee U, Rangel GW, Clark MA, Duraisingh MT. Molecular and cellular interactions defining the tropism of Plasmodium vivax for reticulocytes. Curr Opin Microbiol 2018; 46:109-115. [PMID: 30366310 DOI: 10.1016/j.mib.2018.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/19/2023]
Abstract
Plasmodium vivax is uniquely restricted to invading reticulocytes, the youngest of red blood cells. Parasite invasion relies on the sequential deployment of multiple parasite invasion ligands. Correct targeting of the host reticulocyte is mediated by two families of invasion ligands: the reticulocyte binding proteins (RBPs) and erythrocyte binding proteins (EBPs). The Duffy receptor has long been established as a key determinant for P. vivax invasion. However, recently, the RBP protein PvRBP2b has been shown to bind to transferrin receptor, which is expressed on reticulocytes but lost on normocytes, implicating the ligand-receptor in the reticulocyte tropism of P. vivax. Furthermore there is increasing evidence for P. vivax growth and sexual development in reticulocyte-enriched tissues such as the bone marrow.
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Affiliation(s)
- Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabriel W Rangel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martha A Clark
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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20
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In silico analysis of putative dormancy genes in Plasmodium vivax. Acta Trop 2018; 186:24-34. [PMID: 29959903 DOI: 10.1016/j.actatropica.2018.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/21/2018] [Accepted: 06/26/2018] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is the most widely spread species causing human malaria. The control of malaria caused by P. vivax has been largely hampered by its ability to develop a dormant liver stage that can generate a new blood infection at different periods of time. Unfortunately, the mechanisms of dormancy in P. vivax have not been thoroughly elucidated to date. In this study, the putative dormancy genes were analyzed to select genes with less genetic variability to maintain the function of relapsing. Expression data concerning these genes were searched to support the selection. Protein interactions among selected gene products were identified based on known and predicted protein-protein interaction using String database. Potentially interacting proteins (n = 15) were used to propose a mechanism involved in dormancy based on the differential vesicular transport due to the iron available in the hepatocyte.
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21
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Li H, Guo H, Chen T, Yu L, Chen Y, Zhao J, Yan H, Chen M, Sun Q, Zhang C, Zhou L, Chen L. Genome-wide SNP and InDel mutations in Mycobacterium tuberculosis associated with rifampicin and isoniazid resistance. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3903-3914. [PMID: 31949778 PMCID: PMC6962771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/19/2018] [Indexed: 06/10/2023]
Abstract
OBJECTIVE Multiple resistances to isoniazid and rifampicin lead to the majority of death associated with M. tuberculosis infection. This study aimed to characterize the single nucleotide polymorphisms (SNPs) and insertion and deletion (InDel) mutations associated with isoniazid and rifampicin resistance. METHODS The M. tuberculosis strain H37Rv was cultured and treated with isoniazid or rifampicin for generations. Total DNA samples from different generations were extracted for construction of DNA library, and the SNP and InDel mutation in different samples were detected by whole genome sequencing. Bioinformatics analysis such as phylogenetic tree and heap map were also performed. RESULTS Totally 58 nonsynonymous SNP mutations, 64 synonymous SNP mutations, and 99 SNP mutations in intergenic regions were detected in M. tuberculosis strains treated with rifampicin or isoniazid. Seven InDel mutations were found in the intergenic regions, and also six frameshift InDel mutation and three non-frameshift InDel mutations were also characterized. The phylogenetic tree showed clustering of all samples into three main subgroups. A great number of known and newly identified genes associated with drug resistance were detected in M. tuberculosis, showing distinct mutation patterns. CONCLUSION By whole genome sequencing, many genetic mutations in both known and new genes associated with isoniazid and rifampicin resistance were characterized in M. tuberculosis.
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Affiliation(s)
- Haicheng Li
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Huixin Guo
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Tao Chen
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Li Yu
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Yuhui Chen
- Outpatient Office Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Jiao Zhao
- Medical College of Jinan University GuangzhouChina
| | - Huimin Yan
- Guangdong Medical UniversityDongguan, China
| | - Mu Chen
- Department of Pulmonology, The Sixth Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
| | - Qi Sun
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Chenchen Zhang
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Lin Zhou
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Liang Chen
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
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22
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Zhou X, Huang JL, Shen HM, Xu B, Chen JH, Zhou XN. Immunomics analysis of Babesia microti protein markers by high-throughput screening assay. Ticks Tick Borne Dis 2018; 9:1468-1474. [PMID: 30017725 DOI: 10.1016/j.ttbdis.2018.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 11/28/2022]
Abstract
Babesia microti is a protozoan considered to be a major etiological agent of emerging human babesiosis. It imposes an increasing public-health threat and can be overlooked because of low parasitemia or mixed infection with other pathogens. More sensitive and specific antigens are needed to improve the diagnosis of babesiosis. To screen the immune diagnostic antigens of B. microti, 204 sequences from homologue proteins between B. microti and B. bovis genome sequences in PiroplasmaDB were selected. The high throughput cloned and expressed B. microti proteins were screened with the sera from the BALB/c mice infected by B. microti using protein arrays. Ten (5.9%, 10/169) highly immunoreactive proteins were identified, and most (80%, 8/10) of these highly immunoreactive proteins had not been characterized before, making them potentially useful as candidate antigens for the development of diagnostic tools for babesiosis.
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Affiliation(s)
- Xia Zhou
- Medical School of Soochow University, No. 199 Renai Road, Suzhou 215123, People's Republic of China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai 200025, People's Republic of China.
| | - Ji-Lei Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese 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 Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese 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 Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese 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 Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai 200025, People's Republic of China.
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, Shanghai 200025, People's Republic of China.
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23
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Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
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Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
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24
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Malaria Epidemiology at the Clone Level. Trends Parasitol 2017; 33:974-985. [PMID: 28966050 DOI: 10.1016/j.pt.2017.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
Abstract
Genotyping to distinguish between parasite clones is nowadays a standard in many molecular epidemiological studies of malaria. It has become crucial in drug trials and to follow individual clones in epidemiological studies, and to understand how drug resistance emerges and spreads. Here, we review the applications of the increasingly available genotyping tools and whole-genome sequencing data, and argue for a better integration of population genetics findings into malaria-control strategies.
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25
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de Oliveira TC, Rodrigues PT, Menezes MJ, Gonçalves-Lopes RM, Bastos MS, Lima NF, Barbosa S, Gerber AL, Loss de Morais G, Berná L, Phelan J, Robello C, de Vasconcelos ATR, Alves JMP, Ferreira MU. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS Negl Trop Dis 2017; 11:e0005824. [PMID: 28759591 PMCID: PMC5552344 DOI: 10.1371/journal.pntd.0005824] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/10/2017] [Accepted: 07/20/2017] [Indexed: 01/15/2023] Open
Abstract
Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. Plasmodium vivax is the most common human malaria parasite in the Americas, but how and when this species arrived in the New World remains unclear. Here we describe high-quality whole-genome sequence data for nine P. vivax isolates from Brazil, a country that accounts for 37% of the malaria burden in this continent, and compare these data with additional publicly available P. vivax genomes from Brazil, Peru, Colombia, and Mexico. P. vivax populations from the New World were found to be as diverse as their counterparts from areas with substantially higher malaria transmission, such as Southeast Asia, and to carry several non-synonymous substitutions in candidate drug-resistance genes. Moreover, genome-wide patterns of linkage disequilibrium between pairs of polymorphic sites are consistent with very frequent outcrossing in these populations. Interestingly, local P. vivax is more polymorphic, with less between-population differentiation, than sympatric populations of P. falciparum, possibly as a result of different demographic histories of these two species in the Americas. We hypothesize that local P. vivax lineages originated from successive migratory waves and subsequent admixture between parasites from geographically diverse sites.
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Affiliation(s)
- Thais C. de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria José Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Raquel M. Gonçalves-Lopes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S. Bastos
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandra L. Gerber
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Luisa Berná
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Robello
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Ana Tereza R. de Vasconcelos
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Li J, Tao Z, Li Q, Brashear A, Wang Y, Xia H, Fang Q, Cui L. Further evaluation of the NWF filter for the purification of Plasmodium vivax-infected erythrocytes. Malar J 2017; 16:201. [PMID: 28514968 PMCID: PMC5436455 DOI: 10.1186/s12936-017-1855-3] [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: 03/17/2017] [Accepted: 05/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Isolation of Plasmodium-infected red blood cells (iRBCs) from clinical blood samples is often required for experiments, such as ex vivo drug assays, in vitro invasion assays and genome sequencing. Current methods for removing white blood cells (WBCs) from malaria-infected blood are time-consuming or costly. A prototype non-woven fabric (NWF) filter was developed for the purification of iRBCs, which showed great efficiency for removing WBCs in a pilot study. Previous work was performed with prototype filters optimized for processing 5-10 mL of blood. With the commercialization of the filters, this study aims to evaluate the efficiency and suitability of the commercial NWF filter for the purification of Plasmodium vivax-infected RBCs in smaller volumes of blood and to compare its performance with that of Plasmodipur® filters. METHODS Forty-three clinical P. vivax blood samples taken from symptomatic patients attending malaria clinics at the China-Myanmar border were processed using the NWF filters in a nearby field laboratory. The numbers of WBCs and iRBCs and morphology of P. vivax parasites in the blood samples before and after NWF filtration were compared. The viability of P. vivax parasites after filtration from 27 blood samples was examined by in vitro short-term culture. In addition, the effectiveness of the NWF filter for removing WBCs was compared with that of the Plasmodipur® filter in six P. vivax blood samples. RESULTS Filtration of 1-2 mL of P. vivax-infected blood with the NWF filter removed 99.68% WBCs. The densities of total iRBCs, ring and trophozoite stages before and after filtration were not significantly different (P > 0.05). However, the recovery rates of schizont- and gametocyte-infected RBCs, which were minor parasite stages in the clinical samples, were relatively low. After filtration, the P. vivax parasites did not show apparent morphological changes. Culture of 27 P. vivax-infected blood samples after filtration showed that parasites successfully matured into the schizont stage. The WBC removal rates and iRBC recovery rates were not significantly different between the NWF and Plasmodipur® filters (P > 0.05). CONCLUSIONS When tested with 1-2 mL of P. vivax-infected blood, the NWF filter could effectively remove WBCs and the recovery rates for ring- and trophozoite-iRBCs were high. P. vivax parasites after filtration could be successfully cultured in vitro to reach maturity. The performance of the NWF and Plasmodipur® filters for removing WBCs and recovering iRBCs was comparable.
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Affiliation(s)
- Jiangyan Li
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Zhiyong Tao
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Qian Li
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Awtum Brashear
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA, USA
| | - Ying Wang
- Institute of Tropical Medicine, Third Military Medical University, Chongqing, China
| | - Hui Xia
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Qiang Fang
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, China. .,Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China.
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA, USA.
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27
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Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Roper C, Campino S, Clark TG. Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PLoS One 2017; 12:e0177134. [PMID: 28493919 PMCID: PMC5426636 DOI: 10.1371/journal.pone.0177134] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/21/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors. RESULTS We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents. Using population genetic methods we identified hotspots of selection pressure, including the previously reported MRP1 and DHPS genes, both putative drug resistance loci. Extra copies and deletions in the promoter region of another drug resistance candidate, MDR1 gene, and duplications in the Duffy binding protein gene (PvDBP) potentially involved in erythrocyte invasion, were also identified. For surveillance applications, continental-informative markers were found in putative drug resistance loci, and we show that organellar polymorphisms could classify P. vivax populations across continents and differentiate between Plasmodia spp. CONCLUSIONS This study has shown that genomic diversity that lies within and between P. vivax populations can be used to elucidate potential drug resistance and invasion mechanisms, as well as facilitate the molecular barcoding of the parasite for surveillance applications.
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Affiliation(s)
- Ernest Diez Benavente
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Zoe Ward
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- The Bioinformatics Group, School of Water Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Wilson Chan
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Fady R. Mohareb
- Department of Pathology & Laboratory Medicine, Diagnostic & Scientific Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colin J. Sutherland
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Cally Roper
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Susana Campino
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Taane G. Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
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Folegatti PM, Siqueira AM, Monteiro WM, Lacerda MVG, Drakeley CJ, Braga ÉM. A systematic review on malaria sero-epidemiology studies in the Brazilian Amazon: insights into immunological markers for exposure and protection. Malar J 2017; 16:107. [PMID: 28270152 PMCID: PMC5341168 DOI: 10.1186/s12936-017-1762-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/28/2017] [Indexed: 01/11/2023] Open
Abstract
Background Considerable success in reducing malaria incidence and mortality has been achieved in Brazil, leading to discussions over the possibility of moving towards elimination. However, more than reporting and counting clinical cases, elimination will require the use of efficient tools and strategies for measuring transmission dynamics and detecting the infectious reservoir as the primary indicators of interest for surveillance and evaluation. Because acquisition and maintenance of anti-malarial antibodies depend on parasite exposure, seroprevalence rates could be used as a reliable tool for assessing malaria endemicity and an adjunct measure for monitoring transmission in a rapid and cost-effective manner. Methods This systematic review synthesizes the existing literature on seroprevalence of malaria in the Brazilian Amazon Basin. Different study designs (cross-sectional surveys and longitudinal studies) with reported serological results in well-defined Brazilian populations were considered. Medline (via PubMed), EMBASE and LILACS databases were screened and the articles were included per established selection criteria. Data extraction was performed by two authors and a modified critical appraisal tool was applied to assess the quality and completeness of cross-sectional studies regarding defined variables of interest. Results From 220 single records identified, 23 studies were included in this systematic review for the qualitative synthesis. Five studies reported serology results on Plasmodium falciparum, 14 papers assessed Plasmodium vivax and four articles reported results on both Plasmodium species. Considerable heterogeneity among the evaluated malarial antigens, including sporozoite and blood stage antigens, was observed. The majority of recent studies analysed IgG responses against P. vivax antigens reflecting the species distribution pattern in Brazil over the last decades. Most of the published papers were cross-sectional surveys (73.9%) and only six cohort studies were included in this review. Three studies pointed to an association between antibodies against circumsporozoite protein of both P. falciparum and P. vivax and malaria exposure. Furthermore, five out 13 cross-sectional studies evidenced a positive association between IgG antibodies to the conserved 19-kDa C-terminal region of the merozoite surface protein 1 of P. vivax (PvMSP119) and malaria exposure. Conclusions This systematic review identifies potential biomarkers of P. falciparum and P. vivax exposure in areas with variable and unstable malaria transmission in Brazil. However, this study highlights the need for standardization of further studies to provide an ideal monitoring tool to evaluate trends in malaria transmission and the effectiveness of malaria intervention programmes in Brazil. Moreover, the score-based weighted tool developed and used in this study still requires further validation.
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Affiliation(s)
- Pedro M Folegatti
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - André M Siqueira
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Wuelton M Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil.,Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Marcus Vinícius G Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil.,Instituto de Pesquisas Leônidas e Maria Deane, Manaus, Amazonas, Brazil
| | - Chris J Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Érika M Braga
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. .,Departamento de Parasitologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
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Chen SB, Wang Y, Kassegne K, Xu B, Shen HM, Chen JH. Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area. BMC Genomics 2017; 18:131. [PMID: 28166727 PMCID: PMC5294834 DOI: 10.1186/s12864-017-3523-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/27/2017] [Indexed: 11/29/2022] Open
Abstract
Background Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. Results The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area. Conclusion Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3523-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Yue Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.,Institute of Parasitic Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, People's Republic of China
| | - Kokouvi Kassegne
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology Ministry of Health, Shanghai, 200025, People's Republic of China.
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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.
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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.
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Auburn S, Böhme U, Steinbiss S, Trimarsanto H, Hostetler J, Sanders M, Gao Q, Nosten F, Newbold CI, Berriman M, Price RN, Otto TD. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Res 2016; 1:4. [PMID: 28008421 PMCID: PMC5172418 DOI: 10.12688/wellcomeopenres.9876.1] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous
ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of
P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200
Plasmodium interspersed repeat (
pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ulrike Böhme
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Jessica Hostetler
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Mandy Sanders
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Qi Gao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Jiangsu, China
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Chris I Newbold
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, UK
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33
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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.
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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
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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.
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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.
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35
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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.
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36
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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.
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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
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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.
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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
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Expression of Plasmodium vivax crt-o Is Related to Parasite Stage but Not Ex Vivo Chloroquine Susceptibility. Antimicrob Agents Chemother 2015; 60:361-7. [PMID: 26525783 PMCID: PMC4704153 DOI: 10.1128/aac.02207-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
Chloroquine (CQ)-resistant Plasmodium vivax is present in most countries where P. vivax infection is endemic, but the underlying molecular mechanisms responsible remain unknown. Increased expression of P. vivaxcrt-o (pvcrt-o) has been correlated with in vivo CQ resistance in an area with low-grade resistance. We assessed pvcrt-o expression in isolates from Papua (Indonesia), where P. vivax is highly CQ resistant. Ex vivo drug susceptibilities to CQ, amodiaquine, piperaquine, mefloquine, and artesunate were determined using a modified schizont maturation assay. Expression levels of pvcrt-o were measured using a novel real-time quantitative reverse transcription-PCR method. Large variations in pvcrt-o expression were observed across the 51 isolates evaluated, with the fold change in expression level ranging from 0.01 to 59 relative to that seen with the P. vivax β-tubulin gene and from 0.01 to 24 relative to that seen with the P. vivax aldolase gene. Expression was significantly higher in isolates with the majority of parasites at the ring stage of development (median fold change, 1.7) compared to those at the trophozoite stage (median fold change, 0.5; P < 0.001). Twenty-nine isolates fulfilled the criteria for ex vivo drug susceptibility testing and showed high variability in CQ responses (median, 107.9 [range, 6.5 to 345.7] nM). After controlling for the parasite stage, we found that pvcrt-o expression levels did not correlate with the ex vivo response to CQ or with that to any of the other antimalarials tested. Our results highlight the importance of development-stage composition for measuring pvcrt-o expression and suggest that pvcrt-o transcription is not a primary determinant of ex vivo drug susceptibility. A comprehensive transcriptomic approach is warranted for an in-depth investigation of the role of gene expression levels and P. vivax drug resistance.
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Gonçalves LA, Cravo P, Ferreira MU. Emerging Plasmodium vivax resistance to chloroquine in South America: an overview. Mem Inst Oswaldo Cruz 2015. [PMID: 25184999 PMCID: PMC4156446 DOI: 10.1590/0074-0276130579] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The global emergence of Plasmodium vivax strains resistant to
chloroquine (CQ) since the late 1980s is complicating the current international
efforts for malaria control and elimination. Furthermore, CQ-resistant vivax malaria
has already reached an alarming prevalence in Indonesia, East Timor and Papua New
Guinea. More recently, in vivo studies have documented CQ-resistant P.
vivax infections in Guyana, Peru and Brazil. Here, we summarise the
available data on CQ resistance across P. vivax-endemic areas of
Latin America by combining published in vivo and in vitro studies. We also review the
current knowledge regarding the molecular mechanisms of CQ resistance in P.
vivax and the prospects for developing and standardising reliable
molecular markers of drug resistance. Finally, we discuss how the Worldwide
Antimalarial Resistance Network, an international collaborative effort involving
malaria experts from all continents, might contribute to the current regional efforts
to map CQ-resistant vivax malaria in South America.
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Affiliation(s)
| | - Pedro Cravo
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Marcelo Urbano Ferreira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
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Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, Abraham M, Sanchez JF, Santolalla ML, Baldeviano GC, Edgel KA, Rosales LA, Lescano AG, Bafna V, Vinetz JM, Winzeler EA. Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. ACS Infect Dis 2015; 1:367-79. [PMID: 26719854 DOI: 10.1021/acsinfecdis.5b00049] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms of drug resistance in Plasmodium vivax, the parasite that causes the most widespread form of human malaria, is complicated by the lack of a suitable long-term cell culture system for this parasite. In contrast to P. falciparum, which can be more readily manipulated in the laboratory, insights about parasite biology need to be inferred from human studies. Here we analyze the genomes of parasites within 10 human P. vivax infections from the Peruvian Amazon. Using next-generation sequencing we show that some P. vivax infections analyzed from the region are likely polyclonal. Despite their polyclonality we observe limited parasite genetic diversity by showing that three or fewer haplotypes comprise 94% of the examined genomes, suggesting the recent introduction of parasites into this geographic region. In contrast we find more than three haplotypes in putative drug-resistance genes, including the gene encoding dihydrofolate reductase-thymidylate synthase and the P. vivax multidrug resistance associated transporter, suggesting that resistance mutations have arisen independently. Additionally, several drug-resistance genes are located in genomic regions with evidence of increased copy number. Our data suggest that whole genome sequencing of malaria parasites from patients may provide more insight about the evolution of drug resistance than genetic linkage or association studies, especially in geographical regions with limited parasite genetic diversity.
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Affiliation(s)
| | | | | | | | | | | | | | - Juan F. Sanchez
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Meddly L. Santolalla
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - G. Christian Baldeviano
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Kimberly A. Edgel
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Luis A. Rosales
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Andrés G. Lescano
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
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41
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Yuan S, Johnston HR, Zhang G, Li Y, Hu YJ, Qin ZS. One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. PLoS Comput Biol 2015; 11:e1004448. [PMID: 26267278 PMCID: PMC4534450 DOI: 10.1371/journal.pcbi.1004448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/13/2015] [Indexed: 12/13/2022] Open
Abstract
With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor.
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Affiliation(s)
- Shuai Yuan
- Mathematics & Computer Science Department, Emory University, Atlanta, Georgia, United States of America
| | - H. Richard Johnston
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Guosheng Zhang
- Department of Genetics, Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yun Li
- Department of Genetics, Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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42
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Isolation, characterization, interaction of a thiazolekinase (Plasmodium falciparum) with silver nanoparticles. Int J Biol Macromol 2015; 79:644-53. [DOI: 10.1016/j.ijbiomac.2015.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 05/22/2015] [Accepted: 05/23/2015] [Indexed: 01/14/2023]
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43
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Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. BMC SYSTEMS BIOLOGY 2015; 9 Suppl 4:S1. [PMID: 26100579 PMCID: PMC4474416 DOI: 10.1186/1752-0509-9-s4-s1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627,000 deaths in 2012 alone. During the past decade, new therapeutic targets have been identified and are at various stages of characterization, thanks to the emerging omics-based technologies. However, the mechanism of malaria pathogenesis remains largely unknown. In this paper, we employ a novel neighborhood subnetwork alignment approach to identify network components that are potentially involved in pathogenesis. RESULTS Our module-based subnetwork alignment approach identified 24 functional homologs of pathogenesis-related proteins in the malaria parasite P. falciparum, using the protein-protein interaction networks in Escherichia coli as references. Eighteen out of these 24 proteins are associated with 418 other proteins that are related to DNA replication, transcriptional regulation, translation, signaling, metabolism, cell cycle regulation, as well as cytoadherence and entry to the host. CONCLUSIONS The subnetwork alignments and subsequent protein-protein association network mining predicted a group of malarial proteins that may be involved in parasite development and parasite-host interaction, opening a new systems-level view of parasite pathogenesis and virulence.
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Barry AE, Waltmann A, Koepfli C, Barnadas C, Mueller I. Uncovering the transmission dynamics of Plasmodium vivax using population genetics. Pathog Glob Health 2015; 109:142-52. [PMID: 25891915 DOI: 10.1179/2047773215y.0000000012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes.
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Key Words
- Control,
- Elimination
- Genetic diversity,
- Genetics,
- Genomics,
- Linkage disequilibrium,
- Malaria,
- Microsatellites,
- Mitochondrial DNA,
- Plasmodium vivax,
- Population structure,
- Relapse,
- Single nucleotide polymorphisms,
- Transmission,
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45
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Yu X, Korkmaz T, Lilburn TG, Cai H, Gu J, Wang Y. Heavy path mining of protein-protein associations in the malaria parasite. Methods 2015; 83:63-70. [PMID: 25861922 DOI: 10.1016/j.ymeth.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023] Open
Abstract
Annotating and understanding the function of proteins and other elements in a genome can be difficult in the absence of a well-studied and evolutionarily close relative. The causative agent of malaria, one of the oldest and most deadly global infectious diseases, is a good example of this problem. The burden of malaria is huge and there is a pressing need for new, more effective antimalarial strategies. However, techniques such as homology-dependent annotation transfer are severely impaired in this parasite because there are no well-understood close relatives. To circumvent this approach we developed a network-based method that uses a heavy path network-mining algorithm. We uncovered the protein-protein associations that are implicated in important cellular processes including genome integrity, DNA repair, transcriptional regulation, invasion, and pathogenesis, thus demonstrating the utility of this method. The URL of the source code for super-sequence mining method is http://www.cs.utsa.edu/~korkmaz/research/heavy-path-mining/.
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Affiliation(s)
- Xinran Yu
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Turgay Korkmaz
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | | | - Hong Cai
- Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA.
| | - Yufeng Wang
- Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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46
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Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. PLoS Negl Trop Dis 2015; 9:e0003539. [PMID: 25781890 PMCID: PMC4362761 DOI: 10.1371/journal.pntd.0003539] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/15/2015] [Indexed: 12/30/2022] Open
Abstract
Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections. Plasmodium vivax malaria is a major global public health problem, with nearly 2.5 billion people at risk for infection and approximately 132–391 million clinical infections annually. It has a wide geographical range, with a high disease burden in Asia, Central and South America, the Middle East, Oceania, and East Africa. Advances in sequencing technology and sample processing have made it possible to characterize the genetic diversity of P. vivax populations. This genetic variation provides a means to identify parasites by unique genetic signatures, or “barcodes.” We developed such a genetic barcode for P. vivax, composed of 42 robust and informative variants. Here we report its development and validation based on 87 clinical samples identified by microscopy to contain P. vivax from geographically diverse parasite populations from South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We show that the SNP barcode provides a genotyping tool that can be performed at low cost, providing a means to uniquely identify parasite infections and distinguish geographic origins, and that barcode data may offer new insights into P. vivax population structure and diversity.
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Affiliation(s)
- Mary Lynn Baniecki
- Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Aubrey L. Faust
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Daniel J. Park
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Kevin Galinsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rachel F. Daniels
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Elizabeth Hamilton
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Nadira D. Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - David Serre
- Department of Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Peter A. Zimmerman
- Department of International Health, Biology and Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Lise Musset
- Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana
| | - Eric Legrand
- Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana
| | | | | | - Sarah K. Volkman
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- School of Nursing and Health Sciences, Simmons College, Boston, Massachusetts, United States of America
| | - Dyann F. Wirth
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Pardis C. Sabeti
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Chan ER, Barnwell JW, Zimmerman PA, Serre D. Comparative analysis of field-isolate and monkey-adapted Plasmodium vivax genomes. PLoS Negl Trop Dis 2015; 9:e0003566. [PMID: 25768941 PMCID: PMC4358935 DOI: 10.1371/journal.pntd.0003566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 01/26/2015] [Indexed: 11/23/2022] Open
Abstract
Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology. In this study we compare the genome sequences of Plasmodium vivax collected directly from patients with those of parasites propagated in laboratory monkeys. We show that the adaptation and continuous propagation of Plasmodium vivax in monkeys does not induce systematic changes in the genome and, therefore, that these parasites constitute an unbiased resource for studying this important pathogen. Our analyses also reveal that some monkey-adapted Plasmodium vivax strains are not genetically homogenous and retain multiple genetically different parasites present in the original patient infection. Overall, our study confirms the utility of monkey-adapted Plasmodium vivax strains for malaria research but also shows that this resource should be analyzed cautiously as different samples of the same strain might provide different biological material.
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Affiliation(s)
- Ernest R. Chan
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John W. Barnwell
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Peter A. Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- * E-mail:
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48
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Liu J, Yuan Y, Wu Z, Li N, Chen Y, Qin T, Geng H, Xiong L, Liu D. A novel sterol regulatory element-binding protein gene (sreA) identified in penicillium digitatum is required for prochloraz resistance, full virulence and erg11 (cyp51) regulation. PLoS One 2015; 10:e0117115. [PMID: 25699519 PMCID: PMC4336317 DOI: 10.1371/journal.pone.0117115] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 12/17/2014] [Indexed: 11/26/2022] Open
Abstract
Penicilliumdigitatum is the most destructive postharvest pathogen of citrus fruits, causing fruit decay and economic loss. Additionally, control of the disease is further complicated by the emergence of drug-resistant strains due to the extensive use of triazole antifungal drugs. In this work, an orthologus gene encoding a putative sterol regulatory element-binding protein (SREBP) was identified in the genome of P. digitatum and named sreA. The putative SreA protein contains a conserved domain of unknown function (DUF2014) at its carboxyl terminus and a helix-loop-helix (HLH) leucine zipper DNA binding domain at its amino terminus, domains that are functionally associated with SREBP transcription factors. The deletion of sreA (ΔsreA) in a prochloraz-resistant strain (PdHS-F6) by Agrobacteriumtumefaciens-mediated transformation led to increased susceptibility to prochloraz and a significantly lower EC50 value compared with the HS-F6 wild-type or complementation strain (COsreA). A virulence assay showed that the ΔsreA strain was defective in virulence towards citrus fruits, while the complementation of sreA could restore the virulence to a large extent. Further analysis by quantitative real-time PCR demonstrated that prochloraz-induced expression of cyp51A and cyp51B in PdHS-F6 was completely abolished in the ΔsreA strain. These results demonstrate that sreA is a critical transcription factor gene required for prochloraz resistance and full virulence in P. digitatum and is involved in the regulation of cyp51 expression.
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Affiliation(s)
- Jing Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Zhi Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Na Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Yuanlei Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Tingting Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Hui Geng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Li Xiong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan, 430079, China
- * E-mail:
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49
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Luo Z, Sullivan SA, Carlton JM. The biology of Plasmodium vivax explored through genomics. Ann N Y Acad Sci 2015; 1342:53-61. [PMID: 25693446 DOI: 10.1111/nyas.12708] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/29/2014] [Accepted: 01/07/2015] [Indexed: 12/16/2022]
Abstract
Malaria is a mosquito-borne disease caused by the Plasmodium parasite. Of the four Plasmodium species that routinely cause human malaria, Plasmodium vivax is the most widespread species outside Africa, causing ∼18.9 million cases in 2012. P. vivax cannot be cultured continuously in vitro, which severely hampers research in nonendemic and endemic countries alike. Consequently, whole-genome sequencing has become an effective means to interrogate the biology of the P. vivax parasite. Our comparative genomic analysis of five P. vivax reference genomes and several whole-genome sequences of the closely related monkey malaria species P. cynomolgi has revealed an extraordinary level of genetic diversity and enabled characterization of novel multigene families and important single-copy genes. The generation of whole-genome sequences from multiple clinical isolates is also driving forward knowledge concerning the biology and evolution of the species. Understanding the biology of P. vivax is crucial to develop potential antimalarial drugs and vaccines and to achieve the goal of eliminating malaria.
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Affiliation(s)
- Zunping Luo
- Center for Genomics and Systems Biology, New York University, New York, New York
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50
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Bright AT, Manary MJ, Tewhey R, Arango EM, Wang T, Schork NJ, Yanow SK, Winzeler EA. A high resolution case study of a patient with recurrent Plasmodium vivax infections shows that relapses were caused by meiotic siblings. PLoS Negl Trop Dis 2014; 8:e2882. [PMID: 24901334 PMCID: PMC4046966 DOI: 10.1371/journal.pntd.0002882] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/07/2014] [Indexed: 12/15/2022] Open
Abstract
Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria. Plasmodium vivax is capable of remaining dormant in the human liver for months to years after an initial infection, creating an asymptomatic human reservoir. This unique aspect of parasite biology makes eliminating P. vivax distinctly different from P. falciparum elimination, and yet very little is known about this dormant parasite stage. Lack of knowledge about the dormant liver stage prevents the creation of new drugs and public health interventions directed at P. vivax. In order to better understand this particular parasite stage, we used whole genome sequencing to analyze three sequential P. vivax infections, two of which could be definitively categorized as having arisen from dormant liver stages. Our whole genome sequencing data demonstrates that dormant liver stage parasites are closely related yet not, as had previously been postulated, identical. These data highlight the need for a new paradigm to investigate P. vivax dormant liver stages in order to design the next generation of P. vivax drugs and effective global health interventions.
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Affiliation(s)
- Andrew Taylor Bright
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Micah J. Manary
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Ryan Tewhey
- Scripps Genomic Medicine, The Scripps Translational Science Institute, La Jolla, California, United States of America
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eliana M. Arango
- Grupo Salud y Comunidad, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Tina Wang
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Nicholas J. Schork
- Scripps Genomic Medicine, The Scripps Translational Science Institute, La Jolla, California, United States of America
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Stephanie K. Yanow
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Provincial Laboratory for Public Health, Edmonton, Alberta, Canada
- * E-mail: (SKY, for clinical questions); (EAW, for sequencing questions)
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (SKY, for clinical questions); (EAW, for sequencing questions)
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