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Ali Albsheer MM, Hubbard A, Dieng CC, Gebremeskel EI, Ahmed S, Rougeron V, Ibrahim ME, Lo E, Abdel Hamid MM. Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105643. [PMID: 39053565 DOI: 10.1016/j.meegid.2024.105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/03/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
Plasmodium vivax, traditionally overlooked has experienced a notable increase in cases in East Africa. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan using 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two different ecogeographical zones, New Halfa and Khartoum, in Sudan. Additionally, 841 geographical samples from the database were incorporated for a global genetic analysis to discern genetic relationships among P. vivax isolates on regional and worldwide scales. On the regional scale, our findings revealed 91 unique and 8 shared haplotypes among the Sudan samples, showcasing a remarkable genetic diversity compared to other geographical isolates and supporting the hypothesis that P. vivax originated from Africa. On a global scale, distinct genetic clustering of P. vivax isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) was observed, with limited admixture among the three clusters. Principal component analysis emphasized the substantial contribution of African isolates to the observed global genetic variation. The Sudanese populations displayed extensive genetic diversity, marked by significant multi-locus linkage disequilibrium, suggesting an ancestral source of P. vivax variation globally and frequent recombination among the isolates. Notably, the East African P. vivax exhibited similarity with some Asian isolates, indicating potential recent introductions. Overall, our results underscore the effectiveness of utilizing microsatellite markers for implementing robust control measures, given their ability to capture extensive genetic diversity and linkage disequilibrium patterns.
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Affiliation(s)
- Musab M Ali Albsheer
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan; Faculty of Medical Laboratory Sciences, Sinnar University, Sudan
| | - Alfred Hubbard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
| | - Cheikh Cambel Dieng
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA 19129, USA
| | | | - Safaa Ahmed
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, 34394 Montpellier, France
| | - Muntaser E Ibrahim
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA 19129, USA.
| | - Muzamil M Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.
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Joste V, Coppée R, Bailly J, Rakotoarivony Y, Toko Tchokoteu FG, Achache S, Pradines B, Cottrell G, Ariey F, Khim N, Popovici J, Mita T, Groger M, Ramharter M, Egbo T, Juma DW, Akala H, Houzé S, Clain J. Plasmodium ovale spp dhfr mutations associated with reduced susceptibility to pyrimethamine in sub-Saharan Africa: a retrospective genetic epidemiology and functional study. THE LANCET. MICROBE 2024; 5:669-678. [PMID: 38761813 DOI: 10.1016/s2666-5247(24)00054-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 02/21/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Mutations in the Plasmodium falciparum dhfr gene confer resistance to pyrimethamine, which is widely used for malaria chemoprevention in Africa. We aimed to evaluate the frequency and evolution of dhfr mutations in Plasmodium ovale spp in Africa and their functional consequences, which are incompletely characterised. METHODS We analysed dhfr mutations and their frequencies in P ovale spp isolates collected between Feb 1, 2004, and Aug 31, 2023, from the French National Malaria Reference Centre collection and from field studies in Benin, Gabon, and Kenya. Genetic patterns of positive selection were investigated. Full-length recombinant wild-type and mutant DHFR enzymes from both P ovale curtisi and P ovale wallikeri were expressed in bacteria to test whether the most common mutations reduced pyrimethamine susceptibility. FINDINGS We included 518 P ovale spp samples (314 P ovale curtisi and 204 P ovale wallikeri). In P ovale curtisi, Ala15Ser-Ser58Arg was the most common dhfr mutation (39%; 124 of 314 samples). In P ovale wallikeri, dhfr mutations were less frequent, with Phe57Leu-Ser58Arg reaching 17% (34 of 204 samples). These two mutants were the most prevalent in central and east Africa and were fixed in Kenyan isolates. We detected six and four other non-synonymous mutations, representing 8% (24 isolates) and 2% (five isolates) of the P ovale curtisi and P ovale wallikeri isolates, respectively. Whole-genome sequencing and microsatellite analyses revealed reduced genetic diversity around the mutant pocdhfr and powdhfr genes. The mutant DHFR proteins showed structural changes at the pyrimethamine binding site in-silico, confirmed by a 4-times increase in pyrimethamine half-maximal inhibitory concentration in an Escherichia coli growth assay for the Phe57Leu-Ser58Arg mutant and 50-times increase for the Ala15Ser-Ser58Arg mutant, compared with the wild-type counterparts. INTERPRETATION The widespread use of sulfadoxine-pyrimethamine for malaria chemoprevention might have exerted fortuitous selection pressure for dhfr mutations in P ovale spp. This calls for closer monitoring of dhfr and dhps mutations in P ovale spp. FUNDING French Ministry of Health, Agence Nationale de la Recherche, and Global Emerging Infections Surveillance branch of the Armed Forces Health Surveillance Division.
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Affiliation(s)
- Valentin Joste
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France.
| | - Romain Coppée
- Université de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, UR 7510 ESCAPE, Centre Hospitalier Universitaire de Rouen, Rouen, France
| | | | - Yann Rakotoarivony
- Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
| | | | | | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France; Université Aix-Marseille, IRD, SSA, VITROME, Marseille, France; IHU Méditerranée Infection, Marseille, France; Centre National de Référence du Paludisme, Marseille, France
| | | | - Frédéric Ariey
- INSERM U1016, Institut Cochin, Laboratoire de Parasitologie-Mycologie, Hôpital Cochin, AP-HP, Université Paris Cité, Paris, France
| | - Nimol Khim
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Mirjam Groger
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Ramharter
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Egbo
- Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Dennis W Juma
- Department of Emerging and Infectious Diseases (DEID), Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Hoseah Akala
- Department of Emerging and Infectious Diseases (DEID), Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Sandrine Houzé
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
| | - Jérôme Clain
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
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Hu Y, Li Y, Brashear AM, Zeng W, Wu Z, Wang L, Wei H, Soe MT, Aung PL, Sattabongkot J, Kyaw MP, Yang Z, Zhao Y, Cui L, Cao Y. Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode. PLoS Negl Trop Dis 2024; 18:e0012299. [PMID: 38959285 PMCID: PMC11251639 DOI: 10.1371/journal.pntd.0012299] [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: 02/05/2024] [Revised: 07/16/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024] Open
Abstract
An improved understanding of the Plasmodium vivax populations in the Great Mekong Subregion (GMS) is needed to monitor the progress of malaria elimination. This study aimed to use a P. vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics and explore the gene flow among P. vivax parasite populations in the western GMS (China, Myanmar and Thailand). A total of 315 P. vivax patient samples collected in 2011 and 2018 from four regions of the western GMS were genotyped for 42 SNPs using the high-throughput MassARRAY SNP genotyping technology. Population genetic analysis was conducted to estimate the genetic diversity, effective population size, and population structure among the P. vivax populations. Overall, 291 samples were successfully genotyped at 39 SNPs. A significant difference was observed in the proportion of polyclonal infections among the five P. vivax populations (P = 0.0012, Pearson Chi-square test, χ2 = 18.1), with western Myanmar having the highest proportion (96.2%, 50/52) in 2018. Likewise, the average complexity of infection was also highest in western Myanmar (1.31) and lowest in northeast Myanmar (1.01) in 2018. The older samples from western China in 2011 had the highest pairwise nucleotide diversity (π, 0.388 ± 0.046), expected heterozygosity (He, 0.363 ± 0.02), and the largest effective population size. In comparison, in the neighboring northeast Myanmar, the more recent samples in 2018 showed the lowest values (π, 0.224 ± 0.036; He, 0.220 ± 0.026). Furthermore, the 2018 northeast Myanmar parasites showed high and moderate genetic differentiation from other populations with FST values of 0.162-0.252, whereas genetic differentiation among other populations was relatively low (FST ≤ 0.059). Principal component analysis, phylogeny, and STRUCTURE analysis showed that the P. vivax population in northeast Myanmar in 2018 substantially diverged from other populations. Although the 42 SNP barcode is a valuable tool for tracking parasite origins of worldwide parasite populations, a more extended barcode with additional SNPs is needed to distinguish the more related parasite populations in the western GMS.
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Affiliation(s)
- Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
- Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Awtum M. Brashear
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zifang Wu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon, Myanmar
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Liwang Cui
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
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Spiliopoulou I, Pervanidou D, Tegos N, Tseroni M, Baka A, Vakali A, Kefaloudi CN, Papavasilopoulos V, Mpimpa A, Patsoula E. Genetic Structure of Introduced Plasmodium vivax Malaria Isolates in Greece, 2015-2019. Trop Med Infect Dis 2024; 9:102. [PMID: 38787035 PMCID: PMC11126073 DOI: 10.3390/tropicalmed9050102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Greece has been malaria-free since 1974, after an intense malaria control program. However, as Greece hosts migrant populations from P. vivax malaria-endemic countries, there is a risk of introducing the disease to specific vulnerable and receptive areas of the country. Knowledge of the genetic diversity of P. vivax populations is essential for understanding the dynamics of malaria disease transmission in a given region. We used nine highly polymorphic markers to genotype 124 P. vivax-infected archived DNA samples from human blood specimens referred to the NMRL from all over Greece throughout 2015-2019. The genotypic variability of the samples studied was noted, as they comprised several unique haplotypes, indicative of the importation of a large number of different P. vivax strains in the country. However, only a few events of local transmission were recorded. Genotyping revealed and confirmed the same clusters as those identified through epidemiological investigation. In only one introduction event was the index case found. No sustained/ongoing malaria transmissions in/between the studied regions or during consecutive years or additional foci of local transmission were observed. Genotyping is an important component in assisting malaria surveillance, as it provides information concerning the patterns of introduction and the effectiveness of implemented malaria control and elimination measures.
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Affiliation(s)
- Ioanna Spiliopoulou
- European Programme for Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), 16973 Stockholm, Sweden;
- National Public Health Organization (NPHO), 15123 Athens, Greece; (D.P.); or (M.T.); (A.B.); (A.V.); (C.-N.K.)
| | - Danai Pervanidou
- National Public Health Organization (NPHO), 15123 Athens, Greece; (D.P.); or (M.T.); (A.B.); (A.V.); (C.-N.K.)
| | - Nikolaos Tegos
- National Malaria Reference Center, Laboratory for the Surveillance of Infectious Diseases, Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece; (N.T.); (V.P.); (A.M.)
| | - Maria Tseroni
- National Public Health Organization (NPHO), 15123 Athens, Greece; (D.P.); or (M.T.); (A.B.); (A.V.); (C.-N.K.)
- Department of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 123 Papadiamantopoulou Str., Goudi, 11527 Athens, Greece
| | - Agoritsa Baka
- National Public Health Organization (NPHO), 15123 Athens, Greece; (D.P.); or (M.T.); (A.B.); (A.V.); (C.-N.K.)
| | - Annita Vakali
- National Public Health Organization (NPHO), 15123 Athens, Greece; (D.P.); or (M.T.); (A.B.); (A.V.); (C.-N.K.)
| | | | - Vasilios Papavasilopoulos
- National Malaria Reference Center, Laboratory for the Surveillance of Infectious Diseases, Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece; (N.T.); (V.P.); (A.M.)
| | - Anastasia Mpimpa
- National Malaria Reference Center, Laboratory for the Surveillance of Infectious Diseases, Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece; (N.T.); (V.P.); (A.M.)
| | - Eleni Patsoula
- National Malaria Reference Center, Laboratory for the Surveillance of Infectious Diseases, Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece; (N.T.); (V.P.); (A.M.)
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Joste V, Colard-Itté E, Guillochon É, Ariey F, Coppée R, Clain J, Houzé S. Genetic Profiling of Plasmodium ovale wallikeri Relapses With Microsatellite Markers and Whole-Genome Sequencing. J Infect Dis 2023; 228:1089-1098. [PMID: 37329228 DOI: 10.1093/infdis/jiad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/14/2023] [Accepted: 06/15/2023] [Indexed: 06/18/2023] Open
Abstract
Like Plasmodium vivax, both Plasmodium ovale curtisi and Plasmodium ovale wallikeri have the ability to cause relapse in humans, defined as recurring asexual parasitemia originating from liver-dormant forms subsequent to a primary infection. Here, we investigated relapse patterns in P ovale wallikeri infections from a cohort of travelers who were exposed to the parasite in sub-Saharan Africa and then experienced relapses after their return to France. Using a novel set of 8 highly polymorphic microsatellite markers, we genotyped 15 P ovale wallikeri relapses. For most relapses, the paired primary and relapse infections were highly genetically related (with 12 being homologous), an observation that was confirmed by whole-genome sequencing for the 4 relapses we further studied. This is, to our knowledge, the first genetic evidence of relapses in P ovale spp.
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Affiliation(s)
- Valentin Joste
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Emma Colard-Itté
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Émilie Guillochon
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
| | - Frédéric Ariey
- Inserm U1016, Institut Cochin, Laboratoire de parasitologie-mycologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité
| | - Romain Coppée
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, Paris, France
| | - Jérôme Clain
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
| | - Sandrine Houzé
- Mère et enfant en milieu tropical, Institut Recherche pour le Développement, Université Paris Cité
- Centre National de Référence du Paludisme, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard
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Li Y, Huang X, Qing L, Zeng W, Zeng X, Meng F, Wang G, Chen Y. Geographical origin of Plasmodium vivax in the Hainan Island, China: insights from mitochondrial genome. Malar J 2023; 22:84. [PMID: 36890523 PMCID: PMC9993381 DOI: 10.1186/s12936-023-04520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Hainan Province, China, has been an endemic region with high transmission of Plasmodium falciparum and Plasmodium vivax. Indigenous malaria caused by P. vivax was eliminated in Hainan in 2011, while imported vivax malaria remains. However, the geographical origin of P. vivax cases in Hainan remains unclear. METHODS Indigenous and imported P. vivax isolates (n = 45) were collected from Hainan Province, and the 6 kb mitochondrial genome was obtained. Nucleotide (π) and haplotype (h) diversity were estimated using DnaSP. The numbers of synonymous nucleotide substitutions per synonymous site (dS) and nonsynonymous nucleotide substitutions per nonsynonymous site (dN) were calculated using the SNAP program. Arlequin software was used to estimate the genetic diversity index and assess population differentiation. Bayesian phylogenetic analysis of P. vivax was performed using MrBayes. A haplotype network was generated using the NETWORK program. RESULTS In total, 983 complete mitochondrial genome sequences were collected, including 45 from this study and 938 publicly available from the NCBI. Thirty-three SNPs were identified, and 18 haplotypes were defined. The haplotype (0.834) and nucleotide (0.00061) diversity in the Hainan populations were higher than China's Anhui and Guizhou population, and the majority of pairwise FST values in Hainan exceeded 0.25, suggesting strong differentiation among most populations except in Southeast Asia. Most Hainan haplotypes were connected to South/East Asian and China's others haplotypes, but less connected with populations from China's Anhui and Guizhou provinces. Mitochondrial lineages of Hainan P. vivax belonged to clade 1 of four well-supported clades in a phylogenetic tree, most haplotypes of indigenous cases formed a subclade of clade 1, and the origin of seven imported cases (50%) could be inferred from the phylogenetic tree, but five imported cases (42.8%) could not be traced using the phylogenetic tree alone, necessitating epidemiological investigation. CONCLUSIONS Indigenous cases in Hainan display high genetic (haplotype and nucleotide) diversity. Haplotype network analysis also revealed most haplotypes in Hainan were connected to the Southeast Asian populations and divergence to a cluster of China's other populations. According to the mtDNA phylogenetic tree, some haplotypes were shared between geographic populations, and some haplotypes have formed lineages. Multiple tests are needed to further explore the origin and expansion of P. vivax populations.
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Affiliation(s)
- Yuchun Li
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China.
| | - Xiaomin Huang
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China
| | - Ling Qing
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China
| | - Wen Zeng
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China
| | - Xiangjie Zeng
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China
| | - Feng Meng
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China
| | - GuangZe Wang
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China.
| | - Yan Chen
- Hainan Provincial Centre for Disease Control and Prevention, Haikou, 570203, China.
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Measurably recombining malaria parasites. Trends Parasitol 2023; 39:17-25. [PMID: 36435688 PMCID: PMC9893849 DOI: 10.1016/j.pt.2022.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
Abstract
Genomic epidemiology has guided research and policy for various viral pathogens and there has been a parallel effort towards using genomic epidemiology to combat diseases that are caused by eukaryotic pathogens, such as the malaria parasite. However, the central concept of viral genomic epidemiology, namely that of measurably mutating pathogens, does not apply easily to sexually recombining parasites. Here we introduce the related but different concept of measurably recombining malaria parasites to promote convergence around a unifying theoretical framework for malaria genomic epidemiology. Akin to viral phylodynamics, we anticipate that an inferential framework developed around recombination will help guide practical research and thus realize the full public health potential of genomic epidemiology for malaria parasites and other sexually recombining pathogens.
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PvMSP-3α and PvMSP-3β genotyping reveals higher genetic diversity in Plasmodium vivax parasites from migrant workers than residents at the China-Myanmar border. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105387. [PMID: 36403920 DOI: 10.1016/j.meegid.2022.105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The genetic diversity of malaria parasites traces the origin and spread of new variants and can be used to evaluate the effectiveness of malaria control measures. Therefore, this study aims to improve the understanding of the molecular epidemiology of Plasmodium vivax malaria at the China-Myanmar border by genotyping the PvMSP-3α and PvMSP-3β genes. METHODS Blood samples were collected from P. vivax malaria patients along the China-Myanmar border. The PvMSP-3α and PvMSP-3β genes were amplified by polymerase chain reaction (PCR) and the genetic polymorphism and haplotype of the two genes were analyzed. RESULTS A total of 422 blood samples were used for this study, of which 224 were analyzed at PvMSP-3α and 126 at PvMSP-3β. Samples mainly were from young adults aged 18-45 years, although local patients were significantly younger than migrant laborers crossing the border at Tengchong (P < 0.0001). Molecular evolutionary analysis revealed that PvMSP-3α and PvMSP-3β underwent diversifying natural selection, and intragenic recombination contributed to the diversity of the isolates. Based on the length of the genes, we identified three types of PvMSP-3α [1.9-2.0 kb (Type-A), 1.4-1.5 kb (Type-B), and 1.1-1.3 kb (Type-C)] and two types of PvMSP-3β [1.7-2.2 kb (Type-A) and 1.4-1.5 kb (Type-B)]. Migrant laborers returning to China through Tengchong bore P. vivax infections displaying significantly higher genetic diversity than local residents. CONCLUSIONS Both PvMSP-3 paralogs were subjected to diversifying selection in each sample population. Clustering of alleles supports ephemeral endemic differentiation of alleles, but the broader phylogeny suggests that alleles transit the globe, perhaps accelerated by movements of migrants such as those transiting Tengchong.
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Rougeron V, Daron J, Fontaine MC, Prugnolle F. Evolutionary history of Plasmodium vivax and Plasmodium simium in the Americas. Malar J 2022; 21:141. [PMID: 35505431 PMCID: PMC9066938 DOI: 10.1186/s12936-022-04132-7] [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: 11/30/2021] [Accepted: 03/18/2022] [Indexed: 11/12/2022] Open
Abstract
Malaria is a vector-borne disease caused by protozoan parasites of the genus Plasmodium. Plasmodium vivax is the most prevalent human-infecting species in the Americas. However, the origins of this parasite in this continent are still debated. Similarly, it is now accepted that the existence of Plasmodium simium is explained by a P. vivax transfer from humans to monkey in America. However, many uncertainties still exist concerning the origin of the transfer and whether several transfers occurred. In this review, the most recent studies that addressed these questions using genetic and genomic approaches are presented.
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Affiliation(s)
- Virginie Rougeron
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa.
| | - Josquin Daron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France
| | - Michael C Fontaine
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Franck Prugnolle
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa
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Lopez L, Koepfli C. Systematic review of Plasmodium falciparum and Plasmodium vivax polyclonal infections: Impact of prevalence, study population characteristics, and laboratory procedures. PLoS One 2021; 16:e0249382. [PMID: 34115783 PMCID: PMC8195386 DOI: 10.1371/journal.pone.0249382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/17/2021] [Indexed: 12/27/2022] Open
Abstract
Multiple infections of genetically distinct clones of the same Plasmodium species are common in many malaria endemic settings. Mean multiplicity of infection (MOI) and the proportion of polyclonal infections are often reported as surrogate marker of transmission intensity, yet the relationship with traditional measures such as parasite prevalence is not well understood. We have searched Pubmed for articles on P. falciparum and P. vivax multiplicity, and compared the proportion of polyclonal infections and mean MOI to population prevalence. The impact of the genotyping method, number of genotyping markers, method for diagnosis (microscopy/RDT vs. PCR), presence of clinical symptoms, age, geographic region, and year of sample collection on multiplicity indices were assessed. For P. falciparum, 153 studies met inclusion criteria, yielding 275 individual data points and 33,526 genotyped individuals. The proportion of polyclonal infections ranged from 0-96%, and mean MOI from 1-6.1. For P. vivax, 54 studies met inclusion criteria, yielding 115 data points and 13,325 genotyped individuals. The proportion of polyclonal infections ranged from 0-100%, and mean MOI from 1-3.8. For both species, the proportion of polyclonal infections ranged from very low to close to 100% at low prevalence, while at high prevalence it was always high. Each percentage point increase in prevalence resulted in a 0.34% increase in the proportion of polyclonal P. falciparum infections (P<0.001), and a 0.78% increase in the proportion of polyclonal P. vivax infections (P<0.001). In multivariable analysis, higher prevalence, typing multiple markers, diagnosis of infections by PCR, and sampling in Africa were found to result in a higher proportion of P. falciparum polyclonal infections. For P. vivax, prevalence, year of study, typing multiple markers, and geographic region were significant predictors. In conclusion, polyclonal infections are frequently present in all settings, but the association between multiplicity and prevalence is weak.
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Affiliation(s)
- Luis Lopez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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11
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:genes12060843. [PMID: 34070769 PMCID: PMC8228830 DOI: 10.3390/genes12060843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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12
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Ertabaklar H, Malatyali E, Özün Özbay EP, Yildiz İ, Sinecen M, Ertuğ S, Bozdoğan B, Güçlü Ö. Microsatellite-Based Genotyping, Analysis of Population Structure, Presence of Trichomonas vaginalis Virus (TVV) and Mycoplasma hominis in T. vaginalis Isolates from Southwest of Turkey. IRANIAN JOURNAL OF PARASITOLOGY 2021; 16:81-90. [PMID: 33786050 PMCID: PMC7988665 DOI: 10.18502/ijpa.v16i1.5515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: The present study aimed to determine genetic diversity of Trichomonas vaginalis (T. vaginalis) isolates with microsatellite markers in Turkey (Nov 2015 to 2016) and to create a web-based microsatellite typing (MT) approach for the global interpretation of the data. In addition, the endosymbiosis of Mycoplasma hominis (M. hominis) and T. vaginalis virus (TVV) in the isolates was also examined. Methods: The allele sizes for each locus were calculated and microsatellite types were determined according to the allele profiles. The population structure was examined with Bayesian clustering method. A website (http://mttype.adu.edu.tr) was created for collection and sharing of microsatellite data. Presence of TVV and M. hominis in T. vaginalis isolates were investigated with electrophoresis and PCR. Results: Of 630 vaginal samples T. vaginalis was detected in 30 (4.7%) and those were used for further analysis. The structure produced by a clustering algorithm revealed eight genetic groups. The typing of isolates according to microsatellites revealed 23 different microsatellite types. Three clones were determined among isolates (MT10 16.7%; MT18 10% and MT3 6.7%). The frequency of TVV and M. hominis was 16.6% (n=5) and 20% (n=6), respectively. Conclusion: Presence of three clones among 30 T. vaginalis isolates indicated that microsatellite-based genotyping was efficient to determine the clonal distribution of T. vaginalis isolates. Therefore, a promising tool might be developed further and adapted to the studies dealing with molecular epidemiology of T. vaginalis. Microsatellite data from forthcoming studies will be deposited and presented on the website. In addition, we also presented the frequency of two endosymbionts in T. vaginalis isolates for the first time in Turkey.
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Affiliation(s)
- Hatice Ertabaklar
- Department of Parasitology, Faculty of Medicine, Adnan Menderes University, Aydin, Turkey
| | - Erdoğan Malatyali
- Department of Parasitology, Faculty of Medicine, Adnan Menderes University, Aydin, Turkey
| | | | - İbrahim Yildiz
- Department of Parasitology, Faculty of Medicine, Adnan Menderes University, Aydin, Turkey
| | - Mahmut Sinecen
- Department of Computer Engineering, Faculty of Engineering, Adnan Menderes University, Aydin, Turkey
| | - Sema Ertuğ
- Department of Parasitology, Faculty of Medicine, Adnan Menderes University, Aydin, Turkey
| | - Bülent Bozdoğan
- Department of Medical Microbiology, Faculty of Medicine, Adnan Menderes University, Aydin, Turkey.,Recombinant DNA and Recombinant Protein Research Center (REDPROM), Adnan Menderes University, Aydin, Turkey
| | - Özgür Güçlü
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Adnan Menderes University, Aydin, Turkey.,Department of Plant and Animal Production, Sultanhisar MYO, Adnan Menderes University, Aydin, Turkey
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13
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Kattenberg JH, Razook Z, Keo R, Koepfli C, Jennison C, Lautu-Gumal D, Fola AA, Ome-Kaius M, Barnadas C, Siba P, Felger I, Kazura J, Mueller I, Robinson LJ, Barry AE. Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea. Mol Ecol 2020; 29:4525-4541. [PMID: 32985031 PMCID: PMC10008436 DOI: 10.1111/mec.15654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of two major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), following nationwide distribution of long-lasting insecticide-treated nets (LLINs) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-2006) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik Province: Pf = 54.9%-8.5%, Pv = 35.7%-5.6%, Madang Province: Pf = 38.0%-9.0%, Pv: 31.8%-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, HE = 0.77-0.71; Madang: Rs = 8.2-6.1, HE = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs = 11.4-9.3, HE = 0.83-0.80; Madang: Rs = 12.2-14.5, HE = 0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium post-LLIN were positive indicators of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
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Affiliation(s)
- Johanna Helena Kattenberg
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea
| | - Zahra Razook
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Raksmei Keo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Charlie Jennison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Abebe A Fola
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Ome-Kaius
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Céline Barnadas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - James Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Leanne J Robinson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Alyssa E Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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14
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Dewasurendra RL, Baniecki ML, Schaffner S, Siriwardena Y, Moon J, Doshi R, Gunawardena S, Daniels RF, Neafsey D, Volkman S, Chandrasekharan NV, Wirth DF, Karunaweera ND. Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka. Malar J 2020; 19:342. [PMID: 32958025 PMCID: PMC7504840 DOI: 10.1186/s12936-020-03386-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/25/2020] [Indexed: 11/18/2022] Open
Abstract
Background Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P. vivax parasite isolates from Sri Lanka and to assess the ability of the SNP barcode for tracking the parasites to its origin. Methods A total of 51 P. vivax samples collected during 2005–2011, mainly from three provinces of the country, were genotyped for 40 previously identified P. vivax SNPs using a high-resolution melting (HRM), single-nucleotide barcode method. Minor allele frequencies, linkage disequilibrium, pair-wise FST values, and complexity of infection (COI) were evaluated to determine the genetic diversity. Structure analysis was carried out using STRUCTURE software (Version 2.3.4) and SNP barcode was used to identify the genetic diversity of the local parasite populations collected from different years. Principal component analysis (PCA) was used to determine the clustering according to global geographic regions. Results The proportion of multi-clone infections was significantly higher in isolates collected during an infection outbreak in year 2007. The minor allele frequencies of the SNPs changed dramatically from year to year. Significant linkage was observed in sample sub-sets from years 2005 and 2007. The majority of the isolates from 2007 consisted of at least two genetically distinct parasite strains. The overall percentage of multi-clone infections for the entire parasite sample was 39.21%. Analysis using STRUCTURE software (Version 2.3.4) revealed the high genetic diversity of the sample sub-set from year 2007. In-silico analysis of these data with those available from other global geographical regions using PCA showed distinct clustering of parasite isolates according to geography, demonstrating the usefulness of the barcode in determining an isolate to be indigenous. Conclusions Plasmodium vivax parasite isolates collected during a disease outbreak in year 2007 were more genetically diverse compared to those collected from other years. In-silico analysis using the 40 SNP barcode is a useful tool to track the origin of an isolate of uncertain origin, especially to differentiate indigenous from imported cases. However, an extended barcode with more SNPs may be needed to distinguish highly clonal populations within the country.
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Affiliation(s)
- Rajika L Dewasurendra
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Mary Lynn Baniecki
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stephen Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yamuna Siriwardena
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Jade Moon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Boston, MA, 02138, USA
| | - R Doshi
- Department of Public Health, John Hopkins University, Baltimore, MD, 21218, USA
| | - Sharmini Gunawardena
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniel Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Sarah Volkman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | - Dyann F Wirth
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka.
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15
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Mathema VB, Nakeesathit S, White NJ, Dondorp AM, Imwong M. Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi. Parasite 2020; 27:34. [PMID: 32410726 PMCID: PMC7227371 DOI: 10.1051/parasite/2020034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1-10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18-29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms "cell parts," "binding," "developmental processes," and "metabolic processes." The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.
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Affiliation(s)
- Vivek Bhakta Mathema
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
| | - Supatchara Nakeesathit
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
| | - Nicholas J. White
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford OX1 2JD Oxford United Kingdom
| | - Arjen M. Dondorp
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford OX1 2JD Oxford United Kingdom
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
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16
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Li Y, Hu Y, Zhao Y, Wang Q, Ngassa Mbenda HG, Kittichai V, Lawpoolsri S, Sattabongkot J, Menezes L, Liu X, Cui L, Cao Y. Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination. Malar J 2020; 19:145. [PMID: 32268906 PMCID: PMC7140319 DOI: 10.1186/s12936-020-03221-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Countries within the Greater Mekong Sub-region (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although the malaria situation has greatly improved, malaria transmission remains at international border regions. In some areas, Plasmodium vivax has become the predominant parasite. To gain a better understanding of transmission dynamics, knowledge on the changes of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. Methods This study investigated genetic diversity and population structures in 206 P. vivax clinical samples collected at two time points in two international border areas: the China-Myanmar border (CMB) (n = 50 in 2004 and n = 52 in 2016) and Thailand-Myanmar border (TMB) (n = 50 in 2012 and n = 54 in 2015). Parasites were genotyped using 10 microsatellite markers. Results Despite intensified control efforts, genetic diversity remained high (HE = 0.66–0.86) and was not significantly different among the four populations (P > 0.05). Specifically, HE slightly decreased from 0.76 in 2004 to 0.66 in 2016 at the CMB and increased from 0.80 in 2012 to 0.86 in 2015 at the TMB. The proportions of polyclonal infections varied significantly among the four populations (P < 0.05), and showed substantial decreases from 48.0% in 2004 to 23.7 at the CMB and from 40.0% in 2012 to 30.7% in 2015 at the TMB, with corresponding decreases in the multiplicity of infection. Consistent with the continuous decline of malaria incidence in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and sub-division among the four tested populations. Temporal genetic differentiation was observed at each site (FST = 0.081 at the CMB and FST = 0.133 at the TMB). Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB and the 2016 CMB and 2012 TMB populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 TMB population was genetically distinctive, which may reflect a process of population replacement. Whereas the effective population size (Ne) at the CMB showed a decrease from 4979 in 2004 to 3052 in 2016 with the infinite allele model, the Ne at the TMB experienced an increase from 6289 to 10,259. Conclusions With enhanced control efforts on malaria, P. vivax at the TMB and CMB showed considerable spatial and temporal differentiation, but the presence of large P. vivax reservoirs still sustained genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in these border areas of the GMS. Coordinated and integrated control efforts on both sides of international borders are essential to reach the goal of regional malaria elimination.
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Affiliation(s)
- Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.,Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, Liaoning, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Huguette Gaelle Ngassa Mbenda
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Saranath Lawpoolsri
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Lynette Menezes
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA. .,Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
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17
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Mathema VB, Nakeesathit S, Pagornrat W, Smithuis F, White NJ, Dondorp AM, Imwong M. Polymorphic markers for identification of parasite population in Plasmodium malariae. Malar J 2020; 19:48. [PMID: 31992308 PMCID: PMC6988369 DOI: 10.1186/s12936-020-3122-2] [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: 11/20/2019] [Accepted: 01/13/2020] [Indexed: 11/17/2022] Open
Abstract
Background Molecular genotyping in Plasmodium serves many aims including providing tools for studying parasite population genetics and distinguishing recrudescence from reinfection. Microsatellite typing, insertion-deletion (INDEL) and single nucleotide polymorphisms is used for genotyping, but only limited information is available for Plasmodium malariae, an important human malaria species. This study aimed to provide a set of genetic markers to facilitate the study of P. malariae population genetics. Methods Markers for microsatellite genotyping and pmmsp1 gene polymorphisms were developed and validated in symptomatic P. malariae field isolates from Myanmar (N = 37). Fragment analysis was used to determine allele sizes at each locus to calculate multiplicity of infections (MOI), linkage disequilibrium, heterozygosity and construct dendrograms. Nucleotide diversity (π), number of haplotypes, and genetic diversity (Hd) were assessed and a phylogenetic tree was constructed. Genome-wide microsatellite maps with annotated regions of newly identified markers were constructed. Results Six microsatellite markers were developed and tested in 37 P. malariae isolates which showed sufficient heterozygosity (0.530–0.922), and absence of linkage disequilibrium (IAS=0.03, p value > 0.05) (N = 37). In addition, a tandem repeat (VNTR)-based pmmsp1 INDEL polymorphisms marker was developed and assessed in 27 P. malariae isolates showing a nucleotide diversity of 0.0976, haplotype gene diversity of 0.698 and identified 14 unique variants. The size of VNTR consensus repeat unit adopted as allele was 27 base pairs. The markers Pm12_426 and pmmsp1 showed greatest diversity with heterozygosity scores of 0.920 and 0.835, respectively. Using six microsatellites markers, the likelihood that any two parasite strains would have the same microsatellite genotypes was 8.46 × 10−4 and was further reduced to 1.66 × 10−4 when pmmsp1 polymorphisms were included. Conclusions Six novel microsatellites genotyping markers and a set of pmmsp1 VNTR-based INDEL polymorphisms markers for P. malariae were developed and validated. Each marker could be independently or in combination employed to access genotyping of the parasite. The newly developed markers may serve as a useful tool for investigating parasite diversity, population genetics, molecular epidemiology and for distinguishing recrudescence from reinfection in drug efficacy studies.
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Affiliation(s)
- Vivek Bhakta Mathema
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Supatchara Nakeesathit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Watcharee Pagornrat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Frank Smithuis
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Medical Action Myanmar, Yangon, Myanmar.,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
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Thanapongpichat S, Khammanee T, Sawangjaroen N, Buncherd H, Tun AW. Genetic Diversity of Plasmodium vivax in Clinical Isolates from Southern Thailand using PvMSP1, PvMSP3 (PvMSP3α, PvMSP3β) Genes and Eight Microsatellite Markers. THE KOREAN JOURNAL OF PARASITOLOGY 2019; 57:469-479. [PMID: 31715687 PMCID: PMC6851248 DOI: 10.3347/kjp.2019.57.5.469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/21/2019] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is usually considered morbidity in endemic areas of Asia, Central and South America, and some part of Africa. In Thailand, previous studies indicated the genetic diversity of P. vivax in malaria-endemic regions such as the western part of Thailand bordering with Myanmar. The objective of the study is to investigate the genetic diversity of P. vivax circulating in Southern Thailand by using 3 antigenic markers and 8 microsatellite markers. Dried blood spots were collected from Chumphon, Phang Nga, Ranong and, Surat Thani provinces of Thailand. By PCR, 3 distinct sizes of PvMSP3α, 2 sizes of PvMSP3β and 2 sizes of PvMSP1 F2 were detected based on the length of PCR products, respectively. PCR/RFLP analyses of these antigen genes revealed high levels of genetic diversity. The genotyping of 8 microsatellite loci showed high genetic diversity as indicated by high alleles per locus and high expected heterozygosity (HE). The genotyping markers also showed multiple-clones of infection. Mixed genotypes were detected in 4.8% of PvMSP3α, 29.1% in PvMSP3β and 55.3% of microsatellite markers. These results showed that there was high genetic diversity of P. vivax isolated from Southern Thailand, indicating that the genetic diversity of P. vivax in this region was comparable to those observed other areas of Thailand.
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Affiliation(s)
| | - Thunchanok Khammanee
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Nongyao Sawangjaroen
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Nakhon Pathom, Thailand
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Emergence of Plasmodium vivax Resistance to Chloroquine in French Guiana. Antimicrob Agents Chemother 2019; 63:AAC.02116-18. [PMID: 31481442 PMCID: PMC6811453 DOI: 10.1128/aac.02116-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
In South America, Plasmodium vivax resistance to chloroquine was recently reported in Brazil and Bolivia. The objective of this study was to collect data on chloroquine resistance in French Guiana by associating a retrospective evaluation of therapeutic efficacy with an analysis of recurrent parasitemia from any patients. Patients with P. vivax infection, confirmed by microscopy and a body temperature of ≥37.5°C, were retrospectively identified at Cayenne Hospital between 2009 and 2015. Follow-up and treatment responses were performed according to the World Health Organization protocol. Parasite resistance was confirmed after dosage of a plasma concentration of chloroquine and microsatellite characterization. The pvmdr1 and pvcrt-o genes were analyzed for sequence and gene copy number variation. Among the 172 patients followed for 28 days, 164 presented adequate clinical and parasitological responses. Eight cases of treatment failures were identified (4.7%; n = 8/172), all after 14 days. The therapeutic efficacy of chloroquine was estimated at 95.3% (95% confidence interval [CI], 92.5 to 98.1%; n = 164/172). Among the eight failures, five were characterized: two cases were true P. vivax chloroquine resistance (1.2%; 95% CI, 0 to 2.6%; n = 2/172), and three cases were found with subtherapeutic concentrations of chloroquine. No particular polymorphism in the Plasmodium vivax pvmdr1 and pvcrt-o genes was identified in the resistant parasites. This identified level of resistance of P. vivax to chloroquine in French Guiana does not require a change in therapeutic recommendations. However, primaquine should be administered more frequently to limit the spread of resistance, and there is still a need for a reliable molecular marker to facilitate the monitoring of P. vivax resistance to chloroquine.
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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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21
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Sibley CH. A Solid Beginning to Understanding Plasmodium vivax in Africa. J Infect Dis 2019; 220:1716-1718. [DOI: 10.1093/infdis/jiz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
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Bahk YY, Kim J, Ahn SK, Na BK, Chai JY, Kim TS. Genetic Diversity of Plasmodium vivax Causing Epidemic Malaria in the Republic of Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:545-552. [PMID: 30630274 PMCID: PMC6327206 DOI: 10.3347/kjp.2018.56.6.545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is more challenging to control and eliminate than P. falciparum due to its more asymptomatic infections with low parasite densities making diagnosis more difficult, in addition to its unique biological characteristics. The potential re-introduction of incidence cases, either through borders or via human migrations, is another major hurdle to sustained control and elimination. The Republic of Korea has experienced re-emergence of vivax malaria in 1993 but is one of the 32 malaria-eliminating countries to-date. Despite achieving successful nationwide control and elimination of vivax malaria, the evolutionary characteristics of vivax malaria isolates in the Republic of Korea have not been fully understood. In this review, we present an overview of the genetic variability of such isolates to increase understanding of the epidemiology, diversity, and dynamics of vivax populations in the Republic of Korea.
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Affiliation(s)
- Young Yil Bahk
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju 27478,
Korea
| | - Jeonga Kim
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, UAB Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294,
USA
| | - Seong Kyu Ahn
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Jong-Yil Chai
- Korea Association of Health Promotion, Seoul 07653,
Korea
| | - Tong-Soo Kim
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
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Saralamba N, Mayxay M, Newton PN, Smithuis F, Nosten F, Archasuksan L, Pukrittayakamee S, White NJ, Day NPJ, Dondorp AM, Imwong M. Genetic polymorphisms in the circumsporozoite protein of Plasmodium malariae show a geographical bias. Malar J 2018; 17:269. [PMID: 30012172 PMCID: PMC6048912 DOI: 10.1186/s12936-018-2413-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/09/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Plasmodium malariae is characterized by its long asymptomatic persistence in the human host. The epidemiology of P. malariae is incompletely understood and is hampered by the limited knowledge of genetic polymorphisms. Previous reports from Africa have shown heterogeneity within the P. malariae circumsporozoite protein (pmcsp) gene. However, comparative studies from Asian countries are lacking. Here, the genetic polymorphisms in pmcsp of Asian isolates have been characterized. METHODS Blood samples from 89 symptomatic P. malariae-infected patients were collected, from Thailand (n = 43), Myanmar (n = 40), Lao PDR (n = 5), and Bangladesh (n = 1). pmcsp was amplified using semi-nested PCR before sequencing. The resulting 89 pmcsp sequences were analysed together with 58 previously published pmcsp sequences representing African countries using BioEdit, MEGA6, and DnaSP. RESULTS Polymorphisms identified in pmcsp were grouped into 3 populations: Thailand, Myanmar, and Kenya. The nucleotide diversity and the ratio of nonsynonymous to synonymous substitutions (dN/dS) in Thailand and Myanmar were higher compared with that in Kenya. Phylogenetic analysis showed clustering of pmcsp sequences according to the origin of isolates (Asia vs. Africa). High genetic differentiation (Fst = 0.404) was observed between P. malariae isolates from Asian and African countries. Sequence analysis of pmcsp showed the presence of tetrapeptide repeat units of NAAG, NDAG, and NAPG in the central repeat region of the gene. Plasmodium malariae isolates from Asian countries carried fewer copies of NAAG compared with that from African countries. The NAPG repeat was only observed in Asian isolates. Additional analysis of 2 T-cell epitopes, Th2R and Th3R, showed limited heterogeneity in P. malariae populations. CONCLUSIONS This study provides valuable information on the genetic polymorphisms in pmcsp isolates from Asia and advances our understanding of P. malariae population in Asia and Africa. Polymorphisms in the central repeat region of pmcsp showed association with the geographical origin of P. malariae isolates and can be potentially used as a marker for genetic epidemiology of P. malariae population.
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Affiliation(s)
- Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Churchill Hospital, University of Oxford, Oxford, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Churchill Hospital, University of Oxford, Oxford, UK
| | - Frank Smithuis
- Medical Action Myanmar, Yangon, Myanmar
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7LF, UK
| | - Francois Nosten
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7LF, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Laypaw Archasuksan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Sasithon Pukrittayakamee
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Churchill Hospital, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Churchill Hospital, University of Oxford, Oxford, UK
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Churchill Hospital, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Kittichai V, Nguitragool W, Ngassa Mbenda HG, Sattabongkot J, Cui L. Genetic diversity of the Plasmodium vivax multidrug resistance 1 gene in Thai parasite populations. INFECTION GENETICS AND EVOLUTION 2018; 64:168-177. [PMID: 29936038 DOI: 10.1016/j.meegid.2018.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022]
Abstract
Plasmodium vivax resistance to chloroquine (CQ) was first reported over 60 years ago. Here we analyzed sequence variations in the multidrug resistance 1 gene (Pvmdr1), a putative molecular marker for P. vivax CQ resistance, in field isolates collected from three sites in Thailand during 2013-2016. Several single nucleotide polymorphisms previously implicated in reduced CQ sensitivity were found. These genetic variations encode amino acids in the two nucleotide-binding domains as well as the transmembrane domains of the protein. The high level of genetic diversity of Pvmdr1 provides insights into the evolutionary history of this gene. Specifically, there was little evidence of positive selection at amino acid F1076L in global isolates to be promoted as a possible marker for CQ resistance. Population genetic analysis clearly divided the parasites into eastern and western populations, which is consistent with their geographical separation by the central malaria-free area of Thailand. With CQ-primaquine remaining as the frontline treatment for vivax malaria in all regions of Thailand, such a population subdivision could be shaped and affected by the current drugs for P. falciparum since mixed P. falciparum/P. vivax infections often occur in this region.
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Affiliation(s)
- Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Liwang Cui
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA.
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25
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Ventocilla JA, Nuñez J, Tapia LL, Lucas CM, Manock SR, Lescano AG, Edgel KA, Graf PCF. Genetic Variability of Plasmodium vivax in the North Coast of Peru and the Ecuadorian Amazon Basin. Am J Trop Med Hyg 2018; 99:27-32. [PMID: 29761758 DOI: 10.4269/ajtmh.17-0498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the Peruvian North Coast (PNC), the number of Plasmodium vivax malaria cases increased steadily from 2007 to 2010 despite a significant decline in the overall number of cases in Peru during the same period. To better understand the transmission dynamics of P. vivax populations in the PNC and the neighboring Ecuadorian Amazon Basin (EAB), we studied the genetic variability and population structure of P. vivax in these areas. One hundred and twenty P. vivax isolates (58 from Piura and 37 from Tumbes in the PNC collected from 2008 to 2010 and 25 from the EAB collected in Pastaza from 2001 to 2004) were assessed by five polymorphic microsatellite markers. Genetic variability was determined by expected heterozygosity (He) and population structure by Bayesian inference cluster analysis. We found very low genetic diversity in the PNC (He = 0-0.32) but high genetic diversity in the EAB (He = 0.43-0.70). Population structure analysis revealed three distinct populations in the three locations. Six of 37 (16%) isolates from Tumbes had an identical haplotype to that found in Piura, suggesting unidirectional flow from Piura to Tumbes. In addition, one haplotype from Tumbes showed similarity to a haplotype found in Pastaza, suggesting that this could be an imported case from EAB. These findings strongly suggest a minimal population flow and different levels of genetic variability between these two areas divided by the Andes Mountains. This work presents molecular markers that could be used to increase our understanding of regional malaria transmission dynamics, which has implications for the development of strategies for P. vivax control.
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Affiliation(s)
| | - Jorge Nuñez
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - L Lorena Tapia
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - Carmen M Lucas
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | | | - Andrés G Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration Universidad Peruana Cayetano Heredia, Lima, Peru.,U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
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26
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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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Figan CE, Sá JM, Mu J, Melendez-Muniz VA, Liu CH, Wellems TE. A set of microsatellite markers to differentiate Plasmodium falciparum progeny of four genetic crosses. Malar J 2018; 17:60. [PMID: 29394891 PMCID: PMC5797376 DOI: 10.1186/s12936-018-2210-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Four Plasmodium falciparum genetic crosses (HB3×3D7, HB3×Dd2, 7G8×GB4, and 803×GB4) have produced sets of recombinant progeny that are widely used for malaria research, including investigations of anti-malarial drug resistance. It is critical to maintain the progeny free from cross-contamination. Microsatellite polymorphisms can be used to validate parasite identity. Results A set of 12 markers was developed that differentiates the parents of the four P. falciparum crosses. This typing set identified distinguishing patterns of inheritance (fingerprints) in segregant collections of 15 progeny clones from HB3×3D7, 32 from HB3×Dd2, 33 from 7G8×GB4, and 81 from 803×GB4. Stronger amplification was observed with shorter relative to longer alleles of individual microsatellites. In experiments with mixed parental DNAs, electropherograms showed that signals of cross-contamination can be missed when minor peaks less than 1/4 or 1/3 the height of the major peak are disregarded by threshold settings commonly used for population studies. Conclusions Microsatellite typing is an effective method to check the identity of P. falciparum lines and detect parasite cross-contamination in cultures; however, care must be taken not to ignore minor peaks that can be overlooked. The 12 microsatellite markers presented here provide a rapid and efficient means to distinguish the segregants of laboratory crosses. Fingerprint patterns from these markers are useful to maintain the integrity of diverse parasite lines in and between research laboratories. Electronic supplementary material The online version of this article (10.1186/s12936-018-2210-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine E Figan
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Juliana M Sá
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Viviana A Melendez-Muniz
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chia Hao Liu
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research (LMVR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
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Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific. PLoS Negl Trop Dis 2018; 12:e0006146. [PMID: 29373596 PMCID: PMC5802943 DOI: 10.1371/journal.pntd.0006146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 02/07/2018] [Accepted: 12/01/2017] [Indexed: 01/17/2023] Open
Abstract
The human malaria parasite Plasmodium vivax is more resistant to malaria control strategies than Plasmodium falciparum, and maintains high genetic diversity even when transmission is low. To investigate whether declining P. vivax transmission leads to increasing population structure that would facilitate elimination, we genotyped samples from across the Southwest Pacific region, which experiences an eastward decline in malaria transmission, as well as samples from two time points at one site (Tetere, Solomon Islands) during intensified malaria control. Analysis of 887 P. vivax microsatellite haplotypes from hyperendemic Papua New Guinea (PNG, n = 443), meso-hyperendemic Solomon Islands (n = 420), and hypoendemic Vanuatu (n = 24) revealed increasing population structure and multilocus linkage disequilibrium yet a modest decline in diversity as transmission decreases over space and time. In Solomon Islands, which has had sustained control efforts for 20 years, and Vanuatu, which has experienced sustained low transmission for many years, significant population structure was observed at different spatial scales. We conclude that control efforts will eventually impact P. vivax population structure and with sustained pressure, populations may eventually fragment into a limited number of clustered foci that could be targeted for elimination. Plasmodium vivax is a major human malaria parasite, common in endemic areas outside sub-Saharan Africa, and more difficult to control than other malaria parasite species. The distinct lifecycle biology of P. vivax is thought to contribute to its more stable and efficient transmission allowing the maintenance of high diversity and potentially, gene flow. Independent studies are therefore needed to understand how P. vivax populations respond to changing transmission levels, in order to inform malaria control and elimination efforts. Here we have determined parasite population genetic structure in three countries of the Southwest Pacific, an island chain with a natural west to east decline in transmission intensity (Papua New Guinea > Solomon Islands > Vanuatu). With declining transmission, P. vivax populations experience only a modest decline in diversity but a significant increase in multilocus linkage disequilibrium and population structure, indicating that parasite populations become more inbred and begin to fragment into clustered foci. Analysis of two time points in one study area (Tetere, Solomon Islands) also show similar changes in association with intensifying malaria control. The results indicate that with long term sustained malaria control P. vivax populations will eventually fracture into population clusters that could be targeted for elimination.
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Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations. INFECTION GENETICS AND EVOLUTION 2017; 58:83-95. [PMID: 29313805 DOI: 10.1016/j.meegid.2017.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/27/2017] [Accepted: 11/30/2017] [Indexed: 11/20/2022]
Abstract
The Asia Pacific Leaders in Malaria Alliance (APLMA) have committed to eliminate malaria from the region by 2030. Papua New Guinea (PNG) has the highest malaria burden in the Asia-Pacific region but with the intensification of control efforts since 2005, transmission has been dramatically reduced and Plasmodium vivax is now the dominant malaria infection in some parts of the country. To gain a better understanding of the transmission dynamics and migration patterns of P. vivax in PNG, here we investigate population structure in eight geographically and ecologically distinct regions of the country. A total of 219 P. vivax isolates (16-30 per population) were successfully haplotyped using 10 microsatellite markers. A wide range of genetic diversity (He=0.37-0.87, Rs=3.60-7.58) and significant multilocus linkage disequilibrium (LD) was observed in six of the eight populations (IAS=0.08-0.15 p-value<0.05) reflecting a spectrum of transmission intensities across the country. Genetic differentiation between regions was evident (Jost's D=0.07-0.72), with increasing divergence of populations with geographic distance. Overall, P. vivax isolates clustered into three major genetic populations subdividing the Mainland lowland and coastal regions, the Islands and the Highlands. P. vivax gene flow follows major human migration routes, and there was higher gene flow amongst Mainland parasite populations than among Island populations. The Central Province (samples collected in villages close to the capital city, Port Moresby), acts as a sink for imported infections from the three major endemic areas. These insights into P. vivax transmission dynamics and population networks will inform targeted strategies to contain malaria infections and to prevent the spread of drug resistance in PNG.
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Congpuong K, Ubalee R. Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand. THE KOREAN JOURNAL OF PARASITOLOGY 2017; 55:465-472. [PMID: 29103261 PMCID: PMC5678461 DOI: 10.3347/kjp.2017.55.5.465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/02/2017] [Accepted: 08/02/2017] [Indexed: 11/23/2022]
Abstract
Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.
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Affiliation(s)
- Kanungnit Congpuong
- Department of Medical Technology, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok 10600, Thailand
| | - Ratawan Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
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Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission. PLoS Negl Trop Dis 2017; 11:e0005930. [PMID: 29036178 PMCID: PMC5658191 DOI: 10.1371/journal.pntd.0005930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 09/04/2017] [Indexed: 11/23/2022] Open
Abstract
Background Plasmodium vivax transmission in Thailand has been substantially reduced over the past 10 years, yet it remains highly endemic along international borders. Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country. Methodology/Results A total of 127 P. vivax isolates were genotyped from two western provinces (Tak and Kanchanaburi) and one eastern province (Ubon Ratchathani) of Thailand using 10 microsatellite markers. Genetic diversity was high, but recent clonal expansion was detected in all three provinces. Substantial population structure and genetic differentiation of parasites among provinces suggest limited gene flow among these sites. There was no haplotype sharing among the three sites, and a reduced panel of four microsatellite markers was sufficient to assign the parasites to their provincial origins. Conclusion/Significance Significant parasite genetic differentiation between provinces shows successful interruption of parasite spread within Thailand, but high diversity along international borders implies a substantial parasite population size in these regions. The provincial origin of P. vivax cases can be reliably determined by genotyping four microsatellite markers, which should be useful for monitoring parasite reintroduction after malaria elimination. This study presents an updated view of the P. vivax populations along the Thai-Myanmar and the Thai-Cambodian borders. Genotyping of parasite samples collected after intensified malaria control demonstrated that despite the decline in overall transmission intensity, the genetic diversity of the P. vivax parasites remained high. Parasite populations from three border provinces showed clear genetic separation. This indicates successful interruption of parasite gene flow within Thailand, but suggests frequent parasite migration across international borders. From the analysis of 10 microsatellite markers, we further refined a set of four that are sufficient for distinguishing the provincial origins of these parasites, which should allow tracking of parasite introduction among these provinces.
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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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Soontarawirat I, Andolina C, Paul R, Day NPJ, Nosten F, Woodrow CJ, Imwong M. Plasmodium vivax genetic diversity and heterozygosity in blood samples and resulting oocysts at the Thai-Myanmar border. Malar J 2017; 16:355. [PMID: 28870214 PMCID: PMC5584506 DOI: 10.1186/s12936-017-2002-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/29/2017] [Indexed: 11/30/2022] Open
Abstract
Background Polyclonal blood-stage infections of Plasmodium vivax are frequent even in low transmission settings, allowing meiotic recombination between heterologous parasites. Empirical data on meiotic products are however lacking. This study examined microsatellites in oocysts derived by membrane feeding of mosquitoes from blood-stage P. vivax infections at the Thai–Myanmar border. Methods Blood samples from patients presenting with vivax malaria were fed to Anopheles cracens by membrane feeding and individual oocysts from midguts were obtained by dissection after 7 days. DNA was extracted from oocysts and parental blood samples and tested by microsatellite analysis. Results A focused study of eight microsatellite markers was undertaken for nine blood stage infections from 2013, for which derived oocysts were studied in six cases. One or more alleles were successfully amplified for 131 oocysts, revealing high levels of allelic diversity in both blood and oocyst stages. Based on standard criteria for defining minor alleles, there was evidence of clear deviation from random mating (inbreeding) with relatively few heterozygous oocysts compared to variance across the entire oocyst population (FIT = 0.89). The main explanation appeared to be natural compartmentalisation at mosquito (FSC = 0.27) and human stages (FCT = 0.68). One single human case produced a total of 431 successfully amplified loci (across 70 oocysts) that were homozygous and identical to parental alleles at all markers, indicating clonal infection and transmission. Heterozygous oocyst alleles were found at 15/176 (8.5%) successfully amplified loci in the other five cases. There was apparently reduced oocyst heterozygosity in individual oocysts compared to diversity within individual mosquitoes (FIS = 0.55), but this may simply reflect the difficulty of detecting minor alleles in oocysts, given the high rate of amplification failure. Inclusion of minor allele peaks (irrespective of height) when matching peaks were found in related blood or oocyst samples, added 11 minor alleles for 9 oocysts, increasing the number of heterozygous loci to 26/176 (14.8%; p = 0.096). Conclusion There was an apparently low level of heterozygous oocysts but this can be explained by a combination of factors: relatively low complexity of parental infection, natural compartmentalisation in humans and mosquitoes, and the methodological challenge of detecting minor alleles. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2002-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ingfar Soontarawirat
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chiara Andolina
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Richard Paul
- Unité de Génétique Fonctionnelle Des Maladies Infectieuses, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris, France.,Centre National de la Recherche Scientifique, URA3012, 28 rue du Docteur Roux, 75724, Paris, France
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Charles J Woodrow
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK.,Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mallika Imwong
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Abstract
Plasmodium vivax is the second most prevalent cause of malaria worldwide and the leading cause of malaria outside of Africa. Although infections are seldom fatal clinical disease can be debilitating and imposes significant health and economic impacts on affected populations. Estimates of transmission and prevalence intensity can be problematic because many episodes of vivax originate from hypnozoite stages in the liver that have remained dormant from previous infections by an unknown mechanism. Lack of treatment options to clear hypnozoites and the ability to infect mosquitoes before disease symptoms present represent major challenges for control and eradication of vivax malaria. Compounding these challenges is the unique biology of P. vivax and limited progress in development of experimental research tools, thereby hindering development of new drugs and vaccines. Renewed emphasis on vivax malaria research is beginning to make progress in overcoming some of these challenges.
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Affiliation(s)
- John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Victoria 3052, Australia
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Wang B, Nyunt MH, Yun SG, Lu F, Cheng Y, Han JH, Ha KS, Park WS, Hong SH, Lim CS, Cao J, Sattabongkot J, Kyaw MP, Cui L, Han ET. Variable number of tandem repeats of 9 Plasmodium vivax genes among Southeast Asian isolates. Acta Trop 2017; 170:161-168. [PMID: 28119047 DOI: 10.1016/j.actatropica.2017.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 02/01/2023]
Abstract
The variable number of tandem repeats (VNTRs) provides valuable information about both the functional and evolutionary aspects of genetic diversity. Comparative analysis of 3 Plasmodium falciparum genomes has shown that more than 9% of its open reading frames (ORFs) harbor VNTRs. Although microsatellites and VNTR genes of P. vivax were reported, the VNTR polymorphism of genes has not been examined widely. In this study, 230 P. vivax genes were analyzed for VNTRs by SERV, and 33 kinds of TR deletions or insertions from 29 P. vivax genes (12.6%) were found. Of these, 9 VNTR fragments from 8 P. vivax genes were used for PCR amplification and sequence analysis to examine the genetic diversity among 134 isolates from four Southeast Asian countries (China, Republic of Korea, Thailand, and Myanmar) with different malaria endemicity. We confirmed the existence of extensive polymorphism of VNTR fragments in field isolates. This detection provides several suitable markers for analysis of the molecular epidemiology of P. vivax field isolates.
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Affiliation(s)
- Bo Wang
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Myat Htut Nyunt
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Department of Medical Research, Yangon 11191, Myanmar
| | - Seung-Gyu Yun
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Feng Lu
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, People's Republic of China
| | - Yang Cheng
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Laboratory of Pathogen Infection and Immunity, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Kwon-Soo Ha
- Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Chae-Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Jun Cao
- Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, People's Republic of China
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea.
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Maneerattanasak S, Gosi P, Krudsood S, Chimma P, Tongshoob J, Mahakunkijcharoen Y, Sukasem C, Imwong M, Snounou G, Khusmith S. Molecular and immunological analyses of confirmed Plasmodium vivax relapse episodes. Malar J 2017; 16:228. [PMID: 28558712 PMCID: PMC5450361 DOI: 10.1186/s12936-017-1877-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Relapse infections resulting from the activation hypnozoites produced by Plasmodium vivax and Plasmodium ovale represent an important obstacle to the successful control of these species. A single licensed drug, primaquine is available to eliminate these liver dormant forms. To date, investigations of vivax relapse infections have been few in number. Results Genotyping, based on polymorphic regions of two genes (Pvmsp1F3 and Pvcsp) and four microsatellite markers (MS3.27, MS3.502, MS6 and MS8), of 12 paired admission and relapse samples from P. vivax-infected patients were treated with primaquine, revealed that in eight of the parasite populations in the admission and relapse samples were homologous, and heterologous in the remaining four patients. The patients’ CYP2D6 genotypes did not suggest that any were poor metabolisers of primaquine. Parasitaemia tended to be higher in the heterologous as compared to the homologous relapse episodes as was the IgG3 response. For the twelve pro- and anti-inflammatory cytokine levels measured for all samples, only those of IL-6 and IL-10 tended to be higher in patients with heterologous as compared to homologous relapses in both admission and relapse episodes. Conclusions The data from this limited number of patients with confirmed relapse episodes mirror previous observations of a significant proportion of heterologous parasites in relapses of P. vivax infections in Thailand. Failure of the primaquine treatment that the patients received is unlikely to be due to poor drug metabolism, and could indicate the presence of P. vivax populations in Thailand with poor susceptibility to 8-aminoquinolines. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1877-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarunya Maneerattanasak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Panita Gosi
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Science-United States Army Military Component, Bangkok, Thailand
| | - Srivicha Krudsood
- Clinical Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pattamawan Chimma
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jarinee Tongshoob
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Yuvadee Mahakunkijcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Georges Snounou
- UPMC Univ Paris 06, Inserm (Institut National de la Santé et de la Recherche Medicale), Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, ERL CNRS 8255 (Centre National de la Recherche Scientifique), Sorbonne Universités, 91 Boulevard de l'Hôpital, 75013, Paris, France
| | - Srisin Khusmith
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand. .,Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand.
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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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Abreha T, Hwang J, Thriemer K, Tadesse Y, Girma S, Melaku Z, Assef A, Kassa M, Chatfield MD, Landman KZ, Chenet SM, Lucchi NW, Udhayakumar V, Zhou Z, Shi YP, Kachur SP, Jima D, Kebede A, Solomon H, Mekasha A, Alemayehu BH, Malone JL, Dissanayake G, Teka H, Auburn S, von Seidlein L, Price RN. Comparison of artemether-lumefantrine and chloroquine with and without primaquine for the treatment of Plasmodium vivax infection in Ethiopia: A randomized controlled trial. PLoS Med 2017; 14:e1002299. [PMID: 28510573 PMCID: PMC5433686 DOI: 10.1371/journal.pmed.1002299] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/03/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Recent efforts in malaria control have resulted in great gains in reducing the burden of Plasmodium falciparum, but P. vivax has been more refractory. Its ability to form dormant liver stages confounds control and elimination efforts. To compare the efficacy and safety of primaquine regimens for radical cure, we undertook a randomized controlled trial in Ethiopia. METHODS AND FINDINGS Patients with normal glucose-6-phosphate dehydrogenase status with symptomatic P. vivax mono-infection were enrolled and randomly assigned to receive either chloroquine (CQ) or artemether-lumefantrine (AL), alone or in combination with 14 d of semi-supervised primaquine (PQ) (3.5 mg/kg total). A total of 398 patients (n = 104 in the CQ arm, n = 100 in the AL arm, n = 102 in the CQ+PQ arm, and n = 92 in the AL+PQ arm) were followed for 1 y, and recurrent episodes were treated with the same treatment allocated at enrolment. The primary endpoints were the risk of P. vivax recurrence at day 28 and at day 42. The risk of recurrent P. vivax infection at day 28 was 4.0% (95% CI 1.5%-10.4%) after CQ treatment and 0% (95% CI 0%-4.0%) after CQ+PQ. The corresponding risks were 12.0% (95% CI 6.8%-20.6%) following AL alone and 2.3% (95% CI 0.6%-9.0%) following AL+PQ. On day 42, the risk was 18.7% (95% CI 12.2%-28.0%) after CQ, 1.2% (95% CI 0.2%-8.0%) after CQ+PQ, 29.9% (95% CI 21.6%-40.5%) after AL, and 5.9% (95% CI 2.4%-13.5%) after AL+PQ (overall p < 0.001). In those not prescribed PQ, the risk of recurrence by day 42 appeared greater following AL treatment than CQ treatment (HR = 1.8 [95% CI 1.0-3.2]; p = 0.059). At the end of follow-up, the incidence rate of P. vivax was 2.2 episodes/person-year for patients treated with CQ compared to 0.4 for patients treated with CQ+PQ (rate ratio: 5.1 [95% CI 2.9-9.1]; p < 0.001) and 2.3 episodes/person-year for AL compared to 0.5 for AL+PQ (rate ratio: 6.4 [95% CI 3.6-11.3]; p < 0.001). There was no difference in the occurrence of adverse events between treatment arms. The main limitations of the study were the early termination of the trial and the omission of haemoglobin measurement after day 42, resulting in an inability to estimate the cumulative risk of anaemia. CONCLUSIONS Despite evidence of CQ-resistant P. vivax, the risk of recurrence in this study was greater following treatment with AL unless it was combined with a supervised course of PQ. PQ combined with either CQ or AL was well tolerated and reduced recurrence of vivax malaria by 5-fold at 1 y. TRIAL REGISTRATION ClinicalTrials.gov NCT01680406.
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Affiliation(s)
- Tesfay Abreha
- ICAP, Columbia University Mailman School of Public Health, Addis Ababa, Ethiopia
| | - Jimee Hwang
- US President’s Malaria Initiative, Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Global Health Group, University of California San Francisco, San Francisco, California, United States of America
| | - Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- * E-mail:
| | - Yehualashet Tadesse
- ICAP, Columbia University Mailman School of Public Health, Addis Ababa, Ethiopia
| | - Samuel Girma
- ICAP, Columbia University Mailman School of Public Health, Addis Ababa, Ethiopia
| | - Zenebe Melaku
- ICAP, Columbia University Mailman School of Public Health, Addis Ababa, Ethiopia
| | - Ashenafi Assef
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Moges Kassa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mark D. Chatfield
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Keren Z. Landman
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stella M. Chenet
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Naomi W. Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Zhiyong Zhou
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ya Ping Shi
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - S. Patrick Kachur
- Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Daddi Jima
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Amha Kebede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Addis Mekasha
- Oromia Regional Health Bureau, Addis Ababa, Ethiopia
| | | | - Joseph L. Malone
- US President’s Malaria Initiative, Malaria Branch, Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Gunewardena Dissanayake
- US President’s Malaria Initiative, US Agency for International Development, Addis Ababa, Ethiopia
| | - Hiwot Teka
- US President’s Malaria Initiative, US Agency for International Development, Addis Ababa, Ethiopia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Lorenz von Seidlein
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Fola AA, Harrison GLA, Hazairin MH, Barnadas C, Hetzel MW, Iga J, Siba PM, Mueller I, Barry AE. Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea. Am J Trop Med Hyg 2017; 96:630-641. [PMID: 28070005 DOI: 10.4269/ajtmh.16-0716] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Plasmodium falciparum and Plasmodium vivax have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of P. vivax and P. falciparum throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive P. vivax samples were genotyped at PvMS16 and PvmspF3, and 758 positive P. falciparum samples were genotyped at Pfmsp2. The data were analyzed for multiplicity of infection (MOI) and genetic diversity. Overall, P. vivax had higher polyclonality (71%) and mean MOI (2.32) than P. falciparum (20%, 1.39). These measures were significantly associated with prevalence for P. falciparum but not for P. vivax. The genetic diversity of P. vivax (PvMS16: expected heterozygosity = 0.95, 0.85-0.98; PvMsp1F3: 0.78, 0.66-0.89) was higher and less variable than that of P. falciparum (Pfmsp2: 0.89, 0.65-0.97). Significant associations of MOI with allelic richness (rho = 0.69, P = 0.009) and expected heterozygosity (rho = 0.87, P < 0.001) were observed for P. falciparum. Conversely, genetic diversity was not correlated with polyclonality nor mean MOI for P. vivax. The results demonstrate higher complexity of infection and genetic diversity of P. vivax across the country. Although P. falciparum shows a strong association of these parameters with prevalence, a lack of association was observed for P. vivax and is consistent with higher potential for outcrossing of this species.
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Affiliation(s)
- Abebe A Fola
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - G L Abby Harrison
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mita Hapsari Hazairin
- Department of Epidemiology and Preventative Medicine, Monash University, Clayton, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Céline Barnadas
- Statens Serum Institut, Copenhagen, Denmark.,European Public Health Microbiology (EUPHEM) Training Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Manuel W Hetzel
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Jonah Iga
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ivo Mueller
- Institut Pasteur, Paris, France.,Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Alyssa E Barry
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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Fontoura PS, Finco BF, Lima NF, de Carvalho JF, Vinetz JM, Castro MC, Ferreira MU. Reactive Case Detection for Plasmodium vivax Malaria Elimination in Rural Amazonia. PLoS Negl Trop Dis 2016; 10:e0005221. [PMID: 27941968 PMCID: PMC5179126 DOI: 10.1371/journal.pntd.0005221] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/22/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022] Open
Abstract
Background Malaria burden in Brazil has reached its lowest levels in 35 years and Plasmodium vivax now accounts for 84% of cases countrywide. Targeting residual malaria transmission entrenched in the Amazon is the next major challenge for ongoing elimination efforts. Better strategies are urgently needed to address the vast reservoir of asymptomatic P. vivax carriers in this and other areas approaching malaria elimination. Methods We evaluated a reactive case detection (RCD) strategy tailored for P. vivax transmission in farming settlements in the Amazon Basin of Brazil. Over six months, 41 cases detected by passive surveillance triggered four rounds of RCD (0, 30, 60, and 180 days after index case enrollment), using microscopy- and quantitative real-time polymerase chain reaction (qPCR)-based diagnosis, comprising subjects sharing the household (HH) with the index case (n = 163), those living in the 5 nearest HHs within 3 km (n = 878), and individuals from 5 randomly chosen control HHs located > 5 km away from index cases (n = 841). Correlates of infection were identified with mixed-effects logistic regression models. Molecular genotyping was used to infer local parasite transmission networks. Principal findings/Conclusions Subjects in index and neighbor HHs were significantly more likely to be parasitemic than control HH members, after adjusting for potential confounders, and together harbored > 90% of the P. vivax biomass in study subjects. Clustering patterns were temporally stable. Four rounds of microscopy-based RCD would identify only 49.5% of the infections diagnosed by qPCR, but 76.8% of the total parasite biomass circulating in the proximity of index HHs. However, control HHs accounted for 27.6% of qPCR-positive samples, 92.6% of them from asymptomatic carriers beyond the reach of RCD. Molecular genotyping revealed high P. vivax diversity, consistent with complex transmission networks and multiple sources of infection within clusters, potentially complicating malaria elimination efforts. Addressing the vast reservoir of asymptomatic Plasmodium vivax carriers clustered in hard-to-reach rural communities is a major challenge faced by countries approaching malaria elimination across Latin America and Asia. Routine surveillance targets subjects presenting with fever or reporting recent fever, but overlooks asymptomatic infections that might be otherwise detected by periodic mass blood surveys of the entire population at risk. Here we show that subjects living in close proximity to malaria cases detected by routine passive surveillance are much more likely to carry both symptomatic and asymptomatic infections than randomly selected inhabitants in the same farming settlements in the Amazon Basin of Brazil. Four rounds of microscopy-based screening for malaria parasites targeted at these high-risk subjects would identify 49.5% of the parasite carriers (who together harbored 76.8% of the total P. vivax biomass circulating in the proximity of index cases) detected by a more sensitive molecular method. Whether subpatent and asymptomatic carriers outside the identified clusters of symptomatic infections, beyond the reach of our screening, represent a significant parasite reservoir remains undetermined. The extensive genetic diversity found in local P. vivax populations suggests that multiple sources of infection fuel ongoing residual transmission within malaria clusters, further complicating current elimination efforts.
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Affiliation(s)
- Pablo S. Fontoura
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Bruna F. Finco
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Jaques F. de Carvalho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Joseph M. Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, United States of America
- Alexander von Humboldt Institute of Tropical Medicine and Faculty of Sciences, Department of Cellular and Molecular Sciences, Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Márcia C. Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, United States of America
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- * E-mail:
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Zhu X, Zhao P, Wang S, Liu F, Liu J, Wang J, Yang Z, Yan G, Fan Q, Cao Y, Cui L. Analysis of Pvama1 genes from China-Myanmar border reveals little regional genetic differentiation of Plasmodium vivax populations. Parasit Vectors 2016; 9:614. [PMID: 27899135 PMCID: PMC5129220 DOI: 10.1186/s13071-016-1899-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Background With the premise of diminishing parasite genetic diversity following the reduction of malaria incidence, the analysis of polymorphic antigenic markers may provide important information about the impact of malaria control on local parasite populations. Here we evaluated the genetic diversity of Plasmodium vivax apical membrane antigen 1 (Pvama1) gene in a parasite population from the China-Myanmar border and compared it with global P. vivax populations. Methods We performed evolutionary analysis to examine the genetic diversity, natural selection, and population differentiation of 73 Pvama1 sequences acquired from the China-Myanmar border as well as 615 publically available Pvama1 sequences from seven global P. vivax populations. Results A total of 308 Pvama1 haplotypes were identified among the global P. vivax isolates. The overall nucleotide diversity of Pvama1 gene among the 73 China-Myanmar border parasite isolates was 0.008 with 41 haplotypes being identified (Hd = 0.958). Domain I (DI) harbored the majority (26/33) of the polymorphic sites. The McDonald Kreitman test showed a significant positive selection across the ectodomain and the DI of Pvama1. The fixation index (FST) estimation between the China-Myanmar border, Thailand (0.01) and Myanmar (0.10) showed only slight geographical genetic differentiation. Notably, the Sal-I haplotype was not detected in any of the analyzed global isolates, whereas the Belem strain was restricted to the Thai population. The detected mutations are mapped outside the overlapped region of the predicted B-cell epitopes and intrinsically unstructured/disordered regions. Conclusions This study revealed high levels of genetic diversity of Pvama1 in the P. vivax parasite population from the China-Myanmar border with DI displaying stronger diversifying selection than other domains. There were low levels of population subdivision among parasite populations from the Greater Mekong Subregion. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1899-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaotong Zhu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, 110122, China
| | - Pan Zhao
- Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, 110122, China
| | - Si Wang
- Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, 110122, China
| | - Fei Liu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, 110122, China
| | - Jun Liu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, 110122, China
| | - Jian Wang
- Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, 110122, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, CA, USA
| | - Qi Fan
- Dalian Institute of Biotechnology, Dalian, Liaoning, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, 110122, China.
| | - Liwang Cui
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, 110122, China. .,Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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Friedrich LR, Popovici J, Kim S, Dysoley L, Zimmerman PA, Menard D, Serre D. Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax. PLoS Negl Trop Dis 2016; 10:e0004526. [PMID: 27018585 PMCID: PMC4809505 DOI: 10.1371/journal.pntd.0004526] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plasmodium vivax is the most widely distributed human malaria parasite with 2.9 billion people living in endemic areas. Despite intensive malaria control efforts, the proportion of cases attributed to P. vivax is increasing in many countries. Genetic analyses of the parasite population and its dynamics could provide an assessment of the efficacy of control efforts, but, unfortunately, these studies are limited in P. vivax by the lack of informative markers and high-throughput genotyping methods. METHODOLOGY/PRINCIPAL FINDINGS We developed a sequencing-based assay to simultaneously genotype more than 100 SNPs and applied this approach to ~500 P. vivax-infected individuals recruited across nine locations in Cambodia between 2004 and 2013. Our analyses showed that the vast majority of infections are polyclonal (92%) and that P. vivax displays high genetic diversity in Cambodia without apparent geographic stratification. Interestingly, our analyses also revealed that the proportion of monoclonal infections significantly increased between 2004 and 2013, possibly suggesting that malaria control strategies in Cambodia may be successfully affecting the parasite population. CONCLUSIONS/SIGNIFICANCE Our findings demonstrate that this high-throughput genotyping assay is efficient in characterizing P. vivax diversity and can provide valuable insights to assess the efficacy of malaria elimination programs or to monitor the spread of specific parasites.
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Affiliation(s)
- Lindsey R. Friedrich
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Jean Popovici
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Saorin Kim
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lek Dysoley
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Peter A. Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Didier Menard
- Unite d’Epidemiologie Moleculaire, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- * E-mail:
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Kim JY, Goo YK, Zo YG, Ji SY, Trimarsanto H, To S, Clark TG, Price RN, Auburn S. Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years. PLoS One 2016; 11:e0151514. [PMID: 26990869 PMCID: PMC4798397 DOI: 10.1371/journal.pone.0151514] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/29/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Vivax malaria was successfully eliminated from the Republic of Korea (ROK) in the late 1970s but re-emerged in 1993. Two decades later as the ROK enters the final stages of malaria elimination, dedicated surveillance of the local P. vivax population is critical. We apply a population genetic approach to gauge P. vivax transmission dynamics in the ROK between 2010 and 2012. METHODOLOGY/PRINCIPAL FINDINGS P. vivax positive blood samples from 98 autochthonous cases were collected from patients attending health centers in the ROK in 2010 (n = 27), 2011 (n = 48) and 2012 (n = 23). Parasite genotyping was undertaken at 9 tandem repeat markers. Although not reaching significance, a trend of increasing population diversity was observed from 2010 (HE = 0.50 ± 0.11) to 2011 (HE = 0.56 ± 0.08) and 2012 (HE = 0.60 ± 0.06). Conversely, linkage disequilibrium declined during the same period: IAS = 0.15 in 2010 (P = 0.010), 0.09 in 2011 (P = 0.010) and 0.05 in 2012 (P = 0.010). In combination with data from other ROK studies undertaken between 1994 and 2007, our results are consistent with increasing parasite divergence since re-emergence. Polyclonal infections were rare (3% infections) suggesting that local out-crossing alone was unlikely to explain the increased divergence. Cases introduced from an external reservoir may therefore have contributed to the increased diversity. Aside from one isolate, all infections carried a short MS20 allele (142 or 149 bp), not observed in other studies in tropical endemic countries despite high diversity, inferring that these regions are unlikely reservoirs. CONCLUSIONS Whilst a number of factors may explain the observed population genetic trends, the available evidence suggests that an external geographic reservoir with moderate diversity sustains the majority of P. vivax infection in the ROK, with important implications for malaria elimination.
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Affiliation(s)
- Jung-Yeon Kim
- Division of Malaria and Parasitic Diseases, National Institute of Health, Korea CDC, Osong Saeng-myeong, 2 ro, Osong Health Technology Administration, Osong, Republic of Korea
| | - Youn-Kyoung Goo
- Division of Malaria and Parasitic Diseases, National Institute of Health, Korea CDC, Osong Saeng-myeong, 2 ro, Osong Health Technology Administration, Osong, Republic of Korea
- Department of Parasitology and Tropical Medicine, Kyungpook National University School of Medicine, Daegu, 700–422, Republic of Korea
| | - Young-Gun Zo
- Department of Molecular Parasitology, Sungkyunkwan University School of Medicine and Center for Molecular Medicine, Samsung Biomedical Research Institute, Suwon, Gyeonggi-do 440–746, Republic of Korea
| | - So-Young Ji
- Division of Malaria and Parasitic Diseases, National Institute of Health, Korea CDC, Osong Saeng-myeong, 2 ro, Osong Health Technology Administration, Osong, Republic of Korea
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta Pusat, 10430, Indonesia
- Agency for Assessment and Application of Technology, Jl. MH Thamrin 8, Jakarta, 10340, Indonesia
| | - Sheren To
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810, Australia
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810, Australia
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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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Abstract
The relapsing peculiarity of Plasmodium vivax is one of the prime reasons for sustained global malaria transmission. Global containment of P. vivax is more challenging and crucial compared to other species for achieving total malaria control/elimination. Primaquine (PQ) failure and P. vivax relapse is a major global public health concern. Identification and characterization of different relapse strains of P. vivax prevalent across the globe should be one of the thrust areas in malaria research. Despite renewed and rising global concern by researchers on this once 'neglected' species, research and development on the very topic of P. vivax reappearance remains inadequate. Many malaria endemic countries have not mandated routine glucose-6-phosphate dehydrogenase (G6PD) testing before initiating PQ radical cure in P. vivax malaria. This results in either no PQ prescription or thoughtless prescription and administration of PQ to P. vivax patients by healthcare providers without being concerned about patients' G6PD status and associated complications. It is imperative to ascertain the G6PD status and optimum dissemination of PQ radical cure in all cases of P. vivax malaria across the globe. There persists a compelling need to develop/validate a rapid, easy-to-perform, easy-to-interpret, quality controllable, robust, and cost-effective G6PD assay. High-dose PQ of both standard and short duration appears to be safe and more effective for preventing relapses and should be practiced among patients with normal G6PD activity. Multicentric studies involving adequately representative populations across the globe with reference PQ dose must be carried out to determine the true distribution of PQ failure. Study proving role of cytochrome P450-2D6 gene in PQ metabolism and association of CYP2D6 metabolizer phenotypes and P. vivax relapse is of prime importance and should be carried forward in multicentric systems across the globe.
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Affiliation(s)
- Kumar Rishikesh
- a Department of Medicine , Kasturba Medical College, Manipal University , Madhav Nagar, Manipal 576104 , Karnataka , India.,b Tropical Medicine Research Centre, Kasturba Medical College, Manipal University , Madhav Nagar, Manipal 576104 , Karnataka , India
| | - Kavitha Saravu
- a Department of Medicine , Kasturba Medical College, Manipal University , Madhav Nagar, Manipal 576104 , Karnataka , India.,b Tropical Medicine Research Centre, Kasturba Medical College, Manipal University , Madhav Nagar, Manipal 576104 , Karnataka , India
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Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam. PLoS Negl Trop Dis 2016; 10:e0004434. [PMID: 26872387 PMCID: PMC4752448 DOI: 10.1371/journal.pntd.0004434] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/14/2016] [Indexed: 12/03/2022] Open
Abstract
Background The burden of malaria in Vietnam has drastically reduced, prompting the National Malaria Control Program to officially engage in elimination efforts. Plasmodium vivax is becoming increasingly prevalent, remaining a major problem in the country's central and southern provinces. A better understanding of P. vivax genetic diversity and structure of local parasite populations will provide baseline data for the evaluation and improvement of current efforts for control and elimination. The aim of this study was to examine the population genetics and structure of P. vivax isolates from four communities in Tra Leng commune, Nam Tra My district in Quang Nam, Central Vietnam. Methodology/Principal Findings P. vivax mono infections collected from 234 individuals between April 2009 and December 2010 were successfully analyzed using a panel of 14 microsatellite markers. Isolates displayed moderate genetic diversity (He = 0.68), with no significant differences between study communities. Polyclonal infections were frequent (71.4%) with a mean multiplicity of infection of 1.91 isolates/person. Low but significant genetic differentiation (FST value from -0.05 to 0.18) was observed between the community across the river and the other communities. Strong linkage disequilibrium ( IAS = 0.113, p < 0.001) was detected across all communities, suggesting gene flow within and among them. Using multiple approaches, 101 haplotypes were grouped into two genetic clusters, while 60.4% of haplotypes were admixed. Conclusions/Significance In this area of Central Vietnam, where malaria transmission has decreased significantly over the past decade, there was moderate genetic diversity and high occurrence of polyclonal infections. Local human populations have frequent social and economic interactions that facilitate gene flow and inbreeding among parasite populations, while decreasing population structure. Findings provide important information on parasites populations circulating in the study area and are relevant to current malaria elimination efforts. In Vietnam, Plasmodium vivax (P. vivax) is the second most frequent human malaria parasite and a major obstacle to countrywide malaria elimination. Knowing the local parasite structure is useful for elimination efforts. Therefore, we analyzed, with a panel of 14 microsatellite markers, 234 P. vivax mono infections in blood samples collected from 4 communities in central Vietnam. Genetic diversity in the population was moderate; a high occurrence of polyclonal infections and significant linkage disequilibrium were detected, suggesting inbreeding or recombination between highly related haplotypes. In addition, both genetic differentiation and population structure was low and only detected between communities at each side of the river. Those results suggest gene flow between study communities with the river defining a moderate geographical barrier. Future studies should determine how this genetic variation is maintained in an area of extremely low transmission.
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Delgado-Ratto C, Gamboa D, Soto-Calle VE, Van den Eede P, Torres E, Sánchez-Martínez L, Contreras-Mancilla J, Rosanas-Urgell A, Rodriguez Ferrucci H, Llanos-Cuentas A, Erhart A, Van geertruyden JP, D’Alessandro U. Population Genetics of Plasmodium vivax in the Peruvian Amazon. PLoS Negl Trop Dis 2016; 10:e0004376. [PMID: 26766548 PMCID: PMC4713096 DOI: 10.1371/journal.pntd.0004376] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
Background Characterizing the parasite dynamics and population structure provides useful information to understand the dynamic of transmission and to better target control interventions. Despite considerable efforts for its control, vivax malaria remains a major health problem in Peru. In this study, we have explored the population genetics of Plasmodium vivax isolates from Iquitos, the main city in the Peruvian Amazon, and 25 neighbouring peri-urban as well as rural villages along the Iquitos-Nauta Road. Methodology/ Results From April to December 2008, 292 P. vivax isolates were collected and successfully genotyped using 14 neutral microsatellites. Analysis of the molecular data revealed a similar proportion of monoclonal and polyclonal infections in urban areas, while in rural areas monoclonal infections were predominant (p = 0.002). Multiplicity of infection was higher in urban (MOI = 1.5–2) compared to rural areas (MOI = 1) (p = 0.003). The level of genetic diversity was similar in all areas (He = 0.66–0.76, p = 0.32) though genetic differentiation between areas was substantial (PHIPT = 0.17, p<0.0001). Principal coordinate analysis showed a marked differentiation between parasites from urban and rural areas. Linkage disequilibrium was detected in all the areas ( IAs = 0.08–0.49, for all p<0.0001). Gene flow among the areas was stablished through Bayesian analysis of migration models. Recent bottleneck events were detected in 4 areas and a recent parasite expansion in one of the isolated areas. In total, 87 unique haplotypes grouped in 2 or 3 genetic clusters described a sub-structured parasite population. Conclusion/Significance Our study shows a sub-structured parasite population with clonal propagation, with most of its components recently affected by bottleneck events. Iquitos city is the main source of parasite spreading for all the peripheral study areas. The routes of transmission and gene flow and the reduction of the parasite population described are important from the public health perspective as well for the formulation of future control policies. We present the population genetics of malaria vivax parasites in a large area of the Peruvian Amazon. Our results showed that the parasite population had a predominant clonal propagation, reproducing themselves with identically or closely related parasites; therefore, the same genetic characteristics are maintained in the offspring. The clonal propagation may favour the higher levels of genetic differentiation among the parasites from isolated areas compared to areas where human migration is common. The patterns of gene flow have been established, finding Iquitos city as a reservoir of parasite genetic variability. Moreover, a recent reduction of the parasite population was observed in areas where recent control activities were performed. This research provides a picture of the nature and dynamics of the parasite population which have a significant impact in the malaria epidemiology; therefore, this knowledge is crucial for the development of efficient control policies.
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Affiliation(s)
| | - Dionicia Gamboa
- Institute of Tropical Medicine 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
| | - Veronica E. Soto-Calle
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter Van den Eede
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Eliana Torres
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis Sánchez-Martínez
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Juan Contreras-Mancilla
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Alejandro Llanos-Cuentas
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Annette Erhart
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Umberto D’Alessandro
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit, Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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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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50
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Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. PLoS One 2015; 10:e0140780. [PMID: 26468643 PMCID: PMC4607408 DOI: 10.1371/journal.pone.0140780] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/30/2015] [Indexed: 12/21/2022] Open
Abstract
Background P. vivax is an important public health burden in Ethiopia, accounting for almost half of all malaria cases. Owing to heterogeneous transmission across the country, a stronger evidence base on local transmission dynamics is needed to optimise allocation of resources and improve malaria interventions. Methodology and Principal Findings In a pilot evaluation of local level P. vivax molecular surveillance in southern Ethiopia, the diversity and population structure of isolates collected between May and November 2013 were investigated. Blood samples were collected from microscopy positive P. vivax patients recruited to clinical and cross-sectional surveys from four sites: Arbaminch, Halaba, Badawacho and Hawassa. Parasite genotyping was undertaken at nine tandem repeat markers. Eight loci were successfully genotyped in 197 samples (between 36 and 59 per site). Heterogeneity was observed in parasite diversity and structure amongst the sites. Badawacho displayed evidence of unstable transmission, with clusters of identical clonal infections. Linkage disequilibrium in Badawacho was higher (IAS = 0.32, P = 0.010) than in the other populations (IAS range = 0.01–0.02) and declined markedly after adjusting for identical infections (IAS = 0.06, P = 0.010). Other than Badawacho (HE = 0.70), population diversity was equivalently high across the sites (HE = 0.83). Polyclonal infections were more frequent in Hawassa (67%) than the other populations (range: 8–44%). Despite the variable diversity, differentiation between the sites was low (FST range: 5 x 10−3–0.03). Conclusions Marked variation in parasite population structure likely reflects differing local transmission dynamics. Parasite genotyping in these heterogeneous settings has potential to provide important complementary information with which to optimise malaria control interventions.
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