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Dombrowski JG, Acford-Palmer H, Campos M, Separovic EPM, Epiphanio S, Clark TG, Campino S, Marinho CRF. Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100407. [PMID: 36844021 PMCID: PMC9950542 DOI: 10.1016/j.lana.2022.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background Each year, 92 million pregnant women are at risk of contracting malaria during pregnancy, with the underestimation of the mortality and morbidity burden associated with Plasmodium vivax. During pregnancy, P. vivax infection is associated with low birth weight, maternal anaemia, premature delivery, and stillbirth. In the State of Acre (Brazil), high transmission leaves pregnant women at greater risk of contracting malaria and having a greater number of recurrences. The study of genetic diversity and the association of haplotypes with adverse pregnancy effects is of great importance for the control of the disease. Here we investigate the genetic diversity of P. vivax parasites infecting pregnant women across their pregnancies. Methods P. vivax DNA was extracted from 330 samples from 177 women followed during pregnancy, collected in the State of Acre, Brazil. All samples were negative for Plasmodium falciparum DNA. Sequence data for the Pvmsp1 gene was analysed alongside data from six microsatellite (MS) markers. Allelic frequencies, haplotype frequencies, expected heterozygosity (HE) were calculated. Whole genome sequencing (WGS) was conducted on four samples from pregnant women and phylogenetic analysis performed with other samples from South American regions. Findings Initially, the pregnant women were stratified into two groups-1 recurrence and 2 or more recurrences-in which no differences were observed in clinical gestational outcomes or in placental histological changes between the two groups. Then we evaluated the parasites genetically. An average of 18.5 distinct alleles were found at each of the MS loci, and the HE calculated for each marker indicates a high genetic diversity occurring within the population. There was a high percentage of polyclonal infections (61.7%, 108/175), and one haplotype (H1) occurred frequently (20%), with only 9 of the haplotypes appearing in more than one patient. Interpretation Most pregnant women had polyclonal infections that could be the result of relapses and/or re-infections. The high percentage of H1 parasites, along with the low frequency of many other haplotypes are suggestive of a clonal expansion. Phylogenetic analysis shows that P. vivax population within pregnant women clustered with other Brazilian samples in the region. Funding FAPESP and CNPq - Brazil.
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Affiliation(s)
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Sabrina Epiphanio
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taane Gregory Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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2
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [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: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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3
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Taylor AR, Watson JA, Chu CS, Puaprasert K, Duanguppama J, Day NPJ, Nosten F, Neafsey DE, Buckee CO, Imwong M, White NJ. Resolving the cause of recurrent Plasmodium vivax malaria probabilistically. Nat Commun 2019; 10:5595. [PMID: 31811128 PMCID: PMC6898227 DOI: 10.1038/s41467-019-13412-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/29/2019] [Indexed: 11/23/2022] Open
Abstract
Relapses arising from dormant liver-stage Plasmodium vivax parasites (hypnozoites) are a major cause of vivax malaria. However, in endemic areas, a recurrent blood-stage infection following treatment can be hypnozoite-derived (relapse), a blood-stage treatment failure (recrudescence), or a newly acquired infection (reinfection). Each of these requires a different prevention strategy, but it was not previously possible to distinguish between them reliably. We show that individual vivax malaria recurrences can be characterised probabilistically by combined modelling of time-to-event and genetic data within a framework incorporating identity-by-descent. Analysis of pooled patient data on 1441 recurrent P. vivax infections in 1299 patients on the Thailand-Myanmar border observed over 1000 patient follow-up years shows that, without primaquine radical curative treatment, 3 in 4 patients relapse. In contrast, after supervised high-dose primaquine only 1 in 40 relapse. In this region of frequent relapsing P. vivax, failure rates after supervised high-dose primaquine are significantly lower (∼3%) than estimated previously.
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Affiliation(s)
- Aimee R Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - James A Watson
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Cindy S Chu
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mae Sot, Tak Province, 63110, Thailand
| | - Kanokpich Puaprasert
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jureeporn Duanguppama
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mae Sot, Tak Province, 63110, Thailand
| | - Daniel E Neafsey
- 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
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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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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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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6
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Longley RJ, Sripoorote P, Chobson P, Saeseu T, Sukasem C, Phuanukoonnon S, Nguitragool W, Mueller I, Sattabongkot J. High Efficacy of Primaquine Treatment for Plasmodium vivax in Western Thailand. Am J Trop Med Hyg 2016; 95:1086-1089. [PMID: 27601524 DOI: 10.4269/ajtmh.16-0410] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/25/2016] [Indexed: 11/07/2022] Open
Abstract
Primaquine is the only licensed antimalarial drug that is capable of clearing dormant Plasmodium vivax liver stage parasites. To date, there is no clear evidence of resistance of the liver stage parasite against this drug, because of the difficulty in ascertaining the cause of recurrent infection. We followed 52 Thai P. vivax patients for 9 months after directly observed treatment of 15 mg primaquine daily for 14 days. Blood samples taken at 2-4 weekly intervals were assessed by microscopy and polymerase chain reaction (PCR) for the presence of parasites. Only four of 52 (7.7%) volunteers had recurrent P. vivax infections, all at least 8 weeks after treatment. This demonstrates that primaquine retains a high efficacy in this population. Although a risk of new infections could not be ruled out, parasite genotyping at two polymorphic markers suggested a high probability of late relapsing infections in these volunteers. Continued monitoring of primaquine efficacy in this region is advisable.
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Affiliation(s)
- Rhea J Longley
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Piyarat Sripoorote
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pornpimol Chobson
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Teerawat Saeseu
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suparat Phuanukoonnon
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia.,ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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7
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Silvino ACR, Costa GL, de Araújo FCF, Ascher DB, Pires DEV, Fontes CJF, Carvalho LH, de Brito CFA, Sousa TN. Variation in Human Cytochrome P-450 Drug-Metabolism Genes: A Gateway to the Understanding of Plasmodium vivax Relapses. PLoS One 2016; 11:e0160172. [PMID: 27467145 PMCID: PMC4965052 DOI: 10.1371/journal.pone.0160172] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/14/2016] [Indexed: 01/08/2023] Open
Abstract
Although Plasmodium vivax relapses are classically associated with hypnozoite activation, it has been proposed that a proportion of these cases are due to primaquine (PQ) treatment failure caused by polymorphisms in cytochrome P-450 2D6 (CYP2D6). Here, we present evidence that CYP2D6 polymorphisms are implicated in PQ failure, which was reinforced by findings in genetically similar parasites, and may explain a number of vivax relapses. Using a computational approach, these polymorphisms were predicted to affect the activity of CYP2D6 through changes in the structural stability that could lead to disruption of the PQ-enzyme interactions. Furthermore, because PQ is co-administered with chloroquine (CQ), we investigated whether CQ-impaired metabolism by cytochrome P-450 2C8 (CYP2C8) could also contribute to vivax recurrences. Our results show that CYP2C8-mutated patients frequently relapsed early (<42 days) and had a higher proportion of genetically similar parasites, suggesting the possibility of recrudescence due to CQ therapeutic failure. These results highlight the importance of pharmacogenetic studies as a tool to monitor the efficacy of antimalarial therapy.
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Affiliation(s)
- Ana Carolina Rios Silvino
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Luiz Costa
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Carolina Faustino de Araújo
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - David Benjamin Ascher
- Biosystems Informatics Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Douglas Eduardo Valente Pires
- Biosystems Informatics Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | | | - Luzia Helena Carvalho
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Tais Nobrega Sousa
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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8
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Do mixed infections matter? Assessing virulence of mixed-clone infections in experimental human and murine malaria. INFECTION GENETICS AND EVOLUTION 2015; 36:82-91. [PMID: 26334940 DOI: 10.1016/j.meegid.2015.08.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Malaria parasites within an individual infection often consist of multiple strains (clonal populations) of a single species, which have the potential to interact both with one another, and with the host immune system. Several effects of these interactions have been measured in different parasite systems including competition and mutualism; however, direct observation of these effects in human malaria has been limited by sampling complexities and inherent ethical limitations. METHODS Using multiple complementary epidemiological models, we propose a suite of analyses to more fully utilize data from challenge experiments, and re-examine historical human challenge studies with mixed-strain Plasmodium vivax inocula. We then compare these results with murine model systems using mixed-strain Plasmodium yoelii or Plasmodium chabaudi, to explore the utility of these methods in fully utilizing these data, including the first quantitative estimates of effect sizes for mixed-strain parasitemia. These models also provide a method to assess consistency within these animal model systems. RESULTS We find that amongst a limited set of P. vivax (incubation time) and P. yoelii infections (time-to-mortality), survival times at a study population-level are intermediate between each single-clone infection, and are not dominated by the more virulent clone; in P. vivax relapses, mixed clone infections also show intermediate survival curves. In these infections, the results strongly suggest that highly virulent clones have their virulence attenuated by the presence of less-virulent clones. The analysis of multiple experiments with P. chabaudi suggests greater nuances in the interactions between strains, and that mortality and time-to-event in mixed-strain infections are both indistinguishable from single infections with the more virulent strain. CONCLUSIONS These divergent dynamics support earlier work that suggested drivers of virulence may differ in fundamental ways between malaria species that are reticulocyte-specific and those that readily infect all red blood cell stages which should be studied in greater detail. The effect sizes (magnitude of biological effects) from these analyses are significant, and suggest the potential for important gains in malaria control by greater incorporation of evolutionary epidemiology theory. Moreover, we suggest that using these epidemiological models may generally allow fuller use of data from experimentally challenging animal model experiments.
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Manrique P, Hoshi M, Fasabi M, Nolasco O, Yori P, Calderón M, Gilman RH, Kosek MN, Vinetz JM, Gamboa D. Assessment of an automated capillary system for Plasmodium vivax microsatellite genotyping. Malar J 2015; 14:326. [PMID: 26293655 PMCID: PMC4546211 DOI: 10.1186/s12936-015-0842-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several platforms have been used to generate the primary data for microsatellite analysis of malaria parasite genotypes. Each has relative advantages but share a limitation of being time- and cost-intensive. A commercially available automated capillary gel cartridge system was assessed in the microsatellite analysis of Plasmodium vivax diversity in the Peruvian Amazon. METHODS The reproducibility and accuracy of a commercially-available automated capillary system, QIAxcel, was assessed using a sequenced PCR product of 227 base pairs. This product was measured 42 times, then 27 P. vivax samples from Peruvian Amazon subjects were analyzed with this instrument using five informative microsatellites. Results from the QIAxcel system were compared with a Sanger-type sequencing machine, the ABI PRISM(®) 3100 Genetic Analyzer. RESULTS Significant differences were seen between the sequenced amplicons and the results from the QIAxcel instrument. Different runs, plates and cartridges yielded significantly different results. Additionally, allele size decreased with each run by 0.045, or 1 bp, every three plates. QIAxcel and ABI PRISM systems differed in giving different values than those obtained by ABI PRISM, and too many (i.e. inaccurate) alleles per locus were also seen with the automated instrument. CONCLUSIONS While P. vivax diversity could generally be estimated using an automated capillary gel cartridge system, the data demonstrate that this system is not sufficiently precise for reliably identifying parasite strains via microsatellite analysis. This conclusion reached after systematic analysis was due both to inadequate precision and poor reproducibility in measuring PCR product size.
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Affiliation(s)
- Paulo Manrique
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Mari Hoshi
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | | | - Oscar Nolasco
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Pablo Yori
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Martiza Calderón
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Robert H Gilman
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Margaret N Kosek
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Joseph M Vinetz
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Dionicia Gamboa
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru.
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10
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Koepfli C, Rodrigues PT, Antao T, Orjuela-Sánchez P, Van den Eede P, Gamboa D, van Hong N, Bendezu J, Erhart A, Barnadas C, Ratsimbasoa A, Menard D, Severini C, Menegon M, Nour BYM, Karunaweera N, Mueller I, Ferreira MU, Felger I. Plasmodium vivax Diversity and Population Structure across Four Continents. PLoS Negl Trop Dis 2015; 9:e0003872. [PMID: 26125189 PMCID: PMC4488360 DOI: 10.1371/journal.pntd.0003872] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 06/02/2015] [Indexed: 01/12/2023] Open
Abstract
Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations. Plasmodium vivax is the predominant malaria parasite in Latin America, Asia and the South Pacific. Different factors are expected to shape diversity and population structure across continents, e.g. transmission intensity which is much lower in South America as compared to Southeast-Asia and the South Pacific, or geographical isolation of P. vivax populations in the South Pacific. We have compiled data from 841 isolates from South and Central America, Africa, Central Asia, Southeast-Asia and the South Pacific typed with a panel of 11 microsatellite markers. Diversity was highest in Southeast-Asia, where transmission is intermediate-high and migration of infected hosts is high, and lowest in South America and Central Asia where malaria transmission is low and focal. Reducing the panel of microsatellites showed that 2–6 markers are sufficient for genotyping for most drug trials and epidemiological studies, as these markers can identify >90% of all haplotypes. Parasites clustered according to continental origin, with high population differentiation between South American and Central Asian populations and the other populations, and lowest differences between Southeast-Asia and the South Pacific. Current attempts to reduce malaria transmission might change this pattern, but only after transmission is reduced for an extended period of time.
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Affiliation(s)
- Cristian Koepfli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Walter and Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago Antao
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Pamela Orjuela-Sánchez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Peter Van den Eede
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nguyen van Hong
- National Institute of Malariology, Parasitology, and Entomology, Hanoi, Vietnam
| | - Jorge Bendezu
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Annette Erhart
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Céline Barnadas
- Walter and Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Arsène Ratsimbasoa
- Immunology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Didier Menard
- Institut Pasteur de Cambodge, Malaria Molecular Epidemiology Unit, Phnom Penh, Cambodia
| | - Carlo Severini
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Michela Menegon
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Bakri Y. M. Nour
- Department of Parasitology, Blue Nile National Institute for Communicable Diseases, University of Gezira, Wad Medani, Sudan
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Sri Lanka
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Barcelona Centre for International Health Research, Barcelona, Spain
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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Daniels RF, Rice BL, Daniels NM, Volkman SK, Hartl DL. The utility of genomic data for Plasmodium vivax population surveillance. Pathog Glob Health 2015; 109:153-61. [PMID: 25892032 DOI: 10.1179/2047773215y.0000000014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genetic polymorphisms identified from genomic sequencing can be used to track changes in parasite populations through time. Such tracking is particularly informative when applying control strategies and evaluating their effectiveness. Using genomic approaches may also enable improved ability to categorise populations and to stratify them according to the likely effectiveness of intervention. Clinical applications of genomic approaches also allow relapses to be classified according to reinfection or recrudescence. These tools can be used not only to assess the effectiveness of malaria interventions but also to appraise the strategies for malaria elimination.
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12
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Lin JT, Hathaway NJ, Saunders DL, Lon C, Balasubramanian S, Kharabora O, Gosi P, Sriwichai S, Kartchner L, Chuor CM, Satharath P, Lanteri C, Bailey JA, Juliano JJ. Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse. J Infect Dis 2015; 212:999-1008. [PMID: 25748326 DOI: 10.1093/infdis/jiv142] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 02/27/2015] [Indexed: 01/31/2023] Open
Abstract
Plasmodium vivax infections often recur due to relapse of hypnozoites from the liver. In malaria-endemic areas, tools to distinguish relapse from reinfection are needed. We applied amplicon deep sequencing to P. vivax isolates from 78 Cambodian volunteers, nearly one-third of whom suffered recurrence at a median of 68 days. Deep sequencing at a highly variable region of the P. vivax merozoite surface protein 1 gene revealed impressive diversity-generating 67 unique haplotypes and detecting on average 3.6 cocirculating parasite clones within individuals, compared to 2.1 clones detected by a combination of 3 microsatellite markers. This diversity enabled a scheme to classify over half of recurrences as probable relapses based on the low probability of reinfection by multiple recurring variants. In areas of high P. vivax diversity, targeted deep sequencing can help detect genetic signatures of relapse, key to evaluating antivivax interventions and achieving a better understanding of relapse-reinfection epidemiology.
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Affiliation(s)
- Jessica T Lin
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester
| | - David L Saunders
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chanthap Lon
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sujata Balasubramanian
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill
| | - Oksana Kharabora
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill
| | - Panita Gosi
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sabaithip Sriwichai
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Laurel Kartchner
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill
| | - Char Meng Chuor
- National Center for Parasitology, Entomology and Malaria Control
| | | | - Charlotte Lanteri
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester Division of Transfusion Medicine, University of Massachusetts Medical School, Worcester
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill
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13
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Simões LR, Alves Jr ER, Ribatski-Silva D, Gomes LT, Nery AF, Fontes CJF. Factors associated with recurrent Plasmodium vivax malaria in Porto Velho, Rondônia State, Brazil, 2009. CAD SAUDE PUBLICA 2014; 30:1403-17. [DOI: 10.1590/0102-311x00169312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 11/26/2013] [Indexed: 12/20/2022] Open
Abstract
This open retrospective cohort study aimed to describe the incidence of recurrent Plasmodium vivax malaria and associated factors in Porto Velho, Rondônia State, Brazil, in 2009. Data were collected from the National Information System for Malaria Epidemiological Surveillance. There were 23,365 reported P. vivax malaria cases in 2009, 23% of which were classified as relapses. Incidence density of P. vivax recurrence was 45.1/100 patient-years, mostly occurring between the 4th and 13th week after initiating treatment. Male gender, shorter time since onset of symptoms, and higher parasitemia in the initial infection increased the risk of relapse during the year, with a 10% reduction in relative risk for longer symptoms and 11% and 15% increases in relative risk for males and higher initial parasitemia, respectively. However, the results show low clinical relevance for these associations, thereby limiting their applicability to decision-making at the public health level.
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14
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McCollum AM, Soberon V, Salas CJ, Santolalla ML, Udhayakumar V, Escalante AA, Graf PCF, Durand S, Cabezas C, Bacon DJ. Genetic variation and recurrent parasitaemia in Peruvian Plasmodium vivax populations. Malar J 2014; 13:67. [PMID: 24568141 PMCID: PMC3941685 DOI: 10.1186/1475-2875-13-67] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/13/2014] [Indexed: 11/12/2022] Open
Abstract
Background Plasmodium vivax is a predominant species of malaria in parts of South America and there is increasing resistance to drugs to treat infections by P. vivax. The existence of latent hypnozoites further complicates the ability to classify recurrent infections as treatment failures due to relapse, recrudescence of hyponozoites or re-infections. Antigen loci are putatively under natural selection and may not be an optimal molecular marker to define parasite haplotypes in paired samples. Putatively neutral microsatellite loci, however, offer an assessment of neutral haplotypes. The objective here was to assess the utility of neutral microsatellite loci to reconcile cases of recurrent parasitaemia in Amazonian P. vivax populations in Peru. Methods Patient blood samples were collected from three locations in or around Iquitos in the Peruvian Amazon. Five putatively neutral microsatellite loci were characterized from 445 samples to ascertain the within and amongst population variation. A total of 30 day 0 and day of recurrent parasitaemia samples were characterized at microsatellite loci and five polymorphic antigen loci for haplotype classification. Results The genetic diversity at microsatellite loci was consistent with neutral levels of variation measured in other South American P. vivax populations. Results between antigen and microsatellite loci for the 30 day 0 and day of recurrent parasitaemia samples were the same for 80% of the pairs. The majority of non-concordant results were the result of differing alleles at microsatellite loci. This analysis estimates that 90% of the paired samples with the same microsatellite haplotype are unlikely to be due to a new infection. Conclusions A population-level approach was used to yield a better estimate of the probability of a new infection versus relapse or recrudescence of homologous hypnozoites; hypnozoite activation was common for this cohort. Population studies are critical with the evaluation of genetic markers to assess P. vivax biology and epidemiology. The additional demonstration of microsatellite loci as neutral markers capable of distinguishing the origin of the recurrent parasites (new infection or originating from the patient) lends support to their use in assessment of treatment outcomes.
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Affiliation(s)
- Andrea M McCollum
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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15
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Delgado-Ratto C, Soto-Calle VE, Van den Eede P, Gamboa D, Rosas A, Abatih EN, Rodriguez Ferrucci H, Llanos-Cuentas A, Van Geertruyden JP, Erhart A, D'Alessandro U. Population structure and spatio-temporal transmission dynamics of Plasmodium vivax after radical cure treatment in a rural village of the Peruvian Amazon. Malar J 2014; 13:8. [PMID: 24393454 PMCID: PMC3893378 DOI: 10.1186/1475-2875-13-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/28/2013] [Indexed: 11/23/2022] Open
Abstract
Background Despite the large burden of Plasmodium vivax, little is known about its transmission dynamics. This study explored the population structure and spatio-temporal dynamics of P. vivax recurrent infections after radical cure in a two-year cohort study carried out in a rural community of the Peruvian Amazon. Methods A total of 37 P. vivax participants recruited in San Carlos community (Peru) between April and December 2008 were treated radically with chloroquine and primaquine and followed up monthly for two years with systematic blood sampling. All samples were screened for malaria parasites and subsequently all P. vivax infections genotyped using 15 microsatellites. Parasite population structure and dynamics were determined by computing different genetic indices and using spatio-temporal statistics. Results After radical cure, 76% of the study participants experienced one or more recurrent P. vivax infections, most of them sub-patent and asymptomatic. The parasite population displayed limited genetic diversity (He = 0.49) and clonal structure, with most infections (84%) being monoclonal. Spatio-temporal clusters of specific haplotypes were found throughout the study and persistence of highly frequent haplotypes were observed over several months within the same participants/households. Conclusions In San Carlos community, P. vivax recurrences were commonly observed after radical treatment, and characterized by asymptomatic, sub-patent and clustered infections (within and between individuals from a few neighbouring households). Moreover low genetic diversity as well as parasite inbreeding are likely to define a clonal parasite population which has important implications on the malaria epidemiology of the study area.
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Affiliation(s)
- Christopher Delgado-Ratto
- Unit of International Health, ESOC Department, Faculty of Medicine, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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16
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Sutton PL. A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity. Malar J 2013; 12:447. [PMID: 24330329 PMCID: PMC3878832 DOI: 10.1186/1475-2875-12-447] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite (MS) markers have become an important tool for studying the population diversity, evolutionary history and multiplicity of infection (MOI) of malaria parasite infections. MS are typically selected on the basis of being highly polymorphic. However, it is known that the polymorphic potential (mutability) of each marker can vary as much as two orders of magnitude, which radically changes how diversity is represented in the genome from one marker to the next. Over the past decade, approximately 240 Plasmodium vivax MS have been published, comprising nine major panels of markers. Inconsistent usage of each panel has resulted in a surfeit of descriptive genetic diversity data that are largely incomparable between populations. The objective of this study was to statistically evaluate the quality of individual MS markers in order to validate a refined panel of markers that will provide a balanced picture of P. vivax population diversity. METHODS All previously published data, including genetic diversity indices, MS parameters, and population parameters, were assembled from 18 different global studies into a flat file to facilitate statistical analysis and modelling using JMP® Genomics 6.0 (SAS Institute Inc, Cary, NC, USA). Statistical modeling was employed to down-select markers with extreme variation among the mean number of alleles, expected heterozygosity, maximum repeat length and/or chromosomal location of the repeat. Individual MS were analysed by step-down whole model linear regression and standard least squares fit models, both stratified by annual parasite incidence to identify MS markers with values significantly different from the mean. RESULTS Of the 42 MS under evaluation in this study, 18 (nine high priority) were identified as ideal candidates for measuring population diversity between global regions, while five (two high priority) additional markers were identified as candidates for MOI studies. CONCLUSIONS MS diversity was found to be a function of endemicity and motif structure. Evaluation of individual MS permitted the assembly of a refined panel of markers that can be reliably utilized in the field to compare population structures between global regions.
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Affiliation(s)
- Patrick L Sutton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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17
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Koepfli C, Colborn KL, Kiniboro B, Lin E, Speed TP, Siba PM, Felger I, Mueller I. A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children. PLoS Negl Trop Dis 2013; 7:e2403. [PMID: 24040428 PMCID: PMC3764149 DOI: 10.1371/journal.pntd.0002403] [Citation(s) in RCA: 48] [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: 11/26/2012] [Accepted: 07/23/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND When both parasite species are co-endemic, Plasmodium vivax incidence peaks in younger children compared to P. falciparum. To identify differences in the number of blood stage infections of these species and its potential link to acquisition of immunity, we have estimated the molecular force of blood-stage infection of P. vivax ((mol)FOB, i.e. the number of genetically distinct blood-stage infections over time), and compared it to previously reported values for P. falciparum. METHODS P. vivax (mol)FOB was estimated by high resolution genotyping parasites in samples collected over 16 months in a cohort of 264 Papua New Guinean children living in an area highly endemic for P. falciparum and P. vivax. In this cohort, P. vivax episodes decreased three-fold over the age range of 1-4.5 years. RESULTS On average, children acquired 14.0 new P. vivax blood-stage clones/child/year-at-risk. While the incidence of clinical P. vivax illness was strongly associated with mol FOB (incidence rate ratio (IRR) = 1.99, 95% confidence interval (CI95) [1.80, 2.19]), (mol)FOB did not change with age. The incidence of P. vivax showed a faster decrease with age in children with high (IRR = 0.49, CI95 [0.38, 0.64] p<0.001) compared to those with low exposure (IRR = 0.63, CI95[0.43, 0.93] p = 0.02). CONCLUSION P. vivax (mol)FOB is considerably higher than P. falciparum (mol)FOB (5.5 clones/child/year-at-risk). The high number of P. vivax clones that infect children in early childhood contribute to the rapid acquisition of immunity against clinical P. vivax malaria.
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Affiliation(s)
- Cristian Koepfli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Kathryn L. Colborn
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- University of California, Berkeley, Department of Biostatistics, Berkeley, California, United States of America
| | - Benson Kiniboro
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | - Enmoore Lin
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | | | - Peter M. Siba
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
- Barcelona Centre for International Health Research, Barcelona, Spain
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18
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Lin JT, Patel JC, Kharabora O, Sattabongkot J, Muth S, Ubalee R, Schuster AL, Rogers WO, Wongsrichanalai C, Juliano JJ. Plasmodium vivax isolates from Cambodia and Thailand show high genetic complexity and distinct patterns of P. vivax multidrug resistance gene 1 (pvmdr1) polymorphisms. Am J Trop Med Hyg 2013; 88:1116-23. [PMID: 23509126 DOI: 10.4269/ajtmh.12-0701] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plasmodium vivax accounts for an increasing fraction of malaria infections in Thailand and Cambodia. We compared P. vivax genetic complexity and antimalarial resistance patterns in the two countries. Use of a heteroduplex tracking assay targeting the merozoite surface protein 1 gene revealed that vivax infections in both countries are frequently polyclonal (84%), with parasites that are highly diverse (HE = 0.86) but closely related (GST = 0.18). Following a history of different drug policies in Thailand and Cambodia, distinct patterns of antimalarial resistance have emerged: most Cambodian isolates harbor the P. vivax multidrug resistance gene 1 (pvmdr1) 976F mutation associated with chloroquine resistance (89% versus 8%, P < 0.001), whereas Thai isolates more often display increased pvmdr1 copy number (39% versus 4%, P < 0.001). Finally, genotyping of paired isolates from individuals suspected of suffering relapse supports a complex scheme of relapse whereby recurrence of multiple identical variants is sometimes accompanied by the appearance of novel variants.
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Affiliation(s)
- Jessica T Lin
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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19
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Abstract
Plasmodium vivax is a major cause of febrile illness in endemic areas of Asia, Central and South America, and the horn of Africa. P. vivax infections are characterized by relapses of malaria arising from persistent liver stages of the parasite (hypnozoites), which can be prevented currently only by 8-aminoquinoline anti-malarials. Tropical P. vivax infections relapse at approximately 3-week intervals if rapidly eliminated anti-malarials are given for treatment, whereas in temperate regions and parts of the sub-tropics, P. vivax infections are characterized by either a long incubation or a long-latency period between illness and relapse - in both cases approximating 8-10 months. The epidemiology of the different relapse phenotypes has not been defined adequately despite obvious relevance to malaria therapeutic assessment, control, and elimination. The number of sporozoites inoculated by the anopheline mosquito is an important determinant of both the timing and the number of relapses. The intervals between P. vivax relapses display a remarkable periodicity which has not been explained. Evidence is presented that the proportion of patients who have successive relapses is relatively constant and that the factor which activates hypnozoites and leads to regular interval relapse in vivax malaria is the systemic febrile illness itself. It is proposed that in endemic areas, a large proportion of the population harbours latent hypnozoites which can be activated by a systemic illness such as vivax or falciparum malaria. This explains the high rates of vivax following falciparum malaria, the high proportion of heterologous genotypes in relapses, the higher rates of relapse in people living in endemic areas compared with artificial infection studies, and, by facilitating recombination between different genotypes, contributes to P. vivax genetic diversity particularly in low transmission settings. Long-latency P. vivax phenotypes may be more widespread and more prevalent than currently thought. These observations have important implications for the assessment of radical treatment efficacy and for malaria control and elimination.
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Affiliation(s)
- Nicholas J White
- Mahidol Oxford Research Unit, Mahidol University, Bangkok, Thailand.
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20
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Orjuela-Sánchez P, Brandi MC, Ferreira MU. Microsatellite analysis of malaria parasites. Methods Mol Biol 2013; 1006:247-58. [PMID: 23546796 DOI: 10.1007/978-1-62703-389-3_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Microsatellites have been increasingly used to investigate the population structure of malaria parasites, to map genetic loci contributing to phenotypes such as drug resistance and virulence in laboratory crosses and genome-wide association studies and to distinguish between treatment failures and new infections in clinical trials. Here, we provide optimized protocols for genotyping highly polymorphic microsatellites sampled from across the genomes of the human malaria parasites Plasmodium falciparum and P. vivax that have been extensively used in research laboratories worldwide.
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Affiliation(s)
- Pamela Orjuela-Sánchez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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21
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Chenet SM, Schneider KA, Villegas L, Escalante AA. Local population structure of Plasmodium: impact on malaria control and elimination. Malar J 2012; 11:412. [PMID: 23232077 PMCID: PMC3538601 DOI: 10.1186/1475-2875-11-412] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regardless of the growing interest in detecting population structures in malarial parasites, there have been limited discussions on how to use this concept in control programmes. In such context, the effects of the parasite population structures will depend on interventions' spatial or temporal scales. This investigation explores the problem of identifying genetic markers, in this case microsatellites, to unveil Plasmodium genetic structures that could affect decisions in the context of elimination. The study was performed in a low-transmission area, which offers a good proxy to better understand problems associated with surveillance at the final stages of malaria elimination. METHODS Plasmodium vivax samples collected in Tumeremo, Venezuela, between March 2003 and November 2004 were analysed. Since Plasmodium falciparum also circulates in many low endemic areas, P. falciparum samples from the same locality and time period were included for comparison. Plasmodium vivax samples were assayed for an original set of 25 microsatellites and P. falciparum samples were assayed for 12 microsatellites. RESULTS Not all microsatellite loci assayed offered reliable local data. A complex temporal-cluster dynamics is found in both P. vivax and P. falciparum. Such dynamics affect the numbers and the type of microsatellites required for identifying individual parasites or parasite clusters when performing cross-sectional studies. The minimum number of microsatellites required to differentiate circulating P. vivax clusters differs from the minimum number of hyper-variable microsatellites required to distinguish individuals within these clusters. Regardless the extended number of microsatellites used in P. vivax, it was not possible to separate all individual infections. CONCLUSIONS Molecular surveillance has great potential; however, it requires preliminary local studies in order to properly interpret the emerging patterns in the context of elimination. Clonal expansions and clusters turnovers need to be taken into account when using molecular markers. Those affect the number and type of microsatellite markers, as well as, the expected genetic patterns in the context of operational investigations. By considering the local dynamics, elimination programmes could cost-effectively use molecular markers. However, population level studies need to consider the local limitations of a given set of loci in terms of providing epidemiologically relevant information.
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Affiliation(s)
- Stella M Chenet
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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22
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Cucunubá ZM, Guerra ÁP, Rivera JA, Nicholls RS. Comparison of asymptomatic Plasmodium spp. infection in two malaria-endemic Colombian locations. Trans R Soc Trop Med Hyg 2012; 107:129-36. [DOI: 10.1093/trstmh/trs021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Arango EM, Samuel R, Agudelo OM, Carmona-Fonseca J, Maestre A, Yanow SK. Genotype comparison of Plasmodium vivax and Plasmodium falciparum clones from pregnant and non-pregnant populations in North-west Colombia. Malar J 2012. [PMID: 23181896 PMCID: PMC3519599 DOI: 10.1186/1475-2875-11-392] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Placental malaria is the predominant pathology secondary to malaria in pregnancy, causing substantial maternal and infant morbidity and mortality in tropical areas. While it is clear that placental parasites are phenotypically different from those in the peripheral circulation, it is not known whether unique genotypes are associated specifically with placental infection or perhaps more generally with pregnancy. In this study, genetic analysis was performed on Plasmodium vivax and Plasmodium falciparum parasites isolated from peripheral and placental blood in pregnant women living in North-west Colombia, and compared with parasites causing acute malaria in non-pregnant populations. METHODS A total of 57 pregnant women at delivery with malaria infection confirmed by real-time PCR in peripheral or placental blood were included, as well as 50 pregnant women in antenatal care and 80 men or non-pregnant women with acute malaria confirmed by a positive thick smear for P. vivax or P. falciparum. Five molecular markers per species were genotyped by nested PCR and capillary electrophoresis. Genetic diversity and the fixation index FST per species and study group were calculated and compared. RESULTS Almost all infections at delivery were asymptomatic with significantly lower levels of infection compared with the groups with acute malaria. Expected heterozygosity for P. vivax molecular markers ranged from 0.765 to 0.928 and for P. falciparum markers ranged from 0.331 to 0.604. For P. vivax infections, the genetic diversity was similar amongst the four study groups and the fixation index from each pairwise comparison failed to show significant genetic differentiation. For P. falciparum, no genetic differentiation was observed between placental and peripheral parasites from the same woman at delivery, but the parasites isolated at delivery showed significant genetic differentiation compared with parasites isolated from subjects with acute malaria. CONCLUSIONS In North-west Colombia, P. vivax parasites have high genetic diversity that is equivalent in pregnant and non-pregnant populations as well as in symptomatic and asymptomatic infections. For P. falciparum, the overall genetic diversity is lower, with specific genotypes associated with asymptomatic infections at delivery.
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Affiliation(s)
- Eliana M Arango
- Grupo Salud y Comunidad, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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de Araujo FCF, de Rezende AM, Fontes CJF, Carvalho LH, Alves de Brito CF. Multiple-clone activation of hypnozoites is the leading cause of relapse in Plasmodium vivax infection. PLoS One 2012. [PMID: 23185469 PMCID: PMC3503861 DOI: 10.1371/journal.pone.0049871] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Plasmodium vivax infection is characterized by a dormant hepatic stage, the hypnozoite that is activated at varying periods of time after clearance of the primary acute blood-stage, resulting in relapse. Differentiation between treatment failure and new infections requires characterization of initial infections, relapses, and clone multiplicity in vivax malaria infections. Methodology/Principal Findings Parasite DNA obtained from primary/relapse paired blood samples of 30 patients with P. vivax infection in Brazil was analyzed using 10 molecular markers (8 microsatellites and MSP-1 blocks 2 and 10). Cloning of PCR products and genotyping was used to identify low-frequency clones of parasites. We demonstrated a high frequency of multiple-clone infections in both primary and relapse infections. Few alleles were identified per locus, but the combination of these alleles produced many haplotypes. Consequently, the majority of parasites involved in relapse showed haplotypes that were distinct from those of primary infections. Plasmodium vivax relapse was characterized by temporal variations in the predominant parasite clones. Conclusions/Significance The high rate of low frequency alleles observed in both primary and relapse infections, along with temporal variation in the predominant alleles, might be the source of reported heterologous hypnozoite activation. Our findings complicate the concept of heterologous activation, suggesting the involvement of undetermined mechanisms based on host or environmental factors in the simultaneous activation of multiple clones of hypnozoites.
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Affiliation(s)
| | - Antônio Mauro de Rezende
- Laboratory of Cellular and Molecular Parasitology, Centro de Pesquisas René Rachou – Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | | | - Luzia Helena Carvalho
- Laboratory of Malaria, Centro de Pesquisas René Rachou – Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Cristiana F. Alves de Brito
- Laboratory of Malaria, Centro de Pesquisas René Rachou – Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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Individual Plasmodium vivax msp1 variants within polyclonal P. vivax infections display different propensities for relapse. J Clin Microbiol 2012; 50:1449-51. [PMID: 22205791 DOI: 10.1128/jcm.06212-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Using a newly developed Plasmodium vivax merozoite surface protein 1 gene (Pvmsp1) heteroduplex tracking assay, we genotyped 107 P. vivax infections in individuals from Cambodia, 45 of whom developed recurrent parasitemia within 42 days. The majority of isolates were polyclonal, but recurrent parasitemias displayed fewer variants compared to initial parasitemias. Two Pvmsp1 gene variants occurred more frequently in the initial genotypes of those who developed recurrent parasitemia, representing the first time P. vivax variants associated with a higher risk of relapse have been described.
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Imwong M, Boel ME, Pagornrat W, Pimanpanarak M, McGready R, Day NPJ, Nosten F, White NJ. The first Plasmodium vivax relapses of life are usually genetically homologous. J Infect Dis 2011; 205:680-3. [PMID: 22194628 PMCID: PMC3266132 DOI: 10.1093/infdis/jir806] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In a prospective infant cohort, 21 infants developed Plasmodium vivax malaria during their first year. Twelve of their mothers also had vivax malaria in the corresponding pregnancies or postpartum period. The genotypes of the maternal and infant infections were all different. Eight of the 12 mothers and 9 of the 21 infants had recurrent infections. Relapse parasite genotypes were different to the initial infection in 13 of 20 (65%) mothers compared with 5 of 24 (21%) infants (P = .02). The first P. vivax relapses of life are usually genetically homologous, whereas relapse in adults may result from activation of heterologous latent hypnozoites acquired from previous inoculations.
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Affiliation(s)
- Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Markus MB. Dormancy in mammalian malaria. Trends Parasitol 2011; 28:39-45. [PMID: 22118814 DOI: 10.1016/j.pt.2011.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
This analysis principally concerns biological aspects of dormancy in mammalian malaria, with particular reference to the hypnozoite. Research is needed to reveal what happens to sporozoites of Plasmodium cynomolgi between the time of inoculation and when hypnozoites are first seen in the liver 36-40 h later. It is likely that hypnozoites of relapsing malarial parasites will prove to be directly sporozoite-derived rather than merozoite-derived. There is indirect evidence that, contrary to what is generally assumed, activation of hypnozoites might not be the only cause of recurrent Plasmodium vivax malaria. Latent stages pose a threat to success in eradicating malaria; some suggestions are therefore made for demystifying work on hypnozoites and quiescent merozoites.
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Affiliation(s)
- Miles B Markus
- School of Animal, Plant and Environmental Sciences, University of Witwatersrand, Johannesburg, South Africa.
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28
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White NJ. Determinants of relapse periodicity in Plasmodium vivax malaria. Malar J 2011; 10:297. [PMID: 21989376 PMCID: PMC3228849 DOI: 10.1186/1475-2875-10-297] [Citation(s) in RCA: 420] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/11/2011] [Indexed: 02/05/2023] Open
Abstract
Plasmodium vivax is a major cause of febrile illness in endemic areas of Asia, Central and South America, and the horn of Africa. Plasmodium vivax infections are characterized by relapses of malaria arising from persistent liver stages of the parasite (hypnozoites) which can be prevented only by 8-aminoquinoline anti-malarials. Tropical P. vivax relapses at three week intervals if rapidly eliminated anti-malarials are given for treatment, whereas in temperate regions and parts of the sub-tropics P. vivax infections are characterized either by a long incubation or a long-latency period between illness and relapse - in both cases approximating 8-10 months. The epidemiology of the different relapse phenotypes has not been defined adequately despite obvious relevance to malaria control and elimination. The number of sporozoites inoculated by the anopheline mosquito is an important determinant of both the timing and the number of relapses. The intervals between relapses display a remarkable periodicity which has not been explained. Evidence is presented that the proportion of patients who have successive relapses is relatively constant and that the factor which activates hypnozoites and leads to regular interval relapse in vivax malaria is the systemic febrile illness itself. It is proposed that in endemic areas a large proportion of the population harbours latent hypnozoites which can be activated by a systemic illness such as vivax or falciparum malaria. This explains the high rates of vivax following falciparum malaria, the high proportion of heterologous genotypes in relapses, the higher rates of relapse in people living in endemic areas compared with artificial infection studies, and, by facilitating recombination between different genotypes, contributes to P. vivax genetic diversity particularly in low transmission settings. Long-latency P. vivax phenotypes may be more widespread and more prevalent than currently thought. These observations have important implications for the assessment of radical treatment efficacy and for malaria control and elimination.
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Affiliation(s)
- Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
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