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Sekine S, Chan CW, Kalkoa M, Yamar S, Iata H, Taleo G, Kc A, Kagaya W, Kido Y, Kaneko A. Tracing the origins of Plasmodium vivax resurgence after malaria elimination on Aneityum Island in Vanuatu. COMMUNICATIONS MEDICINE 2024; 4:91. [PMID: 38762604 PMCID: PMC11102431 DOI: 10.1038/s43856-024-00524-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Five years after successful malaria elimination, Aneityum Island in Vanuatu experienced an outbreak of Plasmodium vivax of unknown origin in 2002. Epidemiological investigations revealed several potential sources of P. vivax. We aimed to identify the genetic origin of P. vivax responsible for the resurgence. METHODS Five P. vivax microsatellite markers were genotyped using DNA extracted from archived blood samples. A total of 69 samples from four P. vivax populations was included: 29 from the outbreak in 2002, seven from Aneityum in 1999 and 2000, 18 from visitors to Aneityum in 2000, and 15 from nearby Tanna Island in 2002. A neighbour-joining phylogenetic tree was constructed to elucidate the relationships among P. vivax isolates. STRUCTURE and principal component analysis were used to assess patterns of genetic structure. RESULTS Here we show distinct genetic origins of P. vivax during the outbreak on Aneityum. While the origin of most P. vivax lineages found during the outbreak remains unidentified, limited genetic diversity among these lineages is consistent with a rapid expansion from a recent common ancestor. Contemporaneous P. vivax from neighboring Tanna and potential relapse of P. vivax acquired from other islands in 1999 and 2000 are also identified as minor contributors to the outbreak. CONCLUSIONS Multiple reintroductions of P. vivax after elimination highlight the high receptivity and vulnerability to malaria resurgence in island settings of Vanuatu, despite robust surveillance and high community compliance to control measures.
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Affiliation(s)
- Sho Sekine
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Medical Technology, Morinomiya University of Medical Sciences, Osaka, Japan
| | - Chim W Chan
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Morris Kalkoa
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Sam Yamar
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Harry Iata
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - George Taleo
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Achyut Kc
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wataru Kagaya
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Eco-epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yasutoshi Kido
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Akira Kaneko
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Huwe T, Kibria MG, Johora FT, Phru CS, Jahan N, Hossain MS, Khan WA, Price RN, Ley B, Alam MS, Koepfli C. Heterogeneity in prevalence of subclinical Plasmodium falciparum and Plasmodium vivax infections but no parasite genomic clustering in the Chittagong Hill Tracts, Bangladesh. Malar J 2022; 21:218. [PMID: 35836171 PMCID: PMC9281141 DOI: 10.1186/s12936-022-04236-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/22/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Malaria remains endemic in Bangladesh, with the majority of cases occurring in forested, mountainous region in the Chittagong Hill Tracts (CHT). This area is home to Bengali and diverse groups of indigenous people (Pahari) residing largely in mono-ethnic villages. METHODS 1002 individuals of the 9 most prominent Pahari and the Bengali population were randomly selected and screened by RDT and qPCR. Parasites were genotyped by msp2 and deep sequencing of 5 amplicons (ama1-D3, cpmp, cpp, csp, and msp7) for Plasmodium falciparum (n = 20), and by microsatellite (MS) typing of ten loci and amplicon sequencing of msp1 for Plasmodium vivax (n = 21). Population structure was analysed using STRUCTURE software. Identity-by-state (IBS) was calculated as a measure of parasite relatedness and used to generate relatedness networks. RESULTS The prevalence of P. falciparum and P. vivax infection was 0.7% by RDT (P. falciparum 6/1002; P. vivax 0/1002, mixed: 1/1002) and 4% by qPCR (P. falciparum 21/1002; P. vivax 16/1002, mixed: 5/1002). Infections were highly clustered, with 64% (27/42) of infections occurring in only two Pahari groups, the Khumi and Mro. Diversity was high; expected heterozygosity was 0.93 for P. falciparum and 0.81 for P. vivax. 85.7% (18/21) of P. vivax and 25% (5/20) of P. falciparum infections were polyclonal. No population structure was evident for either species, suggesting high transmission and gene flow among Pahari groups. CONCLUSIONS High subclinical infection prevalence and genetic diversity mirror ongoing transmission. Control activities should be specifically directed to Pahari groups at greatest risk.
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Affiliation(s)
- Tiffany Huwe
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Mohammad Golam Kibria
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Fatema Tuj Johora
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
- Georgia State University, Atlanta, GA, USA
| | - Ching Swe Phru
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Nusrat Jahan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Mohammad Sharif Hossain
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Wasif Ali Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Benedikt Ley
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh.
| | - Cristian Koepfli
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA.
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Monteiro W, Karl S, Kuehn A, Almeida A, White M, Vitor-Silva S, Melo G, Brito-Sousa JD, Baia-da-Silva DC, Silva-Neto AV, Sampaio V, Bassat Q, Felger I, Mueller I, Lacerda M. Prevalence and force of Plasmodium vivax blood-stage infection and associated clinical malaria burden in the Brazilian Amazon. Mem Inst Oswaldo Cruz 2022; 117:e210330. [PMID: 35766676 PMCID: PMC9239689 DOI: 10.1590/0074-02760210330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Understanding the epidemiology of malaria through the molecular force of the blood-stage infection of Plasmodium vivax (molFOB) may provide a detailed assessment of malaria transmission. OBJECTIVES In this study, we investigated risk factors and spatial-temporal patterns of incidence of Plasmodium infection and clinical malaria episodes in three peri-urban communities of Manaus, Western Brazilian Amazon. METHODS Monthly samples were collected in a cohort of 1,274 individuals between April 2013 and March 2014. DNA samples were subject to Plasmodium species. molFOB was calculated by counting the number of genotypes observed on each visit, which had not been present in the preceding two visits and adjusting these counts by the respective times-at-risk. FINDINGS Respectively, 77.8% and 97.2% of the population remained free of P. vivax and P. falciparum infection. Expected heterozygosity for P. vivax was 0.69 for MSP1_F3 and 0.86 for MS2. Multiplicity of infection in P. vivax was close to the value of 1. The season was associated with P. vivax positivity [adjusted hazard ratio (aHR) 2.6 (1.9-5.7)] and clinical disease [aHR 10.6 (2.4-47.2)]. P. falciparum infection was associated with previous malarial episodes [HR 9.7 (4.5-20.9)]. Subjects who reported possession of a bed net [incidence rate ratio (IRR) 1.6 (1.2-2.2)] or previous malaria episodes [IRR 3.0 (2.0-4.5)] were found to have significantly higher P. vivax molFOB. MAIN CONCLUSIONS Overall, P. vivax infection prevailed in the area and infections were mostly observed as monoclonal. Previous malaria episodes were associated with significantly higher P. vivax molFOB.
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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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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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6
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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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Spatial and genetic clustering of Plasmodium falciparum and Plasmodium vivax infections in a low-transmission area of Ethiopia. Sci Rep 2020; 10:19975. [PMID: 33203956 PMCID: PMC7672087 DOI: 10.1038/s41598-020-77031-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 11/23/2022] Open
Abstract
The distribution of malaria infections is heterogeneous in space and time, especially in low transmission settings. Understanding this clustering may allow identification and targeting of pockets of transmission. In Adama district, Ethiopia, Plasmodium falciparum and P. vivax malaria patients and controls were examined, together with household members and immediate neighbors. Rapid diagnostic test and quantitative PCR (qPCR) were used for the detection of infections that were genetically characterized by a panel of microsatellite loci for P. falciparum (26) and P. vivax (11), respectively. Individuals living in households of clinical P. falciparum patients were more likely to have qPCR detected P. falciparum infections (22.0%, 9/41) compared to individuals in control households (8.7%, 37/426; odds ratio, 2.9; 95% confidence interval, 1.3–6.4; P = .007). Genetically related P. falciparum, but not P. vivax infections showed strong clustering within households. Genotyping revealed a marked temporal cluster of P. falciparum infections, almost exclusively comprised of clinical cases. These findings uncover previously unappreciated transmission dynamics and support a rational approach to reactive case detection strategies for P. falciparum in Ethiopia.
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Fola AA, Kattenberg E, Razook Z, Lautu-Gumal D, Lee S, Mehra S, Bahlo M, Kazura J, Robinson LJ, Laman M, Mueller I, Barry AE. SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics. Malar J 2020; 19:375. [PMID: 33081815 PMCID: PMC7576724 DOI: 10.1186/s12936-020-03440-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. RESULTS From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. CONCLUSIONS High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.
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Affiliation(s)
- Abebe A Fola
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Eline Kattenberg
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Zahra Razook
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Stuart Lee
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Somya Mehra
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James Kazura
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Leanne J Robinson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Alyssa E Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia.
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia.
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9
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Ford A, Kepple D, Abagero BR, Connors J, Pearson R, Auburn S, Getachew S, Ford C, Gunalan K, Miller LH, Janies DA, Rayner JC, Yan G, Yewhalaw D, Lo E. Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes. PLoS Negl Trop Dis 2020; 14:e0008234. [PMID: 33044985 PMCID: PMC7581005 DOI: 10.1371/journal.pntd.0008234] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 10/22/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale. Plasmodium vivax is the most geographically widespread parasite species that causes malaria in humans. Although it occurs in Africa as a member of a mix of Plasmodium species, P. vivax is dominant in other parts of the world outside of Africa (e.g., Brazil). It was previously thought that most African populations were immune to P. vivax infections due to the absence of Duffy antigen chemokine receptor (DARC) gene expression required for erythrocyte invasion. However, several recent reports have indicated the emergence and potential spread of P. vivax across human populations in Africa. Compared to Southeast Asia and South America where P. vivax is highly endemic, data on polymorphisms in erythrocyte binding gene candidates of P. vivax from Africa is limited. Filling this knowlege gap is critical for identifying functional genes in erythrocyte invasion, biomarkers for tracking the P. vivax isolates from Africa, as well as potential gene targets for vaccine development. This paper examined the level of genetic polymorphisms in a panel of 43 potential erythrocyte binding protein genes based on whole genome sequences and described transmission patterns of P. vivax infections from different study sites in Ethiopia based on the genetic variants. Our analyses showed that chromosomes 9 and 10 of the P. vivax genomes isolated in Ethiopia had the most high-quality genetic polymorphisms. Among all erythrocyte binding protein gene candidates, the merozoite surface proteins 1 and merozoite surface protein 3 showed high levels of polymorphism. MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. The expansion of the Duffy binding protein and merozoite surface protein 3 gene copies was an independent process among the P. vivax lineages in Ethiopia. Various levels of gene flow were observed even at a smaller geographical scale. Our study provided baseline data for future comparison with P. vivax in Duffy negative individuals and help develop a panel of genetic markers that are informative at a micro-geographical scale.
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Affiliation(s)
- Anthony Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
| | - Daniel Kepple
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Ethiopia
| | - Jordan Connors
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Richard Pearson
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United States of America
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Colby Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Louis H. Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, United States of America
| | - Julian C. Rayner
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 OXY, United Kingdom
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, United States of America
- * E-mail: (AF); (GY); (EL)
| | | | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, United States of America
- * E-mail: (AF); (GY); (EL)
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Liu Y, Tessema SK, Murphy M, Xu S, Schwartz A, Wang W, Cao Y, Lu F, Tang J, Gu Y, Zhu G, Zhou H, Gao Q, Huang R, Cao J, Greenhouse B. Confirmation of the absence of local transmission and geographic assignment of imported falciparum malaria cases to China using microsatellite panel. Malar J 2020; 19:244. [PMID: 32660491 PMCID: PMC7359230 DOI: 10.1186/s12936-020-03316-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/04/2020] [Indexed: 11/15/2022] Open
Abstract
Background Current methods to classify local and imported malaria infections depend primarily on patient travel history, which can have limited accuracy. Genotyping has been investigated as a complementary approach to track the spread of malaria and identify the origin of imported infections. Methods An extended panel of 26 microsatellites (16 new microsatellites) for Plasmodium falciparum was evaluated in 602 imported infections from 26 sub-Saharan African countries to the Jiangsu Province of People’s Republic of China. The potential of the 26 microsatellite markers to assign imported parasites to their geographic origin was assessed using a Bayesian method with Markov Chain Monte Carlo (MCMC) as implemented in the program Smoothed and Continuous Assignments (SCAT) with a modification to incorporate haploid genotype data. Results The newly designed microsatellites were polymorphic and are not in linkage disequilibrium with the existing microsatellites, supporting previous findings of high rate of recombination in sub-Saharan Africa. Consistent with epidemiology inferred from patients’ travel history, no evidence for local transmission was found; nearly all genetically related infections were identified in people who travelled to the same country near the same time. The smoothing assignment method assigned imported cases to their likely geographic origin with an accuracy (Angola: 59%; Nigeria: 51%; Equatorial Guinea: 40%) higher than would be achieved at random, reaching statistical significance for Angola and Equatorial Guinea. Conclusions Genotyping using an extended microsatellite panel is valuable for malaria case classification and programme evaluation in an elimination setting. A Bayesian method for assigning geographic origin of mammals based on genetic data was adapted for malaria and showed potential for identification of the origin of imported infections.
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Affiliation(s)
- Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China.,Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Sofonias K Tessema
- EPPI Center Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Maxwell Murphy
- EPPI Center Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sui Xu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Alanna Schwartz
- EPPI Center Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Weiming Wang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Yuanyuan Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Feng Lu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China.,Department of Parasitology, Institute of Translational Medicine, Medical College, Yangzhou University, Jiangsu Key Laboratory of Experimental & Translational Non- coding RNA Research, Yangzhou, Jiangsu, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Yaping Gu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Huayun Zhou
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China
| | - Rui Huang
- Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, China. .,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,Public Health Research Center, Jiangnan University, Wuxi, China.
| | - Bryan Greenhouse
- EPPI Center Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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11
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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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12
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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13
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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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14
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Lo E, Lam N, Hemming-Schroeder E, Nguyen J, Zhou G, Lee MC, Yang Z, Cui L, Yan G. Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers. J Infect Dis 2017; 216:1254-1263. [PMID: 28329141 DOI: 10.1093/infdis/jix106] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/02/2017] [Indexed: 11/13/2022] Open
Abstract
Background In Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission. Methods Microsatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission. Results P. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow. Conclusions The admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas.
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Affiliation(s)
- Eugenia Lo
- Program in Public Health, University of California-Irvine
| | - Nancy Lam
- Program in Public Health, University of California-Irvine
| | | | | | - Guofa Zhou
- Program in Public Health, University of California-Irvine
| | - Ming-Chieh Lee
- Program in Public Health, University of California-Irvine
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, China
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park
| | - Guiyun Yan
- Program in Public Health, University of California-Irvine
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15
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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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17
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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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18
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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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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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VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations. PLoS Negl Trop Dis 2017; 11:e0005465. [PMID: 28362818 PMCID: PMC5389845 DOI: 10.1371/journal.pntd.0005465] [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: 12/28/2016] [Revised: 04/12/2017] [Accepted: 03/07/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. RESULTS The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. CONCLUSIONS VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms.
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Hamedi Y, Sharifi-Sarasiabi K, Dehghan F, Safari R, To S, Handayuni I, Trimarsanto H, Price RN, Auburn S. Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1. PLoS One 2016; 11:e0166124. [PMID: 27829067 PMCID: PMC5102416 DOI: 10.1371/journal.pone.0166124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ) as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR). METHODOLOGY AND PRINCIPAL FINDINGS The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR) markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73%) were autochthonous cases, 23 (23%) imported cases from Afghanistan or Pakistan, and 4 (4%) with unknown origin. 97% (97/100) isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71%) isolates, including 57(57%) autochthonous and 11 (11%) imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82) suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited. CONCLUSIONS The contrasting low versus high diversity in the two sub-populations (K1 and K2) infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.
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Affiliation(s)
- Yaghoob Hamedi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran
| | - Khojasteh Sharifi-Sarasiabi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran
| | - Farzaneh Dehghan
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran
| | - Reza Safari
- Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran
| | - Sheren To
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Irene Handayuni
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Hidayat Trimarsanto
- Bioinformatics Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- The Ministry of Research and Technology (RISTEK), Jakarta, Indonesia
- Agency for Assessment and Application of Technology, Jakarta, Indonesia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of 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, Northern Territory, Australia
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22
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Wangchuk S, Drukpa T, Penjor K, Peldon T, Dorjey Y, Dorji K, Chhetri V, Trimarsanto H, To S, Murphy A, von Seidlein L, Price RN, Thriemer K, Auburn S. Where chloroquine still works: the genetic make-up and susceptibility of Plasmodium vivax to chloroquine plus primaquine in Bhutan. Malar J 2016; 15:277. [PMID: 27176722 PMCID: PMC4866075 DOI: 10.1186/s12936-016-1320-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/30/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bhutan has made substantial progress in reducing malaria incidence. The national guidelines recommend chloroquine (CQ) and primaquine (PQ) for radical cure of uncomplicated Plasmodium vivax, but the local efficacy has not been assessed. The impact of cases imported from India on the genetic make-up of the local vivax populations is currently unknown. METHODS Patients over 4 years of age with uncomplicated P. vivax mono-infection were enrolled into a clinical efficacy study and molecular survey. Study participants received a standard dose of CQ (25 mg/kg over 3 days) followed by weekly review until day 28. On day 28 a 14-day regimen of PQ (0.25 mg/kg/day) was commenced under direct observation. After day 42, patients were followed up monthly for a year. The primary and secondary endpoints were risk of treatment failure at day 28 and at 1 year. Parasite genotyping was undertaken at nine tandem repeat markers, and standard population genetic metrics were applied to examine population diversity and structure in infections thought to be acquired inside or outside of Bhutan. RESULTS A total of 24 patients were enrolled in the clinical study between April 2013 and October 2015. Eight patients (33.3 %) were lost to follow-up in the first 6 months and another eight patients lost between 6 and 12 months. No (0/24) treatment failures occurred by day 28 and no (0/8) parasitaemia was detected following PQ treatment. Some 95.8 % (23/24) of patients were aparasitaemic by day 2. There were no haemolytic or serious events. Genotyping was undertaken on parasites from 12 autochthonous cases and 16 suspected imported cases. Diversity was high (H E 0.87 and 0.90) in both populations. There was no notable differentiation between the autochthonous and imported populations. CONCLUSIONS CQ and PQ remains effective for radical cure of P. vivax in Bhutan. The genetic analyses indicate that imported infections are sustaining the local vivax population, with concomitant risk of introducing drug-resistant strains.
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Affiliation(s)
- Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Tobgyel Drukpa
- Vector Borne Disease Control Programme in Gelephu, Communicable Disease Division, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Kinley Penjor
- Sarpang District Hospital, Ministry of Health, Sarpang District, Bhutan
| | - Tashi Peldon
- Gelephu Regional Referral Hospital, Ministry of Health, Gelephu, Bhutan
| | - Yeshey Dorjey
- Yebilaptsa Hospital, Ministry of Health, Zhemgang District, Bhutan
| | - Kunzang Dorji
- Public Health Laboratory, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Vishal Chhetri
- Gelephu Regional Referral Hospital, Ministry of Health, Gelephu, Bhutan
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta Pusat, 10430, Indonesia.,The Ministry of Research and Technology (RISTEK), Jakarta, 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
| | - Amanda Murphy
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, 0810, Australia.,Faculty of Medicine and Biomedical Sciences, School of Population Health, The University of Queensland, Brisbane, Australia
| | - Lorenz von Seidlein
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - 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 Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, 0810, Australia.
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, 0810, Australia.
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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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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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Pacheco MA, Lopez-Perez M, Vallejo AF, Herrera S, Arévalo-Herrera M, Escalante AA. Multiplicity of Infection and Disease Severity in Plasmodium vivax. PLoS Negl Trop Dis 2016; 10:e0004355. [PMID: 26751811 PMCID: PMC4709143 DOI: 10.1371/journal.pntd.0004355] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/11/2015] [Indexed: 11/19/2022] Open
Abstract
Background Multiplicity of infection (MOI) refers to the average number of distinct parasite genotypes concurrently infecting a patient. Although several studies have reported on MOI and the frequency of multiclonal infections in Plasmodium falciparum, there is limited data on Plasmodium vivax. Here, MOI and the frequency of multiclonal infections were studied in areas from South America where P. vivax and P. falciparum can be compared. Methodology/Principal Findings As part of a passive surveillance study, 1,328 positive malaria patients were recruited between 2011 and 2013 in low transmission areas from Colombia. Of those, there were only 38 P. vivax and 24 P. falciparum clinically complicated cases scattered throughout the time of the study. Samples from uncomplicated cases were matched in time and location with the complicated cases in order to compare the circulating genotypes for these two categories. A total of 92 P. vivax and 57 P. falciparum uncomplicated cases were randomly subsampled. All samples were genotyped by using neutral microsatellites. Plasmodium vivax showed more multiclonal infections (47.7%) than P. falciparum (14.8%). Population genetics and haplotype network analyses did not detect differences in the circulating genotypes between complicated and uncomplicated cases in each parasite. However, a Fisher exact test yielded a significant association between having multiclonal P. vivax infections and complicated malaria. No association was found for P. falciparum infections. Conclusion The association between multiclonal infections and disease severity in P. vivax is consistent with previous observations made in rodent malaria. The contrasting pattern between P. vivax and P. falciparum could be explained, at least in part, by the fact that P. vivax infections have lineages that were more distantly related among them than in the case of the P. falciparum multiclonal infections. Future research should address the possible role that acquired immunity and exposure may have on multiclonal infections and their association with disease severity. Previous studies on rodent malarias and mathematical models have postulated a link between multiclonal infections and disease severity. This association has been tested in Plasmodium falciparum mostly in Africa with limited information on P. vivax. Furthermore, there is a paucity of information from areas with low transmission. Here, we used samples available from a passive surveillance carried out in Colombia, South America. We found an association between multiclonal infections and disease severity in P. vivax but not in P. falciparum. Although the number of complicated malaria cases is low, the contrasting pattern between these two species emphasizes their epidemiological differences. We discuss how this pattern could be the result of a higher divergence among the P. vivax lineages co-infecting a patient. We hypothesize that low levels of acquired immunity may play a role in the association between multiclonal infections and disease severity.
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Affiliation(s)
- M. Andreína Pacheco
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | - Mary Lopez-Perez
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Andrés F. Vallejo
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Sócrates Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Ananias A. Escalante
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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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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Escalante AA, Ferreira MU, Vinetz JM, Volkman SK, Cui L, Gamboa D, Krogstad DJ, Barry AE, Carlton JM, van Eijk AM, Pradhan K, Mueller I, Greenhouse B, Andreina Pacheco M, Vallejo AF, Herrera S, Felger I. Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network. Am J Trop Med Hyg 2015; 93:79-86. [PMID: 26259945 PMCID: PMC4574277 DOI: 10.4269/ajtmh.15-0005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 05/15/2015] [Indexed: 01/31/2023] Open
Abstract
Molecular epidemiology leverages genetic information to study the risk factors that affect the frequency and distribution of malaria cases. This article describes molecular epidemiologic investigations currently being carried out by the International Centers of Excellence for Malaria Research (ICEMR) network in a variety of malaria-endemic settings. First, we discuss various novel approaches to understand malaria incidence and gametocytemia, focusing on Plasmodium falciparum and Plasmodium vivax. Second, we describe and compare different parasite genotyping methods commonly used in malaria epidemiology and population genetics. Finally, we discuss potential applications of molecular epidemiological tools and methods toward malaria control and elimination efforts.
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Affiliation(s)
- Ananias A. Escalante
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
| | - Marcelo U. Ferreira
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ingrid Felger
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
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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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Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination. PLoS Negl Trop Dis 2015; 9:e0003739. [PMID: 25951184 PMCID: PMC4423885 DOI: 10.1371/journal.pntd.0003739] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/05/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Outside of Africa, P. falciparum and P. vivax usually coexist. In such co-endemic regions, successful malaria control programs have a greater impact on reducing falciparum malaria, resulting in P. vivax becoming the predominant species of infection. Adding to the challenges of elimination, the dormant liver stage complicates efforts to monitor the impact of ongoing interventions against P. vivax. We investigated molecular approaches to inform the respective transmission dynamics of P. falciparum and P. vivax and how these could help to prioritize public health interventions. METHODOLOGY/PRINCIPAL FINDINGS Genotype data generated at 8 and 9 microsatellite loci were analysed in 168 P. falciparum and 166 P. vivax isolates, respectively, from four co-endemic sites in Indonesia (Bangka, Kalimantan, Sumba and West Timor). Measures of diversity, linkage disequilibrium (LD) and population structure were used to gauge the transmission dynamics of each species in each setting. Marked differences were observed in the diversity and population structure of P. vivax versus P. falciparum. In Bangka, Kalimantan and Timor, P. falciparum diversity was low, and LD patterns were consistent with unstable, epidemic transmission, amenable to targeted intervention. In contrast, P. vivax diversity was higher and transmission appeared more stable. Population differentiation was lower in P. vivax versus P. falciparum, suggesting that the hypnozoite reservoir might play an important role in sustaining local transmission and facilitating the spread of P. vivax infections in different endemic settings. P. vivax polyclonality varied with local endemicity, demonstrating potential utility in informing on transmission intensity in this species. CONCLUSIONS/SIGNIFICANCE Molecular approaches can provide important information on malaria transmission that is not readily available from traditional epidemiological measures. Elucidation of the transmission dynamics circulating in a given setting will have a major role in prioritising malaria control strategies, particularly against the relatively neglected non-falciparum species.
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30
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Barry AE, Waltmann A, Koepfli C, Barnadas C, Mueller I. Uncovering the transmission dynamics of Plasmodium vivax using population genetics. Pathog Glob Health 2015; 109:142-52. [PMID: 25891915 DOI: 10.1179/2047773215y.0000000012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes.
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Key Words
- Control,
- Elimination
- Genetic diversity,
- Genetics,
- Genomics,
- Linkage disequilibrium,
- Malaria,
- Microsatellites,
- Mitochondrial DNA,
- Plasmodium vivax,
- Population structure,
- Relapse,
- Single nucleotide polymorphisms,
- Transmission,
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31
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Plasmodium vivax populations are more genetically diverse and less structured than sympatric Plasmodium falciparum populations. PLoS Negl Trop Dis 2015; 9:e0003634. [PMID: 25874894 PMCID: PMC4398418 DOI: 10.1371/journal.pntd.0003634] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/20/2015] [Indexed: 11/20/2022] Open
Abstract
Introduction The human malaria parasite, Plasmodium vivax, is proving more difficult to control and eliminate than Plasmodium falciparum in areas of co-transmission. Comparisons of the genetic structure of sympatric parasite populations may provide insight into the mechanisms underlying the resilience of P. vivax and can help guide malaria control programs. Methodology/Principle findings P. vivax isolates representing the parasite populations of four areas on the north coast of Papua New Guinea (PNG) were genotyped using microsatellite markers and compared with previously published microsatellite data from sympatric P. falciparum isolates. The genetic diversity of P. vivax (He = 0.83–0.85) was higher than that of P. falciparum (He = 0.64–0.77) in all four populations. Moderate levels of genetic differentiation were found between P. falciparum populations, even over relatively short distances (less than 50 km), with 21–28% private alleles and clear geospatial genetic clustering. Conversely, very low population differentiation was found between P. vivax catchments, with less than 5% private alleles and no genetic clustering observed. In addition, the effective population size of P. vivax (30353; 13043–69142) was larger than that of P. falciparum (18871; 8109–42986). Conclusions/Significance Despite comparably high prevalence, P. vivax had higher diversity and a panmictic population structure compared to sympatric P. falciparum populations, which were fragmented into subpopulations. The results suggest that in comparison to P. falciparum, P. vivax has had a long-term large effective population size, consistent with more intense and stable transmission, and limited impact of past control and elimination efforts. This underlines suggestions that more intensive and sustained interventions will be needed to control and eventually eliminate P. vivax. This research clearly demonstrates how population genetic analyses can reveal deeper insight into transmission patterns than traditional surveillance methods. The neglected human malaria parasite Plasmodium vivax is responsible for a large proportion of the global malaria burden. Efforts to control malaria have revealed that P. vivax is more resilient than the other major human malaria parasite, Plasmodium falciparum. This study utilised population genetics to compare patterns of P. vivax and P. falciparum transmission in Papua New Guinea, a region where infection rates of the two species are similar. The results demonstrated that P. vivax populations are more genetically diverse than those of P. falciparum suggestive of a parasite population that is more resilient to environmental challenges, undergoing higher levels of interbreeding locally and between distant parasite populations. Unique characteristics of P. vivax such as relapse, which allows different strains from past infections to produce subsequent infections, may provide more opportunities for the exchange and dissemination of genetic material. The contrasting patterns observed for the two species may be the result of a differential impact of past elimination attempts and indicate that more rigorous interventions will be needed in efforts to control and eventually eliminate P. vivax.
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32
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Oloifana-Polosovai H, Gwala J, Harrington H, Massey PD, Ribeyro E, Flores A, Speare C, McBride E, MacLaren D, Speare R. A marked decline in the incidence of malaria in a remote region of Malaita, Solomon Islands, 2008 to 2013. Western Pac Surveill Response J 2014; 5:30-9. [PMID: 25320674 PMCID: PMC4197191 DOI: 10.5365/wpsar.2014.5.3.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SETTING Atoifi Adventist Hospital (AAH), Solomon Islands, the only hospital in the East Kwaio region. OBJECTIVE To use routine surveillance data to assess the trends in malaria from 2008 to 2013. DESIGN Descriptive study of records from (1) AAH laboratory malaria records; (2) admissions to AAH for malaria; and (3) malaria treatments from outpatient records. RESULTS AAH examined 35 608 blood films and diagnosed malaria in 4443 samples comprised of 2667 Plasmodium falciparum (Pf) and 1776 Plasmodium vivax (Pv). Between 2008 and 2013 the total number of malaria cases detected annually decreased by 86.5%, Pf by 96.7% and Pv by 65.3%. The ratio of Pf to Pv reversed in 2010 from 2.06 in 2008 to 0.19 in 2013. For 2013, Pf showed a seasonal pattern with no cases diagnosed in four months. From 2008 to 2013 admissions in AAH for malaria declined by 90.8%, and malaria mortality fell from 54 per 100 000 to zero. The annual parasite index (API) for 2008 and 2013 was 195 and 24, respectively. Village API has identified a group of villages with higher malaria incidence rates. CONCLUSION The decline in malaria cases in the AAH catchment area has been spectacular, particularly for Pf. This was supported by three sources of hospital surveillance data (laboratory, admissions and treatment records). The decline was associated with the use of artemisinin-based combined therapy and improved vertical social capital between the AAH and the local communities. Calculating village-specific API has highlighted which villages need to be targeted by the AAH malaria control team.
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Affiliation(s)
| | - John Gwala
- Atoifi Adventist Hospital, Atoifi, Malaita, Solomon Islands
| | | | - Peter D Massey
- Health Protection, Hunter New England Population Health, Tamworth, Australia
| | - Elmer Ribeyro
- Atoifi Adventist Hospital, Atoifi, Malaita, Solomon Islands
| | | | | | - Edwin McBride
- College of Medicine and Dentistry, James Cook University, Cairns, Australia
| | - David MacLaren
- College of Medicine and Dentistry, James Cook University, Cairns, Australia
| | - Rick Speare
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
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Menegon M, Durand P, Menard D, Legrand E, Picot S, Nour B, Davidyants V, Santi F, Severini C. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia. INFECTION GENETICS AND EVOLUTION 2014; 27:244-9. [PMID: 25102032 DOI: 10.1016/j.meegid.2014.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
Abstract
Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.
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Affiliation(s)
- Michela Menegon
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Patrick Durand
- Laboratoire MIVEGEC, UMR 224-5290 CNRS-IRD-UM1-UM2, IRD, Montpellier, France
| | - Didier Menard
- Malaria Molecular Epidemiology Unit, Pasteur Institute in Cambodia, Phnom Penh, Cambodia
| | - Eric Legrand
- National Reference Centre of Malaria Chemoresistance in French Guiana and West Indies, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Stéphane Picot
- Malaria Research Unit, CNRS UMR 5246, Faculté de Médecine, Université Lyon 1, Lyon, France
| | - Bakri Nour
- Department of Parasitology, Blue Nile National Institute for Communicable Diseases, University of Gezira, Wad Medani, Sudan
| | - Vladimir Davidyants
- Department of Epidemiology and Health Informatics, Armenian National Institute of Health, Yerevan, Armenia
| | - Flavia Santi
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Carlo Severini
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Genetic diversity of Plasmodium vivax over time and space: a community-based study in rural Amazonia. Parasitology 2014; 142:374-84. [PMID: 25068581 DOI: 10.1017/s0031182014001176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To examine how community-level genetic diversity of the malaria parasite Plasmodium vivax varies across time and space, we investigated the dynamics of parasite polymorphisms during the early phases of occupation of a frontier settlement in the Amazon Basin of Brazil. Microsatellite characterization of 84 isolates of P. vivax sampled over 3 years revealed a moderate-to-high genetic diversity (mean expected heterozygosity, 0.699), with a large proportion (78.5%) of multiple-clone infections (MCI), but also a strong multilocus linkage disequilibrium (LD) consistent with rare outcrossing. Little temporal and no spatial clustering was observed in the distribution of parasite haplotypes. A single microsatellite haplotype was shared by 3 parasites collected during an outbreak; all other 81 haplotypes were recovered only once. The lowest parasite diversity, with the smallest proportion of MCI and the strongest LD, was observed at the time of the outbreak, providing a clear example of epidemic population structure in a human pathogen. Population genetic parameters returned to pre-outbreak values during last 2 years of study, despite the concomitant decline in malaria incidence. We suggest that parasite genotyping can be useful for tracking the spread of new parasite strains associated with outbreaks in areas approaching malaria elimination.
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Liu Y, Auburn S, Cao J, Trimarsanto H, Zhou H, Gray KA, Clark TG, Price RN, Cheng Q, Huang R, Gao Q. Genetic diversity and population structure of Plasmodium vivax in Central China. Malar J 2014; 13:262. [PMID: 25008859 PMCID: PMC4094906 DOI: 10.1186/1475-2875-13-262] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/29/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In Central China the declining incidence of Plasmodium vivax has been interrupted by epidemic expansions and imported cases. The impact of these changes on the local parasite population, and concurrent risks of future resurgence, was assessed. METHODS Plasmodium vivax isolates collected from Anhui and Jiangsu provinces, Central China between 2007 and 2010 were genotyped using capillary electrophoresis at seven polymorphic short tandem repeat markers. Spatial and temporal analyses of within-host and population diversity, population structure, and relatedness were conducted on these isolates. RESULTS Polyclonal infections were infrequent in the 94 isolates from Anhui (4%) and 25 from Jiangsu (12%), with a trend for increasing frequency from 2008 to 2010 (2 to 19%) when combined. Population diversity was high in both provinces and across the years tested (H(E) = 0.8 - 0.85). Differentiation between Anhui and Jiangsu was modest (F'(ST) = 0.1). Several clusters of isolates with identical multi-locus haplotypes were observed across both Anhui and Jiangsu. Linkage disequilibrium was strong in both populations and in each year tested (I(A)(S) = 0.2 - 0.4), but declined two- to four-fold when identical haplotypes were accounted for, indicative of occasional epidemic transmission dynamics. None of five imported isolates shared identical haplotypes to any of the central Chinese isolates. CONCLUSIONS The population genetic structure of P. vivax in Central China highlights unstable transmission, with limited barriers to gene flow between the central provinces. Despite low endemicity, population diversity remained high, but the reservoirs sustaining this diversity remain unclear. The challenge of imported cases and risks of resurgence emphasize the need for continued surveillance to detect early warning signals. Although parasite genotyping has potential to inform the management of outbreaks, further studies are required to identify suitable marker panels for resolving local from imported P. vivax isolates.
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Affiliation(s)
- Yaobao Liu
- Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People’s Republic of China
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jun Cao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People’s Republic of China
| | | | - Huayun Zhou
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People’s Republic of China
| | - Karen-Ann Gray
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Weary Dunlop Drive, Gallipoli Barracks, Enoggera, Queensland, Australia
| | - Taane G Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Weary Dunlop Drive, Gallipoli Barracks, Enoggera, Queensland, Australia
| | - Rui Huang
- Medical College of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Qi Gao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People’s Republic of China
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Al-Hamidhi S, Mahdy MAK, Idris MA, Bin Dajem SM, Al-Sheikh AAH, Al-Qahtani A, Al-Hashami Z, Al-Farsi H, Al-Mekhlafi AM, Saif-Ali R, Beja-Pereira A, Babiker HA. The prospect of malaria elimination in the Arabian Peninsula: a population genetic approach. INFECTION GENETICS AND EVOLUTION 2014; 27:25-31. [PMID: 24981966 DOI: 10.1016/j.meegid.2014.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 03/21/2014] [Accepted: 06/17/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND In the Arabian Peninsula malaria control is progressing steadily, backed by adequate logistic and political support. As a result, transmission has been interrupted throughout the region, with exception of limited sites in Yemen and Saudi Arabia. Here we examined Plasmodium falciparum parasites in these sites to assess if the above success has limited diversity and gene flow. METHODS We examined 108 P. falciparum isolates in three sites in Yemen (Taiz, Dhamar and Hodeidah) and 91 isolates from Saudi Arabia (Jazan). Nine microsatellites were analyzed for allelic diversity, multi-locus haplotype and inter-population differentiation. RESULTS Diversity at each locus (unbiased heterozygosity [H]) was relatively lower in Yemen; (Hodeidah, H=0.615, Taiz, H=0.66, Dhamar, H=0.481), compared to Saudi Arabia (Jazan, H=0.76). Microsatellites were distributed widely and private alleles, detected in a single population, were rare. Pairwise comparisons revealed that parasites population in Dhamar was relatively distanced (FST=0.19). However, Taiz (Yemen) (FST=0.065) and Hodeidah (FST=0.107) populations were closer to that in Jazan (Saudi Arabia). Nonetheless, parasites in the four sites can be considered as one population. CONCLUSION Although malaria risk in Saudi Arabia has been cut considerably, the extent of diversity and parasite genetic structure are indicative of a large population size. Elimination strategy should target demographic factors that favor parasite dispersal and flow of imported malaria.
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Affiliation(s)
- Salama Al-Hamidhi
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | - Mohammed A K Mahdy
- Research Department, University of Science and Technology, Sana'a, Yemen; Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mohamed Ahmed Idris
- Department of Microbiology and Immunology, Faculty of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | - Saad M Bin Dajem
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Ahmed Al-Qahtani
- Medical Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zainab Al-Hashami
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | - Hissa Al-Farsi
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | - Abdulsalam M Al-Mekhlafi
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Riyadh Saif-Ali
- Biochemistry Department, Faculty of Medicine, Sana'a University, Yemen
| | - Albano Beja-Pereira
- Research Centre in Biodiversity and Genetic Resources (CIBIO), University of Porto, Rua Padre Armando Quintas 7, Vairão 4485-661, Portugal
| | - Hamza A Babiker
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Sultan Qaboos University, Oman.
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Arnott A, Wapling J, Mueller I, Ramsland PA, Siba PM, Reeder JC, Barry AE. Distinct patterns of diversity, population structure and evolution in the AMA1 genes of sympatric Plasmodium falciparum and Plasmodium vivax populations of Papua New Guinea from an area of similarly high transmission. Malar J 2014; 13:233. [PMID: 24930015 PMCID: PMC4085730 DOI: 10.1186/1475-2875-13-233] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/22/2014] [Indexed: 12/19/2022] Open
Abstract
Background As Plasmodium falciparum and Plasmodium vivax co-exist in most malaria-endemic regions outside sub-Saharan Africa, malaria control strategies in these areas must target both species in order to succeed. Population genetic analyses can predict the effectiveness of interventions including vaccines, by providing insight into patterns of diversity and evolution. The aim of this study was to investigate the population genetics of leading malaria vaccine candidate AMA1 in sympatric P. falciparum and P. vivax populations of Papua New Guinea (PNG), an area of similarly high prevalence (Pf = 22.3 to 38.8%, Pv = 15.3 to 31.8%). Methods A total of 72 Pfama1 and 102 Pvama1 sequences were collected from two distinct areas, Madang and Wosera, on the highly endemic PNG north coast. Results Despite a greater number of polymorphic sites in the AMA1 genes of P. falciparum (Madang = 52; Wosera = 56) compared to P. vivax (Madang = 36, Wosera = 34), the number of AMA1 haplotypes, haplotype diversity (Hd) and recombination (R) was far lower for P. falciparum (Madang = 12, Wosera = 20; Hd ≤0.92, R ≤45.8) than for P. vivax (Madang = 50, Wosera = 38; Hd = 0.99, R = ≤70.9). Balancing selection was detected only within domain I of AMA1 for P. vivax, and in both domains I and III for P. falciparum. Conclusions Higher diversity in the genes encoding P. vivax AMA1 than in P. falciparum AMA1 in this highly endemic area has important implications for development of AMA1-based vaccines in PNG and beyond. These results also suggest a smaller effective population size of P. falciparum compared to P. vivax, a finding that warrants further investigation. Differing patterns of selection on the AMA1 genes indicate that critical antigenic sites may differ between the species, highlighting the need for independent investigations of these two leading vaccine candidates.
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Affiliation(s)
| | | | | | | | | | | | - Alyssa E Barry
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.
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Plasmodium vivax population structure and transmission dynamics in Sabah Malaysia. PLoS One 2013; 8:e82553. [PMID: 24358203 PMCID: PMC3866266 DOI: 10.1371/journal.pone.0082553] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/27/2013] [Indexed: 11/19/2022] Open
Abstract
Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (FST = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI = 1.38) and KK (mean MOI = 1.19). However, population diversity remained moderate (HE = 0.583 in KM and HE = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (IAS >0.5 [P<0.0001] in KK and KM) declined sharply when identical haplotypes were represented once (IAS = 0.07 [P = 0.0076] in KM, and IAS = -0.003 [P = 0.606] in KK). All 8 recurrences, likely to be relapses, were homologous to the prior infection. These recurrences may promote the persistence of parasite lineages, sustaining local diversity. In summary, Sabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria elimination.
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Gray KA, Dowd S, Bain L, Bobogare A, Wini L, Shanks GD, Cheng Q. Population genetics of Plasmodium falciparum and Plasmodium vivax and asymptomatic malaria in Temotu Province, Solomon Islands. Malar J 2013; 12:429. [PMID: 24261646 PMCID: PMC4222835 DOI: 10.1186/1475-2875-12-429] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/07/2013] [Indexed: 11/10/2022] Open
Abstract
Background Temotu Province, Solomon Islands is progressing toward malaria elimination. A baseline survey conducted in 2008 showed that most Plasmodium infections in the province were of low parasite density and asymptomatic infections. To better understand mechanisms underlying these malaria transmission characteristics genetic diversity and relationships among Plasmodium falciparum and Plasmodium vivax populations in the province were examined. Methods Forty-five P. falciparum and 67 P. vivax samples collected in the 2008 baseline survey were successfully genotyped using eight P. falciparum and seven P. vivax microsatellite markers. Genetic diversity, relationships and distribution of both P. falciparum and P. vivax populations were analysed. Results Plasmodium falciparum population exhibited low diversity with 19 haplotypes identified and had closely related clusters indicating clonal expansion. Interestingly, a dominant haplotype was significantly associated with fever and high parasite density. In contrast, the P. vivax population was highly diverse with 58 haplotypes identified that were not closely related. Parasite populations between different islands in the province showed low genetic differentiation. Conclusion The low diversity and clonal population of P. falciparum population may partially account for clinical immunity developed against illness. However, it is possible that importation of a new P. falciparum strain was the major cause of illness. High diversity in P. vivax population and low relatedness between strains suggested clinical immunity to P. vivax may be maintained by different mechanisms. The genetic diversity, population structure and distribution of strains indicate that transmission of P. falciparum was low, but that of P. vivax was still high in 2008. These data will be useful for assessing changes in malaria transmission resulting from interventions.
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Affiliation(s)
- Karen-Ann Gray
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Weary Dunlop Drive, Gallipoli Barracks, Enoggera, QLD, 4051, Australia.
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Arnott A, Mueller I, Ramsland PA, Siba PM, Reeder JC, Barry AE. Global Population Structure of the Genes Encoding the Malaria Vaccine Candidate, Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1). PLoS Negl Trop Dis 2013; 7:e2506. [PMID: 24205419 PMCID: PMC3814406 DOI: 10.1371/journal.pntd.0002506] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/16/2013] [Indexed: 12/22/2022] Open
Abstract
Background The Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1) is a promising malaria vaccine candidate, however it remains unclear which regions are naturally targeted by host immunity and whether its high genetic diversity will preclude coverage by a monovalent vaccine. To assess its feasibility as a vaccine candidate, we investigated the global population structure of PvAMA1. Methodology and Principal Findings New sequences from Papua New Guinea (PNG, n = 102) were analysed together with published sequences from Thailand (n = 158), India (n = 8), Sri Lanka (n = 23), Venezuela (n = 74) and a collection of isolates from disparate geographic locations (n = 8). A total of 92 single nucleotide polymorphisms (SNPs) were identified including 22 synonymous SNPs and 70 non-synonymous (NS) SNPs. Polymorphisms and signatures of balancing (positive Tajima's D and low FST values) selection were predominantly clustered in domain I, suggesting it is a dominant target of protective immune responses. To estimate global antigenic diversity, haplotypes comprised of (i) non-singleton (n = 40) and (ii) common (≥10% minor allele frequency, n = 23) polymorphic amino acid sites were then analysed revealing a total of 219 and 210 distinct haplotypes, respectively. Although highly diverse, the 210 haplotypes comprised of only common polymorphisms were grouped into eleven clusters, however substantial geographic differentiation was observed, and this may have implications for the efficacy of PvAMA1 vaccines in different malaria-endemic areas. The PNG haplotypes form a distinct group of clusters not found in any other geographic region. Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines. Conclusions It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule. Traditionally misclassified as benign and neglected as a research priority, it is now understood that P. vivax is an increasingly important cause of human malaria. This important human pathogen poses an enormous obstacle to malaria control and elimination efforts due its broad geographic distribution, ability to cause recurring episodes of malaria after long periods of inactivity and extreme biodiversity. Vaccines are an essential component of global malaria control and elimination campaigns but the diversity of malaria antigens is thought to be a major cause of vaccine failure. Furthermore, at present the majority of current vaccine research is directed toward P. falciparum. The aims of this study were to investigate the global diversity of the P. vivax vaccine candidate, Apical Membrane Antigen 1 (PvAMA1), to determine the feasibility of designing a globally effective PvAMA1 vaccine and to determine which region of PvAMA1 is targeted by host immune responses, in order to identify the most promising vaccine candidates. We report that PvAMA1 diversity is extremely high, and that PvAMA1 domain I is a dominant target of host immune responses. These analyses of PvAMA1 diversity from several geographic regions provide a framework to guide development of a broadly efficacious P. vivax vaccine.
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Affiliation(s)
- Alicia Arnott
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Ivo Mueller
- Barcelona Centre for International Health Research, Barcelona, Spain
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Paul A. Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Peter M. Siba
- Papua New Guinea Institute for Medical Research, Goroka, Papua New Guinea
| | - John C. Reeder
- Centre for Population Health, Burnet Institute, Melbourne, Australia
- Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia
| | - Alyssa E. Barry
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- * E-mail:
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Iwagami M, Hwang SY, Kim SH, Park SJ, Lee GY, Matsumoto-Takahashi ELA, Kho WG, Kano S. Microsatellite DNA analysis revealed a drastic genetic change of Plasmodium vivax population in the Republic of Korea during 2002 and 2003. PLoS Negl Trop Dis 2013; 7:e2522. [PMID: 24205429 PMCID: PMC3814342 DOI: 10.1371/journal.pntd.0002522] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/24/2013] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Vivax malaria was successfully eliminated in the Republic of Korea (South Korea) in the late 1970s, but it was found to have re-emerged from 1993. In order to control malaria and evaluate the effectiveness of malaria controls, it is important to develop a spatiotemporal understanding of the genetic structure of the parasite population. Here, we estimated the population structure and temporal dynamics of the transmission of Plasmodium vivax in South Korea by analyzing microsatellite DNA markers of the parasite. METHODOLOGY/PRINCIPAL FINDINGS We analyzed 14 microsatellite DNA loci of the P. vivax genome from 163 South Korean isolates collected from 1994 to 2008. Allelic data were used to analyze linkage disequilibrium (LD), genetic differentiation and population structure, in order to make a detailed estimate of temporal change in the parasite population. The LD analysis showed a gradual decrease in LD levels, while the levels of genetic differentiation between successive years and analysis of the population structure based on the Bayesian approach suggested that a drastic genetic change occurred in the South Korean population during 2002 and 2003. CONCLUSIONS/SIGNIFICANCE Although relapse and asymptomatic parasite carriage might influence the population structure to some extent, our results suggested the continual introduction of P. vivax into South Korea through other parasite population sources. One possible source, particularly during 2002 and 2003, is North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and temporal dynamics of parasite transmission; information that can assist in the elimination of vivax malaria in endemic areas.
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Affiliation(s)
- Moritoshi Iwagami
- Department of Tropical Medicine and Malaria, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Seung-Young Hwang
- Department of Parasitology, Inje University College of Medicine, Busanjin-gu, Busan, Korea
| | - So-Hee Kim
- Department of Infectious Disease and Malaria, Paik Institute of Clinical Research, Inje University, Busanjin-gu, Busan, Korea
| | - So-Jung Park
- Department of Infectious Disease and Malaria, Paik Institute of Clinical Research, Inje University, Busanjin-gu, Busan, Korea
| | - Ga-Young Lee
- Department of Parasitology, Inje University College of Medicine, Busanjin-gu, Busan, Korea
| | - Emilie Louise Akiko Matsumoto-Takahashi
- Department of Tropical Medicine and Malaria, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- Department of Community and Global Health, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Weon-Gyu Kho
- Department of Parasitology, Inje University College of Medicine, Busanjin-gu, Busan, Korea
- Department of Infectious Disease and Malaria, Paik Institute of Clinical Research, Inje University, Busanjin-gu, Busan, Korea
| | - Shigeyuki Kano
- Department of Tropical Medicine and Malaria, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
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Al-Hamidhi S, Mahdy MAK, Al-Hashami Z, Al-Farsi H, Al-mekhlafi AM, Idris MA, Beja-Pereira A, Babiker HA. Genetic diversity of Plasmodium falciparum and distribution of drug resistance haplotypes in Yemen. Malar J 2013; 12:244. [PMID: 23855834 PMCID: PMC3729657 DOI: 10.1186/1475-2875-12-244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/11/2013] [Indexed: 11/25/2022] Open
Abstract
Background Despite evident success of malaria control in many sites in the Arabian Peninsula, malaria remains endemic in a few spots, in Yemen and south-west of Saudi Arabia. In addition to local transmission, imported malaria sustains an extra source of parasites that can challenge the strengths of local control strategies. This study examined the genetic diversity of Plasmodium falciparum in Yemen and mutations of drug resistant genes, to elucidate parasite structure and distribution of drug resistance genotypes in the region. Methods Five polymorphic loci (MSP-2, Pfg377 and three microsatellites on chromosome 8) not involved in anti-malarial drug resistance, and four drug resistant genes (pfcrt, pfmdr1, dhfr and dhps) were genotyped in 108 P. falciparum isolates collected in three sites in Yemen: Dhamar, Hodeidah and Taiz. Results High diversity was seen in non-drug genes, pfg377 (He = 0.66), msp-2 (He = 0.80) and three microsatellites on chr 8, 7.7 kb (He = 0.88), 4.3 kb (He = 0.77) and 0.8 kb (He = 0.71). There was a high level of mixed-genotype infections (57%), with an average 1.8 genotypes per patient. No linkage disequilibrium was seen between drug resistant genes and the non-drug markers (p < 0.05). Genetic differentiation between populations was low (most pair-wise FST values <0.03), indicating extensive gene flow between the parasites in the three sites. There was a high prevalence of mutations in pfmdr1, pfcrt and dhfr; with four mutant pfmdr1 genotypes (NFCDD[57%], NFSND[21%], YFCDD[13%] and YFSND[8% ]), two mutant pfcrt genotypes (CVIET[89%] and SVMNT[4%]) and one mutant dhfr genotype (ICNI[53.7%]). However, no dhps mutations were detected. Conclusion The high diversity of P. falciparum in Yemen is indicative of a large parasite reservoir, which represents a challenge to control efforts. The presence of two distinct pfcrt genotype, CVIET and SVMNT, suggests that chloroquine resistance can possibly be related to a migratory path from Africa and Asia. The absence of the triple mutant dhfr genotype (IRN) and dhps mutations supports the use of artesunate + sulphadoxine-pyrimethamine as first-line therapy. However, the prevalent pfmdr1 genotype NFSND [21%] has previously been associated with tolerance/resistance response to artemisinin combination therapy (ACT). Regular surveys are, therefore, important to monitor spread of pfmdr1 and dhfr mutations and response to ACT.
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