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De Meulenaere K, Cuypers WL, Gauglitz JM, Guetens P, Rosanas-Urgell A, Laukens K, Cuypers B. Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling. mBio 2024; 15:e0196723. [PMID: 38054750 PMCID: PMC10790762 DOI: 10.1128/mbio.01967-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Malaria is caused by parasites of the genus Plasmodium, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich Plasmodium DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich Plasmodium reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches Plasmodium reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim L. Cuypers
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
| | - Julia M. Gauglitz
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
| | - Pieter Guetens
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | - Bart Cuypers
- Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
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2
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Simpson SV, Nundu SS, Arima H, Kaneko O, Mita T, Culleton R, Yamamoto T. The diversity of Plasmodium falciparum isolates from asymptomatic and symptomatic school-age children in Kinshasa Province, Democratic Republic of Congo. Malar J 2023; 22:102. [PMID: 36941587 PMCID: PMC10025789 DOI: 10.1186/s12936-023-04528-z] [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: 10/13/2022] [Accepted: 03/10/2023] [Indexed: 03/22/2023] Open
Abstract
BACKGROUND Understanding Plasmodium falciparum population diversity and transmission dynamics provides information on the intensity of malaria transmission, which is needed for assessing malaria control interventions. This study aimed to determine P. falciparum allelic diversity and multiplicity of infection (MOI) among asymptomatic and symptomatic school-age children in Kinshasa Province, Democratic Republic of Congo (DRC). METHODS A total of 438 DNA samples (248 asymptomatic and 190 symptomatic) were characterized by nested PCR and genotyping the polymorphic regions of pfmsp1 block 2 and pfmsp2 block 3. RESULTS Nine allele types were observed in pfmsp1 block2. The K1-type allele was predominant with 78% (229/293) prevalence, followed by the MAD20-type allele (52%, 152/293) and RO33-type allele (44%, 129/293). Twelve alleles were detected in pfmsp2, and the 3D7-type allele was the most frequent with 84% (256/304) prevalence, followed by the FC27-type allele (66%, 201/304). Polyclonal infections were detected in 63% (95% CI 56, 69) of the samples, and the MOI (SD) was 1.99 (0.97) in P. falciparum single-species infections. MOIs significantly increased in P. falciparum isolates from symptomatic parasite carriers compared with asymptomatic carriers (2.24 versus 1.69, adjusted b: 0.36, (95% CI 0.01, 0.72), p = 0.046) and parasitaemia > 10,000 parasites/µL compared to parasitaemia < 5000 parasites/µL (2.68 versus 1.63, adjusted b: 0.89, (95% CI 0.46, 1.25), p < 0.001). CONCLUSION This survey showed low allelic diversity and MOI of P. falciparum, which reflects a moderate intensity of malaria transmission in the study areas. MOIs were more likely to be common in symptomatic infections and increased with the parasitaemia level. Further studies in different transmission zones are needed to understand the epidemiology and parasite complexity in the DRC.
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Affiliation(s)
- Shirley V Simpson
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Sabin S Nundu
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan.
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
- Institut National de Recherche Biomédicale (INRB), Kinshasa-Gombe, Democratic Republic of Congo.
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Osamu Kaneko
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Richard Culleton
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Ehime, 790-8577, Japan
| | - Taro Yamamoto
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
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Wang X, Bai Y, Xiang Z, Zeng W, Wu Y, Zhao H, Zhao W, Chen X, Duan M, Li X, Zhu W, Sun K, Wu Y, Zhang Y, Li X, Rosenthal BM, Cui L, Yang Z. Genetic diversity of Plasmodium vivax populations from the China-Myanmar border identified by genotyping merozoite surface protein markers. Trop Med Health 2023; 51:2. [PMID: 36631913 PMCID: PMC9832627 DOI: 10.1186/s41182-022-00492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Parasite diversity and population structure influence malaria control measures. Malaria transmission at international borders affects indigenous residents and migrants, defying management efforts and resulting in malaria re-introduction. Here we aimed to determine the extent and distribution of genetic variations in Plasmodium vivax populations and the complexity of infections along the China-Myanmar border. METHODS We collected clinical P. vivax samples from local and migrant malaria patients from Laiza and Myitsone, Kachin State, Myanmar, respectively. We characterized the polymorphisms in two P. vivax merozoite surface protein markers, Pvmsp-3α and Pvmsp-3β, by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. We sought to determine whether these genetic markers could differentiate these two neighboring parasite populations. RESULTS PCR revealed three major size variants for Pvmsp-3α and four for Pvmsp-3β among the 370 and 378 samples, respectively. PCR-RFLP resolved 26 fragment-size alleles by digesting Pvmsp-3α with Alu I and Hha I and 28 alleles by digesting Pvmsp-3β with Pst I. PCR-RFLP analysis of Pvmsp-3α found that infections in migrant laborers from Myitsone bore more alleles than did infections in residents of Laiza, while such difference was not evident from genotyping Pvmsp-3β. Infections originating from these two places contained distinct but overlapping subpopulations of P. vivax. Infections from Myitsone had a higher multiplicity of infection as judged by the size of the Pvmsp-3α amplicons and alleles after Alu I/Hha I digestion. CONCLUSIONS Migrant laborers from Myitsone and indigenous residents from Laiza harbored overlapping but genetically distinct P. vivax parasite populations. The results suggested a more diverse P. vivax population in Myitsone than in the border town of Laiza. PCR-RFLP of Pvmsp-3α offers a convenient method to determine the complexity of P. vivax infections and differentiate parasite populations.
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Affiliation(s)
- Xun Wang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yao Bai
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Zheng Xiang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Weilin Zeng
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yanrui Wu
- grid.285847.40000 0000 9588 0960Department of Cell Biology and Genetics, Kunming Medical University, Kunming, China
| | - Hui Zhao
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Wei Zhao
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xi Chen
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Mengxi Duan
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xiaosong Li
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Wenya Zhu
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Kemin Sun
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yiman Wu
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yanmei Zhang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xiaomei Li
- grid.285847.40000 0000 9588 0960Faculty of Public Health, Kunming Medical University, Kunming, Yunnan Province China
| | - Benjamin M. Rosenthal
- grid.508984.8Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD USA
| | - Liwang Cui
- grid.170693.a0000 0001 2353 285XDepartment of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Zhaoqing Yang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
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Deora N, Yadav C, Pande V, Sinha A. A systematic review and meta-analysis on sub-microscopic Plasmodium infections in India: Different perspectives and global challenges. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2022; 2:100012. [PMID: 37383294 PMCID: PMC10305983 DOI: 10.1016/j.lansea.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Background The long-term maintenance of parasite biomass below the detection threshold of microscopy may stymie malaria elimination. Variation in microscopists' competencies to detect and correctly identify parasite species reflect in microscopy sensitivity, resulting in incorrect species-specific burden. Methods The study estimated Plasmodium SMI pooled burden from published reports using a random effect model & identifies their hotspots in India. The study applied a prediction model for the first time on Indian data, emphasizing the importance of such models that can predict PCR-prevalence from slide- prevalence. Findings A total of 17,449 samples from 39 districts were examined for Plasmodium by microscopy and PCR. The overall heterogeneity in clinic-based and community-based studies was 91% and 96%, respectively, with the pooled prevalence of 3.63%. The SMI prevalence in individual studies ranged from 38.4% to 0.4%. Sensitivity of microscopy for mono-P. vivax (91%) was found to be better than mono-P. falciparum (82 %). But surprisingly, it was much lower for mixed PfPv (45%). Interpretation Primary regional data in the form of SMIs hot spots should be generated from countries on the verge of malaria elimination, and genetic monitoring should be integrated into national programs, particularly in key areas for successful malaria elimination. Funding Not applicable.
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Affiliation(s)
- Nimita Deora
- ICMR-National Institute of Malaria Research, New Delhi, India
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - C.P. Yadav
- ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Abhinav Sinha
- ICMR-National Institute of Malaria Research, New Delhi, India
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Pinto A, Archaga O, Mejía Á, Escober L, Henríquez J, Montoya A, Valdivia HO, Fontecha G. Evidence of a Recent Bottleneck in Plasmodium falciparum Populations on the Honduran-Nicaraguan Border. Pathogens 2021; 10:pathogens10111432. [PMID: 34832588 PMCID: PMC8617645 DOI: 10.3390/pathogens10111432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 12/04/2022] Open
Abstract
The countries of Central America and the island of Hispaniola have set the goal of eliminating malaria in less than a decade. Although efforts to reduce the malaria burden in the region have been successful, there has been an alarming increase in cases in the Nicaraguan Moskitia since 2014. The continuous decrease in cases between 2000 and 2014, followed by a rapid expansion from 2015 to the present, has generated a potential bottleneck effect in the populations of Plasmodium spp. Consequently, this study aimed to evaluate the genetic diversity of P. falciparum and the decrease in allelic richness in this population. The polymorphic regions of the pfmsp-1 and pfmsp-2 genes of patients with falciparum malaria from Honduras and Nicaragua were analyzed using nested PCR and sequencing. Most of the samples were classified into the K1 allelic subfamily of the pfmsp-1 gene and into the 3D7 subfamily of the pfmsp-2 gene. Despite the low genetic diversity found, more than half of the samples presented a polyclonal K1/RO33 haplotype. No sequence polymorphisms were found within each allelic subfamily. This study describes a notable decrease in the genetic diversity of P. falciparum in the Moskitia region after a bottleneck phenomenon. These results will be useful for future epidemiological investigations and the monitoring of malaria transmission in Central America.
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Affiliation(s)
- Alejandra Pinto
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Osman Archaga
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Ángel Mejía
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
| | - Lenin Escober
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa 11101, Honduras; (L.E.); (J.H.)
| | - Jessica Henríquez
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa 11101, Honduras; (L.E.); (J.H.)
| | - Alberto Montoya
- National Center for Diagnosis and Reference, Health Ministry, Managua 11001, Nicaragua;
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima 07006, Peru;
| | - Gustavo Fontecha
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa 11101, Honduras; (A.P.); (O.A.); (Á.M.)
- Correspondence: ; Tel.: +504-33935443
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6
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Kattenberg JH, Gumal DL, Ome-Kaius M, Kiniboro B, Philip M, Jally S, Kasian B, Sambale N, Siba PM, Karl S, Barry AE, Felger I, Kazura JW, Mueller I, Robinson LJ. The epidemiology of Plasmodium falciparum and Plasmodium vivax in East Sepik Province, Papua New Guinea, pre- and post-implementation of national malaria control efforts. Malar J 2020; 19:198. [PMID: 32503607 PMCID: PMC7275396 DOI: 10.1186/s12936-020-03265-x] [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: 01/20/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
Background In the past decade, national malaria control efforts in Papua New Guinea (PNG) have received renewed support, facilitating nationwide distribution of free long-lasting insecticidal nets (LLINs), as well as improvements in access to parasite-confirmed diagnosis and effective artemisinin-combination therapy in 2011–2012. Methods To study the effects of these intensified control efforts on the epidemiology and transmission of Plasmodium falciparum and Plasmodium vivax infections and investigate risk factors at the individual and household level, two cross-sectional surveys were conducted in the East Sepik Province of PNG; one in 2005, before the scale-up of national campaigns and one in late 2012-early 2013, after 2 rounds of LLIN distribution (2008 and 2011–2012). Differences between studies were investigated using Chi square (χ2), Fischer’s exact tests and Student’s t-test. Multivariable logistic regression models were built to investigate factors associated with infection at the individual and household level. Results The prevalence of P. falciparum and P. vivax in surveyed communities decreased from 55% (2005) to 9% (2013) and 36% to 6%, respectively. The mean multiplicity of infection (MOI) decreased from 1.8 to 1.6 for P. falciparum (p = 0.08) and from 2.2 to 1.4 for P. vivax (p < 0.001). Alongside these reductions, a shift towards a more uniform distribution of infections and illness across age groups was observed but there was greater heterogeneity across the study area and within the study villages. Microscopy positive infections and clinical cases in the household were associated with high rate infection households (> 50% of household members with Plasmodium infection). Conclusion After the scale-up of malaria control interventions in PNG between 2008 and 2012, there was a substantial reduction in P. falciparum and P. vivax infection rates in the studies villages in East Sepik Province. Understanding the extent of local heterogeneity in malaria transmission and the driving factors is critical to identify and implement targeted control strategies to ensure the ongoing success of malaria control in PNG and inform the development of tools required to achieve elimination. In household-based interventions, diagnostics with a sensitivity similar to (expert) microscopy could be used to identify and target high rate households.
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Affiliation(s)
- Johanna H Kattenberg
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea.,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Biomedical Sciences, Institute of Tropical Medicine, Malariology Unit, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Dulcie L Gumal
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea.,Disease Elimination Program, Vector-borne Diseases and Tropical Public Health Group, Burnet Institute, 85 Commercial Rd, Melbourne, VIC, 3004, Australia
| | - Maria Ome-Kaius
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea.,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Benson Kiniboro
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Matthew Philip
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Shadrach Jally
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Bernadine Kasian
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Naomi Sambale
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Peter M Siba
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea
| | - Stephan Karl
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea.,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,School of Medicine, Deakin University, Geelong and Burnet Institute, Melbourne, VIC, Australia
| | - Ingrid Felger
- Medical Parasitology and Infection Biology, Swiss Tropical & Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA
| | - Ivo Mueller
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Parasites and Insect Vectors, Malaria Parasites and Hosts Unit, Pasteur Institute, 25-28 rue du Docteur-Roux, 75724, Paris Cedex 15, France
| | - Leanne J Robinson
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, PO Box 378, Madang, 511, MP, Papua New Guinea. .,Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Disease Elimination Program, Vector-borne Diseases and Tropical Public Health Group, Burnet Institute, 85 Commercial Rd, Melbourne, VIC, 3004, Australia.
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7
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Graumans W, Andolina C, Awandu SS, Grignard L, Lanke K, Bousema T. Plasmodium falciparum Gametocyte Enrichment in Peripheral Blood Samples by Magnetic Fractionation: Gametocyte Yields and Possibilities to Reuse Columns. Am J Trop Med Hyg 2020; 100:572-577. [PMID: 30608048 PMCID: PMC6402936 DOI: 10.4269/ajtmh.18-0773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gametocytes are sexual stage malaria parasites responsible for transmission to mosquitoes. Multiple gametocyte-producing clones may be present in natural infections, but the molecular characterization of gametocytes is challenging. Because of their magnetic properties, gametocyte enrichment can be achieved by magnetic fractionation. This increases detection sensitivity and allows specific genotyping of clones that contribute to malaria transmission. Here, we determined the percentage of Plasmodium falciparum gametocytes successfully bound to magnetic activated cell sorting (MACS) LS columns during magnetic fractionation and assessed whether columns can be reused without risking contamination or affecting column binding efficiency. Bound column fractions were quantified using multiplex quantitative reverse transcription polymerase chain reaction (qRT-PCR) for male (pfMGET) and female (CCp4) gametocytes and ring-stage asexual parasites (SBP1). To investigate cross contamination between columns, parasite strain identity was determined by merozoite surface protein 2 genotyping followed by capillary electrophoresis fragment sizing. A reproducible high percentage of gametocytes was bound to MACS LS columns with < 5% gametocytes appearing in the flow-through and < 0.6% asexual ring-stage parasites appearing in the gametocyte fraction. A high yield (> 94%) of gametocyte enrichment was achieved when columns were used up to five times with lower binding success after eight times (79%). We observed no evidence for cross contamination between columns.
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Affiliation(s)
- Wouter Graumans
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Chiara Andolina
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Shehu S Awandu
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lynn Grignard
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kjerstin Lanke
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.,Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
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8
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PCR correction strategies for malaria drug trials: updates and clarifications. THE LANCET. INFECTIOUS DISEASES 2020; 20:e20-e25. [PMID: 31540841 DOI: 10.1016/s1473-3099(19)30426-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 07/03/2019] [Accepted: 07/19/2019] [Indexed: 11/24/2022]
Abstract
Malaria drug trials conducted in endemic areas face a major challenge in their analysis because it is difficult to establish whether parasitaemia in blood samples collected after treatment indicate drug failure or a new infection acquired after treatment. It is therefore vital to reliably distinguish drug failures from new infections in order to obtain accurate estimates of drug failure rates. This distinction can be achieved for Plasmodium falciparum by comparing parasite genotypes obtained at the time of treatment (the baseline) and on the day of recurring parasitaemia. Such PCR correction is required to obtain accurate failure rates, even for new effective drugs. Despite the routine use of PCR correction in surveillance of drug resistance and in clinical drug trials, limitations inherent to the molecular genotyping methods have led some researchers to question the validity of current PCR correction strategies. Here we describe and discuss recent developments in these genotyping approaches, with a particular focus on method validation and limitations of the genotyping strategies. Our aim is to update scientists from public and private bodies who are working on the development, deployment, and surveillance of new malaria drugs. We aim to promote discussion around these issues and argue for the adoption of improved standardised PCR correction methodologies.
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9
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Improving Methods for Analyzing Antimalarial Drug Efficacy Trials: Molecular Correction Based on Length-Polymorphic Markers msp-1, msp-2, and glurp. Antimicrob Agents Chemother 2019; 63:AAC.00590-19. [PMID: 31307982 PMCID: PMC6709465 DOI: 10.1128/aac.00590-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/02/2019] [Indexed: 01/14/2023] Open
Abstract
Drug efficacy trials monitor the continued efficacy of front-line drugs against falciparum malaria. Overestimating efficacy results in a country retaining a failing drug as first-line treatment with associated increases in morbidity and mortality, while underestimating drug effectiveness leads to removal of an effective treatment with substantial practical and economic implications. Drug efficacy trials monitor the continued efficacy of front-line drugs against falciparum malaria. Overestimating efficacy results in a country retaining a failing drug as first-line treatment with associated increases in morbidity and mortality, while underestimating drug effectiveness leads to removal of an effective treatment with substantial practical and economic implications. Trials are challenging: they require long durations of follow-up to detect drug failures, and patients are frequently reinfected during that period. Molecular correction based on parasite genotypes distinguishes reinfections from drug failures to ensure the accuracy of failure rate estimates. Several molecular correction “algorithms” have been proposed, but which is most accurate and/or robust remains unknown. We used pharmacological modeling to simulate parasite dynamics and genetic signals that occur in patients enrolled in malaria drug clinical trials. We compared estimates of treatment failure obtained from a selection of proposed molecular correction algorithms against the known “true” failure rate in the model. Our findings are as follows. (i) Molecular correction is essential to avoid substantial overestimates of drug failure rates. (ii) The current WHO-recommended algorithm consistently underestimates the true failure rate. (iii) Newly proposed algorithms produce more accurate failure rate estimates; the most accurate algorithm depends on the choice of drug, trial follow-up length, and transmission intensity. (iv) Long durations of patient follow-up may be counterproductive; large numbers of new infections accumulate and may be misclassified, overestimating drug failure rate. (v) Our model was highly consistent with existing in vivo data. The current WHO-recommended method for molecular correction and analysis of clinical trials should be reevaluated and updated.
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Taylor AR, Jacob PE, Neafsey DE, Buckee CO. Estimating Relatedness Between Malaria Parasites. Genetics 2019; 212:1337-1351. [PMID: 31209105 PMCID: PMC6707449 DOI: 10.1534/genetics.119.302120] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the relatedness of individuals within or between populations is a common goal in biology. Increasingly, relatedness features in genetic epidemiology studies of pathogens. These studies are relatively new compared to those in humans and other organisms, but are important for designing interventions and understanding pathogen transmission. Only recently have researchers begun to routinely apply relatedness to apicomplexan eukaryotic malaria parasites, and to date have used a range of different approaches on an ad hoc basis. Therefore, it remains unclear how to compare different studies and which measures to use. Here, we systematically compare measures based on identity-by-state (IBS) and identity-by-descent (IBD) using a globally diverse data set of malaria parasites, Plasmodium falciparum and P. vivax, and provide marker requirements for estimates based on IBD. We formally show that the informativeness of polyallelic markers for relatedness inference is maximized when alleles are equifrequent. Estimates based on IBS are sensitive to allele frequencies, which vary across populations and by experimental design. For portability across studies, we thus recommend estimates based on IBD. To generate estimates with errors below an arbitrary threshold of 0.1, we recommend ∼100 polyallelic or 200 biallelic markers. Marker requirements are immediately applicable to haploid malaria parasites and other haploid eukaryotes. C.I.s facilitate comparison when different marker sets are used. This is the first attempt to provide rigorous analysis of the reliability of, and requirements for, relatedness inference in malaria genetic epidemiology. We hope it will provide a basis for statistically informed prospective study design and surveillance strategies.
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Affiliation(s)
- Aimee R Taylor
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Pierre E Jacob
- Department of Statistics, Harvard University, Cambridge, Massachusetts 02138
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
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Nguitragool W, Karl S, White M, Koepfli C, Felger I, Singhasivanon P, Mueller I, Sattabongkot J. Highly heterogeneous residual malaria risk in western Thailand. Int J Parasitol 2019; 49:455-462. [PMID: 30954453 PMCID: PMC6996282 DOI: 10.1016/j.ijpara.2019.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 01/01/2023]
Abstract
There is a highly heterogenous risk of malaria infection among villagers in western Thailand. The molecular force of infection was determined in a low endemic setting. There is a strong correlation between malaria prevalence and the force of infection.
Over the past decades, the malaria burden in Thailand has substantially declined. Most infections now originate from the national border regions. In these areas, the prevalence of asymptomatic infections is still substantial and poses a challenge for the national malaria elimination program. To determine epidemiological parameters as well as risk factors for malaria infection in western Thailand, we carried out a cohort study in Kanchanaburi and Ratchaburi provinces on the Thailand-Myanmar border. Blood samples from 999 local participants were examined for malaria infection every 4 weeks between May 2013 and Jun 2014. Prevalence of Plasmodium falciparum and Plasmodium vivax was determined by quantitative PCR (qPCR) and showed a seasonal variation with values fluctuating from 1.7% to 4.2% for P. vivax and 0% to 1.3% for P. falciparum. Ninety percent of infections were asymptomatic. The annual molecular force of blood-stage infection (molFOB) was estimated by microsatellite genotyping to be 0.24 new infections per person-year for P. vivax and 0.02 new infections per person-year for P. falciparum. The distribution of infections was heterogenous, that is, the vast majority of infections (>80%) were found in a small number of individuals (<8% of the study population) who tested positive at multiple timepoints. Significant risk factors were detected for P. vivax infections, including previous clinical malaria, occupation in agriculture and travel to Myanmar. In contrast, indoor residual spraying was associated with a protection from infection. These findings provide a recent landscape of malaria epidemiology and emphasize the importance of novel strategies to target asymptomatic and imported infections.
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Affiliation(s)
- Wang Nguitragool
- Department of Molecular Tropical Medicine & Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stephan Karl
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Michael White
- Malaria: Parasites and Hosts Unit, Department of Parasites & Insect Vectors, Institute Pasteur, Paris, France
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid Felger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical & Public Health Institute, Basel, Switzerland
| | - Pratap Singhasivanon
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Malaria: Parasites and Hosts Unit, Department of Parasites & Insect Vectors, Institute Pasteur, Paris, France.
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Ghoshal S, Gajendra P, Datta Kanjilal S, Mitra M, Sengupta S. Diversity analysis of MSP1 identifies conserved epitope organization in block 2 amidst high sequence variability in Indian Plasmodium falciparum isolates. Malar J 2018; 17:447. [PMID: 30509263 PMCID: PMC6276175 DOI: 10.1186/s12936-018-2592-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/23/2018] [Indexed: 02/02/2023] Open
Abstract
Background Despite its immunogenicity, the polymorphic nature of merozoite surface protein 1, an important vaccine candidate for Plasmodium falciparum malaria, remains a concern. This study analyses the impact of genetic variability and parasite population structure on epitope organization of different MSP1 segments. Methods Altogether 98 blood samples collected from P. falciparum infected mild and severe malaria patients of Chhattisgarh and West Bengal were used to sequence regions encoding block 2 and MSP1-19 of msp1. Sequences were analysed using MEGA7, DnaSPv5, Arlequin3.5 and BepiPred. Results All three major MSP1 block 2 allele families namely K1, MAD20 and RO33 were detected in the samples and they together resulted in 41 indel variants. Chhattisgarh samples displayed an average MOI of 2.07 ± 1.59 which was higher in mild malaria and in age group < 18 years. Ultra-structure of block 2 alleles revealed that mutation and repeat expansion were two major mechanisms responsible for allelic variability of K1 and MAD20. Regions flanking block 2 were highly variable in Chhattisgarh with average mismatch differences (k) ranging from 1.198 to 5.156 for three families. In contrast, region encompassing MSP1-19 exhibited limited heterogeneity (kChhattisgarh = 1.45, kWest Bengal = 1.363). Of the 50 possible B cell linear epitopes predicted from block 2 variants, 94.9% (131 of 138) of the parasites could be represented by three conserved antigens. Conclusions Present data indicates that natural selection and transmission intensity jointly play a role in controlling allelic diversity of MSP1 in Indian parasite isolates. Despite remarkable genetic variability, a limited number of predominant and conserved epitopes are present in Indian parasite isolates reinstating the importance of MSP1 as a promising malaria vaccine candidate. Electronic supplementary material The online version of this article (10.1186/s12936-018-2592-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sharmistha Ghoshal
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India
| | - Pragya Gajendra
- School of Studies in Anthropology, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, 492010, India
| | - Sumana Datta Kanjilal
- Department of Pediatric Medicine, Institute of Post Graduate Medical Education & Research, Kolkata, West Bengal, India
| | - Mitashree Mitra
- School of Studies in Anthropology, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, 492010, India
| | - Sanghamitra Sengupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India.
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Fontecha G, Mejía RE, Banegas E, Ade MP, Mendoza L, Ortiz B, Sabillón I, Alvarado G, Matamoros G, Pinto A. Deletions of pfhrp2 and pfhrp3 genes of Plasmodium falciparum from Honduras, Guatemala and Nicaragua. Malar J 2018; 17:320. [PMID: 30170596 PMCID: PMC6119307 DOI: 10.1186/s12936-018-2470-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/27/2018] [Indexed: 01/02/2023] Open
Abstract
Background Malaria remains a public health problem in some countries of Central America. Rapid diagnostic tests (RDTs) are one of the most useful tools to assist in the diagnosis of malaria in remote areas. Since its introduction, a wide variety of RDTs have been developed for the detection of different parasite antigens. PfHRP2 is the most targeted antigen for the detection of Plasmodium falciparum infections. Genetic mutations and gene deletions are important factors influencing or affecting the performance of rapid diagnostic tests. Methods In order to demonstrate the presence or absence of the pfhrp2 and pfhrp3 genes and their flanking regions, a total of 128 blood samples from patients with P. falciparum infection from three Central American countries were analysed through nested or semi-nested PCR approaches. Results In total, 25.8 and 91.4% of the isolates lacked the region located between exon 1 and exon 2 of pfhrp2 and pfhrp3 genes, respectively. Parasites from the three countries showed deletions of one or both genes. The highest proportion of pfhrp2 deletions was found in Nicaragua while the isolates from Guatemala revealed the lowest number of pfhrp2 deletions. Parasites collected from Honduras showed the highest proportion of phfrp3 absence (96.2%). Twenty-one percent of isolates were double negative mutants for the exon 1–2 segment of both genes, and 6.3% of isolates lacked the full-length coding region of both genes. Conclusions This study provides molecular evidence of the existence of P. falciparum isolates lacking the pfhrp2 and pfhrp3 genes, and their flanking regions, in Honduras, Guatemala and Nicaragua. This finding could hinder progress in the control and elimination of malaria in Central America. Continuous evaluation of RDTs and molecular surveillance would be recommended.
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Affiliation(s)
- Gustavo Fontecha
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras.
| | - Rosa E Mejía
- Panamerican Health Organization, Tegucigalpa, Honduras
| | - Engels Banegas
- National Department of Surveillance, Ministry of Health, Tegucigalpa, Honduras
| | | | - Lisandro Mendoza
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
| | - Bryan Ortiz
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
| | - Isaac Sabillón
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
| | - Gerardo Alvarado
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
| | - Gabriela Matamoros
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
| | - Alejandra Pinto
- Microbiology Research Institute, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras
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Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda. Sci Rep 2018; 8:10159. [PMID: 29977002 PMCID: PMC6033881 DOI: 10.1038/s41598-018-28534-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular techniques are not routinely employed for malaria surveillance, while cross-sectional, community-based parasite surveys require significant resources. Here, we describe a novel use of malaria rapid diagnostic tests (RDTs) collected at a single facility as source material for sequencing to esimtate malaria transmission intensity across a relatively large catchment area. We extracted Plasmodium falciparum DNA from RDTs, then amplified and sequenced a region of the apical membrane antigen 1 (pfama1) using targeted amplicon deep sequencing. We determined the multiplicity of infection (MOI) for each sample and examined associations with demographic, clinical, and spatial factors. We successfully genotyped 223 of 287 (77.7%) of the samples. We demonstrated an inverse relationship between the MOI and elevation with individuals presenting from the highest elevation villages harboring infections approximately half as complex as those from the lowest (MOI 1.85 vs. 3.51, AOR 0.25, 95% CI 0.09-0.65, p = 0.004). This study demonstrates the feasibility and validity of using routinely-collected RDTs for molecular surveillance of malaria and has real-world utility, especially as the cost of high-throughpout sequencing continues to decline.
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Affiliation(s)
- Ross M Boyce
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.
| | - Nick Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Travis Fulton
- Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA
| | - Raquel Reyes
- Division of General Medicine & Clinical Epidemiology, University of North Carolina at Chapel Hill, 5039 Old Clinic Building, CB 7110, Chapel Hill, 27599, USA
| | - Michael Matte
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Moses Ntaro
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Edgar Mulogo
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Andreea Waltmann
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, 125 Nashua Street, Suite 722, Boston, 02114, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.,Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA.,Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
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15
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Grignard L, Gonçalves BP, Early AM, Daniels RF, Tiono AB, Guelbéogo WM, Ouédraogo A, van Veen EM, Lanke K, Diarra A, Nebie I, Sirima SB, Targett GA, Volkman SK, Neafsey DE, Wirth DF, Bousema T, Drakeley C. Transmission of molecularly undetectable circulating parasite clones leads to high infection complexity in mosquitoes post feeding. Int J Parasitol 2018; 48:671-677. [PMID: 29738740 PMCID: PMC6018601 DOI: 10.1016/j.ijpara.2018.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/04/2018] [Accepted: 02/26/2018] [Indexed: 11/24/2022]
Abstract
Additional parasite alleles were consistently identified in mosquitoes compared with the human blood sample they had fed on. Assessments of Plasmodium falciparum complexity relying on single time-point collections miss transmissible clones. Low-density gametocyte – producing clones are capable of successfully establishing infections in mosquitoes.
Plasmodium falciparum malaria infections often comprise multiple distinct parasite clones. Few datasets have directly assessed infection complexity in humans and mosquitoes they infect. Examining parasites using molecular tools may provide insights into the selective transmissibility of isolates. Using capillary electrophoresis genotyping and next generation amplicon sequencing, we analysed complexity of parasite infections in human blood and in the midguts of mosquitoes that became infected in membrane feeding experiments using the same blood material in two West African settings. Median numbers of clones in humans and mosquitoes were higher in samples from Burkina Faso (4.5, interquartile range 2–8 for humans; and 2, interquartile range 1–3 for mosquitoes) than in The Gambia (2, interquartile range 1–3 and 1, interquartile range 1–3, for humans and mosquitoes, respectively). Whilst the median number of clones was commonly higher in human blood samples, not all transmitted alleles were detectable in the human peripheral blood. In both study sample sets, additional parasite alleles were identified in mosquitoes compared with the matched human samples (10–88.9% of all clones/feeding assay, n = 73 feeding assays). The results are likely due to preferential amplification of the most abundant clones in peripheral blood but confirm the presence of low density clones that produce transmissible sexual stage parasites.
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Affiliation(s)
- Lynn Grignard
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK.
| | - Bronner P Gonçalves
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Rachel F Daniels
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alfred B Tiono
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Wamdaogo M Guelbéogo
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Alphonse Ouédraogo
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Elke M van Veen
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kjerstin Lanke
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amidou Diarra
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Issa Nebie
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Sodiomon B Sirima
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Geoff A Targett
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; School of Nursing and Health Sciences, Simmons College, Boston, MA, USA
| | | | - Dyann F Wirth
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Teun Bousema
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
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Plasmodium vivax and Plasmodium falciparum infection dynamics: re-infections, recrudescences and relapses. Malar J 2018; 17:170. [PMID: 29665803 PMCID: PMC5905131 DOI: 10.1186/s12936-018-2318-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022] Open
Abstract
Background In malaria endemic populations, complex patterns of Plasmodium vivax and Plasmodium falciparum blood-stage infection dynamics may be observed. Genotyping samples from longitudinal cohort studies for merozoite surface protein (msp) variants increases the information available in the data, allowing multiple infecting parasite clones in a single individual to be identified. msp genotyped samples from two longitudinal cohorts in Papua New Guinea (PNG) and Thailand were analysed using a statistical model where the times of acquisition and clearance of each clone in every individual were estimated using a process of data augmentation. Results For the populations analysed, the duration of blood-stage P. falciparum infection was estimated as 36 (95% Credible Interval (CrI): 29, 44) days in PNG, and 135 (95% CrI 94, 191) days in Thailand. Experiments on simulated data indicated that it was not possible to accurately estimate the duration of blood-stage P. vivax infections due to the lack of identifiability between a single blood-stage infection and multiple, sequential blood-stage infections caused by relapses. Despite this limitation, the method and data point towards short duration of blood-stage P. vivax infection with a lower bound of 24 days in PNG, and 29 days in Thailand. On an individual level, P. vivax recurrences cannot be definitively classified into re-infections, recrudescences or relapses, but a probabilistic relapse phenotype can be assigned to each P. vivax sample, allowing investigation of the association between epidemiological covariates and the incidence of relapses. Conclusion The statistical model developed here provides a useful new tool for in-depth analysis of malaria data from longitudinal cohort studies, and future application to data sets with multi-locus genotyping will allow more detailed investigation of infection dynamics. Electronic supplementary material The online version of this article (10.1186/s12936-018-2318-1) contains supplementary material, which is available to authorized users.
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Examining the human infectious reservoir for Plasmodium falciparum malaria in areas of differing transmission intensity. Nat Commun 2017; 8:1133. [PMID: 29074880 PMCID: PMC5658399 DOI: 10.1038/s41467-017-01270-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/05/2017] [Indexed: 12/20/2022] Open
Abstract
A detailed understanding of the human infectious reservoir is essential for improving malaria transmission-reducing interventions. Here we report a multi-regional assessment of population-wide malaria transmission potential based on 1209 mosquito feeding assays in endemic areas of Burkina Faso and Kenya. Across both sites, we identified 39 infectious individuals. In high endemicity settings, infectious individuals were identifiable by research-grade microscopy (92.6%; 25/27), whilst one of three infectious individuals in the lowest endemicity setting was detected by molecular techniques alone. The percentages of infected mosquitoes in the different surveys ranged from 0.05 (4/7716) to 1.6% (121/7749), and correlate positively with transmission intensity. We also estimated exposure to malaria vectors through genetic matching of blood from 1094 wild-caught bloodfed mosquitoes with that of humans resident in the same houses. Although adults transmitted fewer parasites to mosquitoes than children, they received more mosquito bites, thus balancing their contribution to the infectious reservoir. Heterogeneity in the transmission potential of individual hosts is an important feature of malaria. Here, the authors perform a multi-regional study of the human infectious reservoir in malaria-endemic regions of Burkina Faso and Kenya.
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Hofmann NE, Karl S, Wampfler R, Kiniboro B, Teliki A, Iga J, Waltmann A, Betuela I, Felger I, Robinson LJ, Mueller I. The complex relationship of exposure to new Plasmodium infections and incidence of clinical malaria in Papua New Guinea. eLife 2017; 6:23708. [PMID: 28862132 PMCID: PMC5606846 DOI: 10.7554/elife.23708] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 08/18/2017] [Indexed: 01/20/2023] Open
Abstract
The molecular force of blood-stage infection (molFOB) is a quantitative surrogate metric for malaria transmission at population level and for exposure at individual level. Relationships between molFOB, parasite prevalence and clinical incidence were assessed in a treatment-to-reinfection cohort, where P.vivax (Pv) hypnozoites were eliminated in half the children by primaquine (PQ). Discounting relapses, children acquired equal numbers of new P. falciparum (Pf) and Pv blood-stage infections/year (Pf-molFOB = 0–18, Pv-molFOB = 0–23) resulting in comparable spatial and temporal patterns in incidence and prevalence of infections. Including relapses, Pv-molFOB increased >3 fold (relative to PQ-treated children) showing greater heterogeneity at individual (Pv-molFOB = 0–36) and village levels. Pf- and Pv-molFOB were strongly associated with clinical episode risk. Yearly Pf clinical incidence rate (IR = 0.28) was higher than for Pv (IR = 0.12) despite lower Pf-molFOB. These relationships between molFOB, clinical incidence and parasite prevalence reveal a comparable decline in Pf and Pv transmission that is normally hidden by the high burden of Pv relapses. Clinical trial registration: ClinicalTrials.gov NCT02143934 Malaria is caused by five different species of parasites that are transmitted to humans by bites from parasite-carrying mosquitos. Once in human blood, the parasites rapidly multiply. People who live in countries where malaria is common may become infected and never show any symptoms because their immune systems are able to keep parasite numbers low. Repeated infections, or infection with more than one species of malaria parasite also are common. Some species of malaria, including Plasmodium vivax, can hibernate in the liver for weeks or months after the infection and only become active later. Asymptomatic infections, multi-parasite infections, and reactivating parasites make it hard to measure how often new malaria infections occur. One way scientists can determine if a new infection has occurred is by genotyping the parasites in a person’s blood. Genotyping involves looking for small differences in the parasite DNA. For example, a study in Papua New Guinea, where P. vivax is very common, showed that reactivations of hibernating parasites were more common than new infections. Now, Hofmann et al. use the same study in Papua New Guinea to compare the frequency and consequences of new infections with P. vivax and another malaria parasite, Plasmodium falciparum. In the study, 466 children from 6 villages were followed for 8 months with tests every 2 to 4 weeks to genotype the parasites in their blood. Some of the children were treated with antimalarial drugs to help wipe out any existing parasites including hibernating ones. While P. vivax was about twice as common in blood samples—likely due to reactivation—genotyping showed that new infections with the two parasites occur at equal rates and often at the same times and locations. Hofmann et al. also showed that some villages and some children had much higher rates of infection than others. This difference could not fully be explained by use of bednets or other preventive measures. Children were more likely to become ill from P. falciparum than P. vivax even though P. vivax was more common. But children with more frequent infections with P. falciparum seemed better able to manage the parasites and were less likely to develop symptoms that those with infrequent infections. The experiments show that genotyping may help scientists better track new malaria infections and develop better strategies to prevent or treat malaria.
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Affiliation(s)
- Natalie E Hofmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Stephan Karl
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Rahel Wampfler
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Benson Kiniboro
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Albina Teliki
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Jonah Iga
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Andreea Waltmann
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,University of Melbourne, Melbourne, Australia
| | - Inoni Betuela
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Leanne J Robinson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.,University of Melbourne, Melbourne, Australia.,Burnet Institute, Melbourne, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,University of Melbourne, Melbourne, Australia.,ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic-University of Barcelona, Barcelona, Spain.,Institut Pasteur, Paris, France
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Effects of liver-stage clearance by Primaquine on gametocyte carriage of Plasmodium vivax and P. falciparum. PLoS Negl Trop Dis 2017; 11:e0005753. [PMID: 28732068 PMCID: PMC5540608 DOI: 10.1371/journal.pntd.0005753] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/02/2017] [Accepted: 06/27/2017] [Indexed: 01/08/2023] Open
Abstract
Background Primaquine (PQ) is the only currently licensed antimalarial that prevents Plasmodium vivax (Pv) relapses. It also clears mature P. falciparum (Pf) gametocytes, thereby reducing post-treatment transmission. Randomized PQ treatment in a treatment-to-reinfection cohort in Papua New Guinean children permitted the study of Pv and Pf gametocyte carriage after radical cure and to investigate the contribution of Pv relapses. Methods Children received radical cure with Chloroquine, Artemether-Lumefantrine plus either PQ or placebo. Blood samples were subsequently collected in 2-to 4-weekly intervals over 8 months. Gametocytes were detected by quantitative reverse transcription-PCR targeting pvs25 and pfs25. Results PQ treatment reduced the incidence of Pv gametocytes by 73%, which was comparable to the effect of PQ on incidence of blood-stage infections. 92% of Pv and 79% of Pf gametocyte-positive infections were asymptomatic. Pv and to a lesser extent Pf gametocyte positivity and density were associated with high blood-stage parasite densities. Multivariate analysis revealed that the odds of gametocytes were significantly reduced in mixed-species infections compared to single-species infections for both species (ORPv = 0.39 [95% CI 0.25–0.62], ORPf = 0.33 [95% CI 0.18–0.60], p<0.001). No difference between the PQ and placebo treatment arms was observed in density of Pv gametocytes or in the proportion of Pv infections that carried gametocytes. First infections after blood-stage and placebo treatment, likely caused by a relapsing hypnozoite, were equally likely to carry gametocytes than first infections after PQ treatment, likely caused by an infective mosquito bite. Conclusion Pv relapses and new infections are associated with similar levels of gametocytaemia. Relapses thus contribute considerably to the Pv reservoir highlighting the importance of effective anti-hypnozoite treatment for efficient control of Pv. Trial registration ClinicalTrials.gov NCT02143934 Plasmodium vivax (Pv) mainly affects Asia, Central and South America as well as Ethiopia. In Papua New Guinea (PNG) Pv prevalence is among the highest worldwide. The biggest challenge for the control of Pv infections is the formation of dormant liver stages, which have the ability to relapse and cause disease even after successful clearance of asexual stages in the blood circulation. Primaquine is the only licensed drug that is able to prevent Pv relapses. A randomized treatment-to-reinfection cohort in Papua New Guinean children permitted permitted the study of Pv and P. falciparum gametocyte carriage after radical cure with Primaquine and to investigate the contribution of Pv relapses to transmission. We found that most gametocyte carriers in this study were detected in asymptomatic infections and that relapses and new infections are associated with similar Pv gametocyte production. These are strong arguments emphasizing the importance of sensitive detection and early treatment of asymptomatic and submicroscopic Plasmodium spp. infections and of anti-hypnozoite treatment for an effective control of Pv.
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20
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Mira-Martínez S, van Schuppen E, Amambua-Ngwa A, Bottieau E, Affara M, Van Esbroeck M, Vlieghe E, Guetens P, Rovira-Graells N, Gómez-Pérez GP, Alonso PL, D'Alessandro U, Rosanas-Urgell A, Cortés A. Expression of the Plasmodium falciparum Clonally Variant clag3 Genes in Human Infections. J Infect Dis 2017; 215:938-945. [PMID: 28419281 PMCID: PMC5407054 DOI: 10.1093/infdis/jix053] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/20/2017] [Indexed: 11/13/2022] Open
Abstract
Background Many genes of the malaria parasite Plasmodium falciparum show clonally variant expression regulated at the epigenetic level. These genes participate in fundamental host-parasite interactions and contribute to adaptive processes. However, little is known about their expression patterns during human infections. A peculiar case of clonally variant genes are the 2 nearly identical clag3 genes, clag3.1 and clag3.2, which mediate nutrient uptake and are linked to resistance to some toxic compounds. Methods We developed a procedure to characterize the expression of clag3 genes in naturally infected patients and in experimentally infected human volunteers. Results We provide the first description of clag3 expression during human infections, which revealed mutually exclusive expression and identified the gene predominantly expressed. Adaptation to culture conditions or selection with a toxic compound resulted in isolate-dependent changes in clag3 expression. We also found that clag3 expression patterns were reset during transmission stages. Conclusions Different environment conditions select for parasites with different clag3 expression patterns, implying functional differences between the proteins encoded. The epigenetic memory is likely erased before parasites start infection of a new human host. Altogether, our findings support the idea that clonally variant genes facilitate the adaptation of parasite populations to changing conditions through bet-hedging strategies.
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Affiliation(s)
- Sofía Mira-Martínez
- Institute of Tropical Medicine, Antwerp, Belgium.,Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Evi van Schuppen
- Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | | | - Muna Affara
- Medical Research Council Unit, Fajara, The Gambia
| | | | | | | | - Núria Rovira-Graells
- Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Gloria P Gómez-Pérez
- Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Pedro L Alonso
- Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Umberto D'Alessandro
- Institute of Tropical Medicine, Antwerp, Belgium.,Medical Research Council Unit, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, United Kingdom
| | | | - Alfred Cortés
- Barcelona Institute for Global Health (ISGlobal), Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
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21
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Natural immune response to Plasmodium vivax alpha-helical coiled coil protein motifs and its association with the risk of P. vivax malaria. PLoS One 2017. [PMID: 28651021 PMCID: PMC5484505 DOI: 10.1371/journal.pone.0179863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Protein α-helical coiled coil structures are known to induce antibodies able to block critical functions in different pathogens. In a previous study, a total of 50 proteins of Plasmodium vivax erythrocytic asexual stages containing α-helical coiled coil structural motifs were identified in silico, and the corresponding peptides were chemically synthesized. A total of 43 peptides were recognized by naturally acquired antibodies in plasma samples from both Papua New Guinea (PNG) and Colombian adult donors. In this study, the association between IgG antibodies to these peptides and clinical immunity was further explored by measuring total IgG antibody levels to 24 peptides in baseline samples from a longitudinal study of children aged 1–3 years (n = 164) followed for 16 months. Samples were reactive to all peptides tested. Eight peptides were recognized by >50% of individuals, whereas only one peptide had < 20% reactivity. Children infected at baseline were seropositive to 23/24 peptides. No significant association was observed between antibody titers and age or molecular force of infection, suggesting that antibody levels had already reached an equilibrium. There was a strong association between antibody levels to all peptides and protection against P. vivax clinical episodes during the 16 months follow-up. These results suggest that the selected coiled coil antigens might be good markers of both exposure and acquired immunity to P. vivax malaria, and further preclinical investigation should be performed to determine their potential as P. vivax vaccine antigens.
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22
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Schofield L, Ioannidis LJ, Karl S, Robinson LJ, Tan QY, Poole DP, Betuela I, Hill DL, Siba PM, Hansen DS, Mueller I, Eriksson EM. Synergistic effect of IL-12 and IL-18 induces TIM3 regulation of γδ T cell function and decreases the risk of clinical malaria in children living in Papua New Guinea. BMC Med 2017; 15:114. [PMID: 28615061 PMCID: PMC5471992 DOI: 10.1186/s12916-017-0883-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 05/22/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND γδ T cells are important for both protective immunity and immunopathogenesis during malaria infection. However, the immunological processes determining beneficial or detrimental effects on disease outcome remain elusive. The aim of this study was to examine expression and regulatory effect of the inhibitory receptor T-cell immunoglobulin domain and mucin domain 3 (TIM3) on γδ T cells. While TIM3 expression and function on conventional αβ T cells have been clearly defined, the equivalent characterization on γδ T cells and associations with disease outcomes is limited. This study investigated the functional capacity of TIM3+ γδ T cells and the underlying mechanisms contributing to TIM3 upregulation and established an association with malaria disease outcomes. METHODS We analyzed TIM3 expression on γδ T cells in 132 children aged 5-10 years living in malaria endemic areas of Papua New Guinea. TIM3 upregulation and effector functions of TIM3+ γδ T cells were assessed following in vitro stimulation with parasite-infected erythrocytes, phosphoantigen and/or cytokines. Associations between the proportion of TIM3-expressing cells and the molecular force of infection were tested using negative binomial regression and in a Cox proportional hazards model for time to first clinical episode. Multivariable analyses to determine the association of TIM3 and IL-18 levels were conducted using general linear models. Malaria infection mouse models were utilized to experimentally investigate the relationship between repeated exposure and TIM3 upregulation. RESULTS This study demonstrates that even in the absence of an active malaria infection, children of malaria endemic areas have an atypical population of TIM3-expressing γδ T cells (mean frequency TIM3+ of total γδ T cells 15.2% ± 12). Crucial factors required for γδ T cell TIM3 upregulation include IL-12/IL-18, and plasma IL-18 was associated with TIM3 expression (P = 0.002). Additionally, we show a relationship between TIM3 expression and infection with distinct parasite clones during repeated exposure. TIM3+ γδ T cells were functionally impaired and were associated with asymptomatic malaria infection (hazard ratio 0.54, P = 0.032). CONCLUSIONS Collectively our data demonstrate a novel role for IL-12/IL-18 in shaping the innate immune response and provide fundamental insight into aspects of γδ T cell immunoregulation. Furthermore, we show that TIM3 represents an important γδ T cell regulatory component involved in minimizing malaria symptoms.
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Affiliation(s)
- Louis Schofield
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Lisa J Ioannidis
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Stephan Karl
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Leanne J Robinson
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.,Papua New Guinea Institute of Medical Research, Goroka and Madang, Papua New Guinea.,Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Qiao Y Tan
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Daniel P Poole
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Inoni Betuela
- Papua New Guinea Institute of Medical Research, Goroka and Madang, Papua New Guinea
| | - Danika L Hill
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka and Madang, Papua New Guinea.,School of Veterinary and Biomedical Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Diana S Hansen
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Emily M Eriksson
- Walter and Eliza Hall Institute of Medical Research, Division of Population Health and Immunity, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia. .,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC, 3052, Australia.
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23
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Ruan W, Zhang LL, Feng Y, Zhang X, Chen HL, Lu QY, Yao LN, Hu W. Genetic diversity of Plasmodium Vivax revealed by the merozoite surface protein-1 icb5-6 fragment. Infect Dis Poverty 2017; 6:92. [PMID: 28578709 PMCID: PMC5458480 DOI: 10.1186/s40249-017-0302-6] [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: 08/11/2016] [Accepted: 04/12/2017] [Indexed: 02/04/2023] Open
Abstract
Background Plasmodium vivax remains a potential cause of morbidity and mortality for people living in its endemic areas. Understanding the genetic diversity of P. vivax from different regions is valuable for studying population dynamics and tracing the origins of parasites. The PvMSP-1 gene is highly polymorphic and has been used as a marker in many P. vivax population studies. The aim of this study was to investigate the genetic diversity of the PvMSP-1 gene icb5-6 fragment and to provide more genetic polymorphism data for further studies on P. vivax population structure and tracking of the origin of clinical cases. Methods Nested PCR and sequencing of the PvMSP-1 icb5-6 marker were performed to obtain the nucleotide sequences of 95 P. vivax isolates collected from Zhejiang province, China. To investigate the genetic diversity of PvMSP-1, the 95 nucleotide sequences of the PvMSP-1 icb5-6 fragment were genotyped and analyzed using DnaSP v5, MEGA software. Results The 95 P. vivax isolates collected from Zhejiang province were either indigenous cases or imported cases from different regions around the world. A total of 95 sequences ranging from 390 to 460 bp were obtained. The 95 sequences were genotyped into four allele-types (Sal I, Belem, R-III and R-IV) and 17 unique haplotypes. R-III and Sal I were the predominant allele-types. The haplotype diversity (Hd) and nucleotide diversity (Pi) were estimated to be 0.729 and 0.062, indicating that the PvMSP-1 icb5-6 fragment had the highest level of polymorphism due to frequent recombination processes and single nucleotide polymorphism. The values of dN/dS and Tajima’s D both suggested neutral selection for the PvMSP-1icb5-6 fragment. In addition, a rare recombinant style of R-IV type was identified. Conclusions This study presented high genetic diversity in the PvMSP-1 marker among P. vivax strains from around the world. The genetic data is valuable for expanding the polymorphism information on P. vivax, which could be helpful for further study on population dynamics and tracking the origin of P. vivax. Electronic supplementary material The online version of this article (doi:10.1186/s40249-017-0302-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Ruan
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Ling-Ling Zhang
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Yan Feng
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Xuan Zhang
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Hua-Liang Chen
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Qiao-Yi Lu
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Li-Nong Yao
- Department of Communicable Diseases of Control and Prevention, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China.
| | - Wei Hu
- School of Life Sciences, FuDan University, Shanghai, China.
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24
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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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25
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Das S, Muleba M, Stevenson JC, Pringle JC, Norris DE. Beyond the entomological inoculation rate: characterizing multiple blood feeding behavior and Plasmodium falciparum multiplicity of infection in Anopheles mosquitoes in northern Zambia. Parasit Vectors 2017; 10:45. [PMID: 28122597 PMCID: PMC5267472 DOI: 10.1186/s13071-017-1993-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 01/19/2017] [Indexed: 11/16/2022] Open
Abstract
Background A commonly used measure of malaria transmission intensity is the entomological inoculation rate (EIR), defined as the product of the human biting rate (HBR) and sporozoite infection rate (SIR). The EIR excludes molecular parameters that may influence vector control and surveillance strategies. The purpose of this study was to investigate Anopheles multiple blood feeding behavior (MBF) and Plasmodium falciparum multiplicity of infection (MOI) within the mosquito host in Nchelenge District, northern Zambia. Mosquitoes were collected from light traps and pyrethroid spray catch in Nchelenge in the 2013 wet season. All anophelines were tested for blood meal host, P. falciparum, and MOI using PCR. Circumsporozoite (CSP) ELISA and microsatellite analysis were performed to detect parasites in the mosquito and MBF, respectively. Statistical analyses used regression models to assess MBF and MOI and exact binomial test for human sex bias. Both MBF and MOI can enhance our understanding of malaria transmission dynamics beyond what is currently understood through conventional EIR estimates alone. Results The dominant malaria vectors collected in Nchelenge were Anopheles funestus (sensu stricto) and An. gambiae (s.s.) The EIRs of An. funestus (s.s.) and An. gambiae (s.s.) were 39.6 infectious bites/person/6 months (ib/p/6mo) and 5.9 ib/p/6mo, respectively, and took multiple human blood meals at high rates, 23.2 and 25.7% respectively. There was no bias in human host sex preference in the blood meals. The SIR was further characterized for parasite genetic diversity. The overall P. falciparum MOI was 6.4 in infected vectors, exceeding previously reported average MOIs in humans in Africa. Conclusions Both Anopheles MBF rates and P. falciparum MOI in Nchelenge were among some of the highest reported in sub-Saharan Africa. The results suggest an underestimation of the EIR and large numbers of circulating parasite clones. Together, the results describe important molecular aspects of transmission excluded from the traditional EIR measurement. These elements may provide more sensitive measures with which to assess changes in transmission intensity and risk in vector and parasite surveillance programs.
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Affiliation(s)
- Smita Das
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Mbanga Muleba
- Tropical Disease Research Centre, P.O. Box 71769, Ndola, Zambia
| | - Jennifer C Stevenson
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA.,Macha Research Trust, P.O. Box 630166, Choma, Zambia
| | - Julia C Pringle
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Douglas E Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD, 21205, USA.
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Rovira-Graells N, Aguilera-Simón S, Tintó-Font E, Cortés A. New Assays to Characterise Growth-Related Phenotypes of Plasmodium falciparum Reveal Variation in Density-Dependent Growth Inhibition between Parasite Lines. PLoS One 2016; 11:e0165358. [PMID: 27780272 PMCID: PMC5079629 DOI: 10.1371/journal.pone.0165358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
The growth phenotype of asexual blood stage malaria parasites can influence their virulence and also their ability to survive and achieve transmission to the next host, but there are few methods available to characterise parasite growth parameters in detail. We developed a new assay to measure growth rates at different starting parasitaemias in a 96-well format and applied it to characterise the growth of Plasmodium falciparum lines 3D7-A and 3D7-B, previously shown to have different invasion rates and to use different invasion pathways. Using this simple and accurate assay we found that 3D7-B is more sensitive to high initial parasitaemia than 3D7-A. This result indicates that different parasite lines show variation in their levels of density-dependent growth inhibition. We also developed a new assay to compare the duration of the asexual blood cycle between different parasite lines. The assay is based on the tight synchronisation of cultures to a 1 h parasite age window and the subsequent monitoring of schizont bursting and formation of new rings by flow cytometry. Using this assay we observed differences in the duration of the asexual blood cycle between parasite lines 3D7 and HB3. These two new assays will be useful to characterise variation in growth-related parameters and to identify growth phenotypes associated with the targeted deletion of specific genes or with particular genomic, transcriptomic or proteomic patterns. Furthermore, the identification of density-dependent growth inhibition as an intrinsic parasite property that varies between parasite lines expands the repertoire of measurable growth-related phenotypic traits that have the potential to influence the outcome of a malarial blood infection.
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Affiliation(s)
- Núria Rovira-Graells
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sara Aguilera-Simón
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Elisabet Tintó-Font
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfred Cortés
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain
- ICREA, Barcelona, Catalonia, Spain
- * E-mail:
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Ross A, Koepfli C, Schoepflin S, Timinao L, Siba P, Smith T, Mueller I, Felger I, Tanner M. The Incidence and Differential Seasonal Patterns of Plasmodium vivax Primary Infections and Relapses in a Cohort of Children in Papua New Guinea. PLoS Negl Trop Dis 2016; 10:e0004582. [PMID: 27144482 PMCID: PMC4856325 DOI: 10.1371/journal.pntd.0004582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 03/07/2016] [Indexed: 12/11/2022] Open
Abstract
Plasmodium vivax has the ability to relapse from dormant parasites in the liver weeks or months after inoculation, causing further blood-stage infection and potential onward transmission. Estimates of the force of blood-stage infections arising from primary infections and relapses are important for designing intervention strategies. However, in endemic settings their relative contributions are unclear. Infections are frequently asymptomatic, many individuals harbor multiple infections, and while high-resolution genotyping of blood samples enables individual infections to be distinguished, primary infections and relapses cannot be identified. We develop a model and fit it to longitudinal genotyping data from children in Papua New Guinea to estimate the incidence and seasonality of P vivax primary infection and relapse. The children, aged one to three years at enrolment, were followed up over 16 months with routine surveys every two months. Blood samples were taken at the routine visits and at other times if the child was ill. Samples positive by microscopy or a molecular method for species detection were genotyped using high-resolution capillary electrophoresis for P vivax MS16 and msp1F3, and P falciparum msp2. The data were summarized as longitudinal patterns of success or failure to detect a genotype at each routine time-point (eg 001000001). We assume that the seasonality of P vivax primary infection is similar to that of P falciparum since they are transmitted by the same vectors and, because P falciparum does not have the ability to relapse, the seasonality can be estimated. Relapses occurring during the study period can be a consequence of infections occurring prior to the study: we assume that the seasonal pattern of primary infections repeats over time. We incorporate information from parasitological and entomology studies to gain leverage for estimating the parameters, and take imperfect detection into account. We estimate the force of P vivax primary infections to be 11.5 (10.5, 12.3) for a three-year old child per year and the mean number of relapses per infection to be 4.3 (4.0, 4.6) over 16 months. The peak incidence of relapses occurred in the two month interval following the peak interval for primary infections: the contribution to the force of blood-stage infection from relapses is between 71% and 90% depending on the season. Our estimates contribute to knowledge of the P vivax epidemiology and have implications for the timing of intervention strategies targeting different stages of the life cycle. Plasmodium vivax is the most widespread of the malaria species affecting humans. It has the ability for parasites to lie dormant in liver cells and then to relapse weeks or months later, causing further blood-stage infections and onward transmission. Relapses present a challenge to control and elimination programs. The contribution of relapses to the force of blood-stage infection is not well established. While genotyping can distinguish individual infections, the difficulty lies in the inability to distinguish primary infections (occurring shortly after an infectious mosquito bite) and relapses. This is a gap in the knowledge of the epidemiology of P vivax. We develop a statistical model to tease out and estimate the contributions of primary infections and relapses to the force of blood-stage infection. We use data from a cohort of children in Papua New Guinea with genotyped routine blood samples. The study area has both P vivax and P falciparum malaria: we use the seasonality of P falciparum to estimate the seasonality of P vivax primary infections. We also take into account infections occurring prior to the study period and their subsequent relapses during the study period. We find that approximately 80% of the force of blood-stage infection l is contributed by relapses and that primary infections and relapses have different seasonal patterns. The findings are important to the epidemiology of P vivax and for designing intervention strategies targeting different stages of the parasite life cycle.
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Affiliation(s)
- Amanda Ross
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
| | - Cristian Koepfli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Population Health and Immunity Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Sonja Schoepflin
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Lincoln Timinao
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Thomas Smith
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute, Parkville, Australia
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Barcelona, Spain
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Marcel Tanner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Alam MS, Elahi R, Mohon AN, Al-Amin HM, Kibria MG, Khan WA, Khanum H, Haque R. Plasmodium falciparum Genetic Diversity in Bangladesh Does Not Suggest a Hypoendemic Population Structure. Am J Trop Med Hyg 2016; 94:1245-50. [PMID: 27139455 DOI: 10.4269/ajtmh.15-0446] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 03/28/2016] [Indexed: 11/07/2022] Open
Abstract
Despite the recommendation for the use of merozoite surface protein 1 (msp1), merozoite surface protein 2 (msp2), and glutamate-rich protein (glurp) genes as markers in drug efficacy studies by World Health Organization and their limited use in Bangladesh, the circulating Plasmodium falciparum population genetic structure has not yet been assessed in Bangladesh. This study presents a comprehensive report on the circulating P. falciparum population structure based on msp1, msp2, and glurp polymorphic gene markers in Bangladesh. Among the 130 pretreatment (day 0) P. falciparum samples from seven malaria-endemic districts, 14 distinct genotypes were observed for msp1, 20 for msp2, and 13 for glurp Polyclonal infection was reported in 94.6% (N = 123) of the samples. Multiplicity of infection (MOI) for msp1 was the highest (1.5) among the MOIs of the markers. The heterozygosity for msp1, msp2, and glurp was 0.89, 0.93, and 0.83, respectively. Data according to different malaria-endemic areas are also presented and discussed. Bangladesh is considered as a malaria-hypoendemic country. However, the prevalence of polyclonal infection and the genetic diversity of P. falciparum do not represent hypoendemicity.
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Affiliation(s)
- Mohammad Shafiul Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Rubayet Elahi
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Naser Mohon
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Hasan Mohammad Al-Amin
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Golam Kibria
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Wasif A Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Hamida Khanum
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, Canada; Parasitology Branch, Department of Zoology, University of Dhaka, Dhaka, Bangladesh
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Cook J, Grignard L, Al-Eryani S, Al-Selwei M, Mnzava A, Al-Yarie H, Rand A, Kleinschmidt I, Drakeley C. High heterogeneity of malaria transmission and a large sub-patent and diverse reservoir of infection in Wusab As Safil district, Republic of Yemen. Malar J 2016; 15:193. [PMID: 27059182 PMCID: PMC4826523 DOI: 10.1186/s12936-016-1249-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/30/2016] [Indexed: 11/10/2022] Open
Abstract
Background Yemen remains the country with the highest malaria transmission within the Arabian Peninsula and a source of imported cases to neighbouring countries. Methods This study collected samples from individuals resident in a valley in Western Yemen as a baseline to examine infection prevalence for a future trial. As well as rapid diagnostic test (RDT) and microscopy, a filter paper blood spot was collected for molecular and serological analyses. Results Samples were collected from 2261 individuals from 12 clusters across a study area of approximately 100 km2. Plasmodium falciparum infection prevalence was 12.4, 11.1 and 19.6 % by RDT, microscopy and polymerase chain reaction (PCR), respectively. RDT and microscopy did not detect 45 % of infections present, suggesting many infections were low-density. Infection prevalence and seroprevalence were highly heterogeneous between clusters, with evidence of higher exposure in clusters close to the wadi. The mean multiplicity of infection (MOI) was 2.3 and high heterozygosity and allelic richness were detected. Conclusions This highly diverse parasite population suggests a high degree of transmissibility and coupled with the substantial proportion of low-density infections, may pose challenges for malaria control and elimination efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1249-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jackie Cook
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK.
| | - Lynn Grignard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Samira Al-Eryani
- Department of Medical Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - Mustafa Al-Selwei
- Malaria Control Programme, Ministry of Public Health and Population, Sana'a, Yemen
| | - Abraham Mnzava
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Hafed Al-Yarie
- Malaria Control Programme, Ministry of Public Health and Population, Sana'a, Yemen
| | - Alison Rand
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Immo Kleinschmidt
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Chris Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Mawili-Mboumba DP, Mbondoukwe N, Adande E, Bouyou-Akotet MK. Allelic Diversity of MSP1 Gene in Plasmodium falciparum from Rural and Urban Areas of Gabon. THE KOREAN JOURNAL OF PARASITOLOGY 2015; 53:413-9. [PMID: 26323839 PMCID: PMC4566513 DOI: 10.3347/kjp.2015.53.4.413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/23/2015] [Accepted: 08/05/2015] [Indexed: 11/23/2022]
Abstract
The present study determined and compared the genetic diversity of Plasmodium falciparum strains infecting children living in 2 areas from Gabon with different malaria endemicity. Blood samples were collected from febrile children from 2008 to 2009 in 2 health centres from rural (Oyem) and urban (Owendo) areas. Genetic diversity was determined in P. falciparum isolates by analyzing the merozoite surface protein-1 (msp1) gene polymorphism using nested-PCR. Overall, 168 children with mild falciparum malaria were included. K1, Ro33, and Mad20 alleles were found in 110 (65.5%), 94 (55.9%), and 35 (20.8%) isolates, respectively, without difference according to the site (P>0.05). Allelic families' frequencies were comparable between children less than 5 years old from the 2 sites; while among the older children the proportions of Ro33 and Mad20 alleles were 1.7 to 2.0 fold higher at Oyem. Thirty-three different alleles were detected, 16 (48.5%) were common to both sites, and 10 out of the 17 specific alleles were found at Oyem. Furthermore, multiple infection carriers were frequent at Oyem (57.7% vs 42.2% at Owendo; P=0.04) where the complexity of infection was of 1.88 (±0.95) higher compared to that found at Owendo (1.55±0.75). Extended genetic diversity of P. falciparum strains infecting Gabonese symptomatic children and high multiplicity of infections were observed in rural area. Alleles common to the 2 sites were frequent; the site-specific alleles predominated in the rural area. Such distribution of the alleles should be taken into accounts when designing MSP1 or MSP2 malaria vaccine.
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Affiliation(s)
- Denise Patricia Mawili-Mboumba
- Department of Parasitology-Mycology, Faculty of Medicine, Université des Sciences de la Santé. BP4009, Libreville, Gabon
| | - Noé Mbondoukwe
- Department of Parasitology-Mycology, Faculty of Medicine, Université des Sciences de la Santé. BP4009, Libreville, Gabon
| | - Elvire Adande
- Department of Parasitology-Mycology, Faculty of Medicine, Université des Sciences de la Santé. BP4009, Libreville, Gabon
| | - Marielle Karine Bouyou-Akotet
- Department of Parasitology-Mycology, Faculty of Medicine, Université des Sciences de la Santé. BP4009, Libreville, Gabon
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Tadesse FG, Pett H, Baidjoe A, Lanke K, Grignard L, Sutherland C, Hall T, Drakeley C, Bousema T, Mamo H. Submicroscopic carriage of Plasmodium falciparum and Plasmodium vivax in a low endemic area in Ethiopia where no parasitaemia was detected by microscopy or rapid diagnostic test. Malar J 2015; 14:303. [PMID: 26242243 PMCID: PMC4524028 DOI: 10.1186/s12936-015-0821-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/23/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Motivated by the success in malaria control that was documented over the last decade Ethiopia is aiming at malaria elimination by 2020 in selected districts. It is currently unknown if asymptomatic, submicroscopic malaria parasite carriage may form a hurdle to achieve elimination. The elimination effort may further be complicated by possible glucose-6 phosphate dehydrogenase (G6PD) deficiency which would hinder the use of 8-aminoquinolines in the elimination efforts. METHOD In February 2014 a community-based cross-sectional survey was conducted in Malo, southwest Ethiopia. Finger-prick blood samples (n = 555) were tested for presence of Plasmodium falciparum and Plasmodium vivax with microscopy, rapid diagnostic test (RDT), and nested polymerase chain reaction (nPCR). Multiplicity of P. falciparum infections was determined based on genotyping the polymorphic merozoite surface protein-2 (MSP-2) gene. Individuals were also genotyped for mutations in the gene that produces G6PD. RESULTS All study participants were malaria infection negative by microscopy and RDT. Nested PCR revealed P. falciparum mono-infection in 5.2% (29/555), P. vivax mono-infection in 4.3% (24/555) and mixed infection in 0.2% (1/555) of individuals. All parasitemic individuals were afebrile (axillary temperature <37.5°C). None of the study participants carried mutations for the G6PD African A-(202GA) and Mediterranean (563CT) variants. All infections, except one, were single-clone infection by MSP-2 genotyping. CONCLUSION The detection of a substantial number of subpatent malaria infections in an apparently asymptomatic population without evidence for malaria transmission by conventional diagnostics raises questions about the path to malaria elimination. It is currently unknown how important these infections are for sustaining malaria transmission in the study sites. The absence of G6PD deficiency indicates that 8-aminoquinolines may be safely deployed to accelerate elimination initiatives.
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Affiliation(s)
- Fitsum G Tadesse
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525GA, Nijmegen, The Netherlands.
- Medical Biotechnology Unit, Institute of Biotechnology, Addis Ababa University, POBox 1176, Addis Ababa, Ethiopia.
| | - Helmi Pett
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525GA, Nijmegen, The Netherlands.
| | - Amrish Baidjoe
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525GA, Nijmegen, The Netherlands.
| | - Kjerstin Lanke
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525GA, Nijmegen, The Netherlands.
| | - Lynn Grignard
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Colin Sutherland
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Tom Hall
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Chris Drakeley
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525GA, Nijmegen, The Netherlands.
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, POBox 1176, Addis Ababa, Ethiopia.
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Koepfli C, Robinson LJ, Rarau P, Salib M, Sambale N, Wampfler R, Betuela I, Nuitragool W, Barry AE, Siba P, Felger I, Mueller I. Blood-Stage Parasitaemia and Age Determine Plasmodium falciparum and P. vivax Gametocytaemia in Papua New Guinea. PLoS One 2015; 10:e0126747. [PMID: 25996916 PMCID: PMC4440770 DOI: 10.1371/journal.pone.0126747] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/07/2015] [Indexed: 12/18/2022] Open
Abstract
A better understanding of human-to-mosquito transmission is crucial to control malaria. In order to assess factors associated with gametocyte carriage, 2083 samples were collected in a cross-sectional survey in Papua New Guinea. Plasmodium species were detected by light microscopy and qPCR and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all infections were submicroscopic. Gametocytes were detected in 60% of P. falciparum-positive and 51% of P. vivax-positive samples. Each 10-fold increase in parasite density led to a 1.8-fold and 3.3-fold increase in the odds of carrying P. falciparum and P. vivax gametocytes. Thus the proportion of gametocyte positive and gametocyte densities was highest in young children carrying high asexual parasite densities and in symptomatic individuals. Dilution series of gametocytes allowed absolute quantification of gametocyte densities by qRT-PCR and showed that pvs25 expression is 10-20 fold lower than pfs25 expression. Between 2006 and 2010 parasite prevalence in the study site has decreased by half. 90% of the remaining infections were asymptomatic and likely constitute an important reservoir of transmission. However, mean gametocyte densities were low (approx. 1-2 gametocyte/μL) and it remains to be determined to what extent low-density gametocyte positive individuals are infective to mosquitos.
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Affiliation(s)
- Cristian Koepfli
- Walter and Eliza Hall Institute, Population Health and Immunity Division, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
| | - Leanne J. Robinson
- Walter and Eliza Hall Institute, Population Health and Immunity Division, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Patricia Rarau
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Mary Salib
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Naomi Sambale
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Rahel Wampfler
- Swiss Tropical and Public Health Institute, Medical Parasitology and Infection Biology, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Inoni Betuela
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Wang Nuitragool
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Alyssa E. Barry
- Walter and Eliza Hall Institute, Population Health and Immunity Division, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Vector Borne Diseases Unit, Madang, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Medical Parasitology and Infection Biology, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Population Health and Immunity Division, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
- ISGlobal, Barcelona Centre for International Health Research, Barcelona, Spain
- * E-mail:
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Maïga-Ascofaré O, Rakotozandrindrainy R, Girmann M, Hahn A, Randriamampionona N, Poppert S, May J, Schwarz NG. Molecular epidemiology and seroprevalence in asymptomatic Plasmodium falciparum infections of Malagasy pregnant women in the highlands. Malar J 2015; 14:188. [PMID: 25935753 PMCID: PMC4432997 DOI: 10.1186/s12936-015-0704-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/22/2015] [Indexed: 11/29/2022] Open
Abstract
Background Malaria epidemiology in Madagascar is classified into four different areas, ranging from unstable seasonal transmission in the highlands to hyperendemic perennial transmission areas in the costal level. Most malaria studies in Madagascar are focused on symptomatic children. However, because of the low transmission in some areas with correspondingly low level of semi-immunity, adults are also at risk, in particular pregnant women. The objective of this study was to gain information on the genetic epidemiology of malarial infections in pregnant women in order to provide information for malaria control and elimination programmes in Madagascar. Methods Between May and August 2010, we carried out cross-sectional surveys targeting healthy pregnant women in six locations, three in the coastal area and three in the highlands at 850–1300 m. 1244 blood samples were screened for anti-Plasmodium falciparum antibodies by immunofluorescence test and for malarial infection by realtime-PCR. The prevalence of chloroquine and sulphadoxine-pyrimethamine resistance markers was also determined in all Plasmodium falciparum samples by PCR-RFLP as well as the multiplicity of infection through genotyping six neutral microsatellites. Results In the highlands, 67.4% of the women presented antibodies against Plasmodium falciparum and 9.2% were carrying parasites, at the coast 95.6% and 14.8%, respectively. In the mean, 1.2 clones were detected in infected pregnant woman in the highlands and 1.5 at the coast. A higher level of monoclonal infections was found in the highlands (85.4%) compared to the coast (61.8%). Resistance markers for sulphadoxine-pyrimethamine were present only in two sites. Conclusion Immunity is triggered in Malagasy highland populations when they are infected with malaria parasites, but these populations could also serve as a reservoir for epidemics. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0704-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Mirko Girmann
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - Andreas Hahn
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | | | | | - Jürgen May
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
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Jones S, Grignard L, Nebie I, Chilongola J, Dodoo D, Sauerwein R, Theisen M, Roeffen W, Singh SK, Singh RK, Singh S, Kyei-Baafour E, Tetteh K, Drakeley C, Bousema T. Naturally acquired antibody responses to recombinant Pfs230 and Pfs48/45 transmission blocking vaccine candidates. J Infect 2015; 71:117-27. [PMID: 25869538 DOI: 10.1016/j.jinf.2015.03.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 03/13/2015] [Accepted: 03/28/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Pfs48/45 and Pfs230 are Plasmodium falciparum sexual stage proteins and promising malaria transmission-blocking vaccine candidates. Antibody responses against these proteins may be naturally acquired and target antigens may be under selective pressure. This has consequences for the future evaluation of vaccine immunogenicity and efficacy in populations naturally exposed to malaria. METHODS We determined naturally acquired antibody responses to the recombinant proteins Pfs48/45-10C and Pfs230-230CMB in children from three malaria endemic settings in Ghana, Tanzania and Burkina Faso. We also examined genetic polymorphisms in the P. falciparum gene pfs48/45. RESULTS Antibody prevalence was 1.1-18.2% for 10C and 6.7-18.9% for 230CMB. In Burkina Faso we observed evidence of an age-dependent acquisition pattern for both 10C (p < 0.001) and 230CMB (p = 0.031). Membrane feeding assays on a separate dataset demonstrated an association between functional transmission reducing activity and antibody prevalence for both 10C (p = 0.017) and 230CMB (p = 0.049). 17 single nucleotide polymorphisms were found in pfs48/45 (from 126 samples), with 5 non-synonymous SNPs in the Pfs48/45 10C region. CONCLUSIONS We conclude there are naturally acquired antibody responses to both vaccine candidates which have functional relevance by reducing the transmissibility of infected individuals. We identified genetic polymorphisms, in pfs48/45 which exhibited geographical specificity.
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Affiliation(s)
- Sophie Jones
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Lynn Grignard
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Issa Nebie
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Daniel Dodoo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Robert Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Theisen
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark; Centre for Medical Parasitology at Department of International Health, Immunology, and Microbiology, University of Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Will Roeffen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Sanjay Singh
- Gennova Bio Pharmaceuticals Limited, Pune, India
| | - Eric Kyei-Baafour
- Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Kevin Tetteh
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Chris Drakeley
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Teun Bousema
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
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Acquisition of antibodies against Plasmodium falciparum merozoites and malaria immunity in young children and the influence of age, force of infection, and magnitude of response. Infect Immun 2014; 83:646-60. [PMID: 25422270 DOI: 10.1128/iai.02398-14] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Individuals in areas of Plasmodium falciparum endemicity develop immunity to malaria after repeated exposure. Knowledge of the acquisition and nature of protective immune responses to P. falciparum is presently limited, particularly for young children. We examined antibodies (IgM, IgG, and IgG subclasses) to merozoite antigens and their relationship to the prospective risk of malaria in children 1 to 4 years of age in a region of malaria endemicity in Papua New Guinea. IgG, IgG1, and IgG3 responses generally increased with age, were higher in children with active infection, and reflected geographic heterogeneity in malaria transmission. Antigenic properties, rather than host factors, appeared to be the main determinant of the type of IgG subclass produced. High antibody levels were not associated with protection from malaria; in contrast, they were typically associated with an increased risk of malaria. Adjustment for malaria exposure, using a novel molecular measure of the force of infection by P. falciparum, accounted for much of the increased risk, suggesting that the antibodies were markers of higher exposure to P. falciparum. Comparisons between antibodies in this cohort of young children and in a longitudinal cohort of older children suggested that the lack of protective association was explained by lower antibody levels among young children and that there is a threshold level of antibodies required for protection from malaria. Our results suggest that in populations with low immunity, such as young children, antibodies to merozoite antigens may act as biomarkers of malaria exposure and that, with increasing exposure and responses of higher magnitude, antibodies may act as biomarkers of protective immunity.
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Khan SN, Khan A, Khan S, Ayaz S, Attaullah S, Khan J, Khan MA, Ali I, Shah AH. PCR/RFLP-based analysis of genetically distinct Plasmodium vivax population of Pvmsp-3α and Pvmsp-3β genes in Pakistan. Malar J 2014; 13:355. [PMID: 25199951 PMCID: PMC4164714 DOI: 10.1186/1475-2875-13-355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/28/2014] [Indexed: 11/23/2022] Open
Abstract
Background Plasmodium vivax is one of the widespread human malarial parasites accounting for 75% of malaria epidemics. However, there is no baseline information about the status and nature of genetic variation of Plasmodium species circulating in various parts of Pakistan. The present study was aimed at observing the molecular epidemiology and genetic variation of Plasmodium vivax by analysing its merozoite surface protein-3α (msp-3α) and merozoite surface protein-3β (msp-3β) genes, by using suballele, species-specific, combined nested PCR/RFLP detection techniques. Methods A total of 230 blood samples from suspected subjects tested slide positive for vivax malaria were collected from Punjab, Sindh, Khyber Pakhtunkhwa, and Balochistan during the period May 2012 to December 2013. Combined nested PCR/RFLP technique was conducted using Pvmsp-3α and Pvmsp-3β genetic markers to detect extent of genetic variation in clinical isolates of P. vivax in the studied areas of Pakistan. Results By PCR, P. vivax, 202/230 (87.82%), was found to be widely distributed in the studied areas. PCR/RFLP analysis showed a high range of allelic variations for both msp-3α and msp-3β genetic markers of P. vivax, i.e., 21 alleles for msp-3α and 19 for msp-3β. Statistically a significant difference (p ≤ 0.05) was observed in the genetic diversity of the suballelic variants of msp-3α and msp-3β genes of P. vivax. Conclusion It is concluded that P. vivax populations are highly polymorphic and diverse allelic variants of Pvmsp-3α and Pvmsp-3β are present in Pakistan.
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Affiliation(s)
- Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology Kohat 26000, Khyber Pakhtunkhwa, Pakistan.
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Wampfler R, Timinao L, Beck HP, Soulama I, Tiono AB, Siba P, Mueller I, Felger I. Novel genotyping tools for investigating transmission dynamics of Plasmodium falciparum. J Infect Dis 2014; 210:1188-97. [PMID: 24771862 DOI: 10.1093/infdis/jiu236] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Differentiation between gametocyte-producing Plasmodium falciparum clones depends on both high levels of stage-specific transcripts and high genetic diversity of the selected genotyping marker obtained by a high-resolution typing method. By analyzing consecutive samples of one host, the contribution of each infecting clone to transmission and the dynamics of gametocyte production in multiclone infections can be studied. METHODS We have evaluated capillary electrophoresis based differentiation of 6 length-polymorphic gametocyte genes. RNA and DNA of 25 µL whole blood from 46 individuals from Burkina Faso were simultaneously genotyped. RESULTS Highest discrimination power was achieved by pfs230 with 18 alleles, followed by pfg377 with 15 alleles. When assays were performed in parallel on RNA and DNA, 85.7% of all pfs230 samples and 59.5% of all pfg377 samples contained at least one matching genotype in DNA and RNA. CONCLUSIONS The imperfect detection in both, DNA and RNA, was identified as major limitation for investigating transmission dynamics, owing primarily to the volume of blood processed and the incomplete representation of all clones in the sample tested. Abundant low-density gametocyte carriers impede clone detectability, which may be improved by analyzing larger volumes and detecting initially sequestered gametocyte clones in follow-up samples.
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Affiliation(s)
- Rahel Wampfler
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute University of Basel, Switzerland
| | - Lincoln Timinao
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute University of Basel, Switzerland Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province
| | - Hans-Peter Beck
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute University of Basel, Switzerland
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Alfred B Tiono
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia Barcelona Centre for International Health Research (CRESIB), Spain
| | - Ingrid Felger
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute University of Basel, Switzerland
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Genetic diversity of VAR2CSA ID1-DBL2Xb in worldwide Plasmodium falciparum populations: impact on vaccine design for placental malaria. INFECTION GENETICS AND EVOLUTION 2014; 25:81-92. [PMID: 24768682 DOI: 10.1016/j.meegid.2014.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 12/18/2022]
Abstract
In placental malaria (PM), sequestration of infected erythrocytes in the placenta is mediated by an interaction between VAR2CSA, a Plasmodium falciparum protein expressed on erythrocytes, and chondroitin sulfate A (CSA) on syncytiotrophoblasts. Recent works have identified ID1-DBL2Xb as the minimal CSA-binding region within VAR2CSA able to induce strong protective immunity, making it the leading candidate for the development of a vaccine against PM. Assessing the existence of population differences in the distribution of ID1-DBL2Xb polymorphisms is of paramount importance to determine whether geographic diversity must be considered when designing a candidate vaccine based on this fragment. In this study, we examined patterns of sequence variation of ID1-DBL2Xb in a large collection of P. falciparum field isolates (n=247) from different malaria-endemic areas, including Africa (Benin, Senegal, Cameroon and Madagascar), Asia (Cambodia), Oceania (Papua New Guinea), and Latin America (Peru). Detection of variants and estimation of their allele frequencies were performed using next-generation sequencing of DNA pools. A considerable amount of variation was detected along the whole gene segment, suggesting that several allelic variants may need to be included in a candidate vaccine to achieve broad population coverage. However, most sequence variants were common and extensively shared among worldwide parasite populations, demonstrating long term persistence of those polymorphisms, probably maintained through balancing selection. Therefore, a vaccine mixture including such stable antigen variants will be putatively applicable and efficacious in all world regions where malaria occurs. Despite similarity in ID1-DBL2Xb allele repertoire across geographic areas, several peaks of strong population differentiation were observed at specific polymorphic loci, pointing out putative targets of humoral immunity subject to positive immune selection.
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Taylor AR, Flegg JA, Nsobya SL, Yeka A, Kamya MR, Rosenthal PJ, Dorsey G, Sibley CH, Guerin PJ, Holmes CC. Estimation of malaria haplotype and genotype frequencies: a statistical approach to overcome the challenge associated with multiclonal infections. Malar J 2014; 13:102. [PMID: 24636676 PMCID: PMC4004158 DOI: 10.1186/1475-2875-13-102] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/26/2014] [Indexed: 11/16/2022] Open
Abstract
Background Reliable measures of anti-malarial resistance are crucial for malaria control. Resistance is typically a complex trait: multiple mutations in a single parasite (a haplotype or genotype) are necessary for elaboration of the resistant phenotype. The frequency of a genetic motif (proportion of parasite clones in the parasite population that carry a given allele, haplotype or genotype) is a useful measure of resistance. In areas of high endemicity, malaria patients generally harbour multiple parasite clones; they have multiplicities of infection (MOIs) greater than one. However, most standard experimental procedures only allow measurement of marker prevalence (proportion of patient blood samples that test positive for a given mutation or combination of mutations), not frequency. It is misleading to compare marker prevalence between sites that have different mean MOIs; frequencies are required instead. Methods A Bayesian statistical model was developed to estimate Plasmodium falciparum genetic motif frequencies from prevalence data collected in the field. To assess model performance and computational speed, a detailed simulation study was implemented. Application of the model was tested using datasets from five sites in Uganda. The datasets included prevalence data on markers of resistance to sulphadoxine-pyrimethamine and an average MOI estimate for each study site. Results The simulation study revealed that the genetic motif frequencies that were estimated using the model were more accurate and precise than conventional estimates based on direct counting. Importantly, the model did not require measurements of the MOI in each patient; it used the average MOI in the patient population. Furthermore, if a dataset included partially genotyped patient blood samples, the model imputed the data that were missing. Using the model and the Ugandan data, genotype frequencies were estimated and four biologically relevant genotypes were identified. Conclusions The model allows fast, accurate, reliable estimation of the frequency of genetic motifs associated with resistance to anti-malarials using prevalence data collected from malaria patients. The model does not require per-patient MOI measurements and can easily analyse data from five markers. The model will be a valuable tool for monitoring markers of anti-malarial drug resistance, including markers of resistance to artemisinin derivatives and partner drugs.
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Affiliation(s)
- Aimee R Taylor
- WorldWide Antimalarial Resistance Network (WWARN), Oxford, UK.
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Valizadeh V, Zakeri S, Mehrizi AA, Djadid ND. Population genetics and natural selection in the gene encoding the Duffy binding protein II in Iranian Plasmodium vivax wild isolates. INFECTION GENETICS AND EVOLUTION 2013; 21:424-35. [PMID: 24384095 DOI: 10.1016/j.meegid.2013.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 10/25/2022]
Abstract
Region II of Duffy binding protein (PvDBP-II) is one of the most promising blood-stage vaccine candidate antigens against Plasmodium vivax and having knowledge of the nature and genetic polymorphism of PvDBP-II among global P. vivax isolates is important for developing a DBP-based vaccine. By using PCR and sequencing, the present molecular population genetic approach was carried out to investigate sequence diversity and natural selection of dbp-II gene in 63 P. vivax isolates collected from unstable and low transmission malaria-endemic areas of Iran during 2008-2012. Also, phylogenetic analysis, the diversifying natural selection, and recombination across the pvdbp-II gene, including regions containing B-cell epitopes were analyzed using the DnaSP and MEGA4 programs. Twenty two single nucleotide polymorphisms (SNPs, including 20 non-synonymous and 2 synonymous) were identified in PvDBP-II, resulting in 16 different PvDBP-II haplotypes among the Iranian P. vivax isolates. High binding inhibitory B-cell epitope (H3) overlapping with intrinsically unstructured/disordered region (aa: 384-392) appeared to be highly polymorphic (D384G/E385K/ K386N/Q/R390H), and positive selective pressure acted on this region. Most of the polymorphic amino acids, which are located on the surface of the protein, are under selective pressure that implies increased recombination events and exposure to the human immune system. In summary, PvDBP-II gene displays genetic polymorphism among Iranian P. vivax isolates and it is under selective pressure. Mutations, recombination, and positive selection seem to play a role in the resulting genetic diversity, and phylogenetic analysis of DNA sequences demonstrates that Iranian isolates represent a sample of the global population. These results are useful for understanding the nature of the P. vivax population in Iran and also for development of PvDBP-II-based malaria vaccine.
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Affiliation(s)
- Vahideh Valizadeh
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran
| | - Sedigheh Zakeri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran.
| | - Akram Abouie Mehrizi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran
| | - Navid Dinparast Djadid
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran
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Mara SE, Silué KD, Raso G, N'guetta SP, N'goran EK, Tanner M, Utzinger J, Ding XC. Genetic diversity of Plasmodium falciparum among school-aged children from the Man region, western Côte d'Ivoire. Malar J 2013; 12:419. [PMID: 24228865 PMCID: PMC3842749 DOI: 10.1186/1475-2875-12-419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022] Open
Abstract
Background The genetic diversity of Plasmodium falciparum allows the molecular discrimination of otherwise microscopically identical parasites and the identification of individual clones in multiple infections. The study reported here investigated the P. falciparum multiplicity of infection (MOI) and genetic diversity among school-aged children in the Man region, western Côte d’Ivoire. Methods Blood samples from 292 children aged seven to 15 years were collected in four nearby villages located at altitudes ranging from 340 to 883 m above sea level. Giemsa-stained thick and thin blood films were prepared and examined under a microscope for P. falciparum prevalence and parasitaemia. MOI and genetic diversity of the parasite populations were investigated using msp2 typing by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results Plasmodium falciparum prevalence and parasitaemia were both found to be significantly lower in the highest altitude village. Genotyping of the isolates revealed 25 potentially new msp2 alleles. MOI varied significantly across villages but did not correlate with altitude nor children’s age, and only to a limited extent with parasitaemia. An analysis of molecular variance (AMOVA) indicated that a small, but close to statistical significance (p = 0.07), fraction of variance occurs specifically between villages of low and high altitudes. Conclusions Higher altitude was associated with lower prevalence of P. falciparum but not with reduced MOI, suggesting that, in this setting, MOI is not a good proxy for transmission. The evidence for partially parted parasite populations suggests the existence of local geographical barriers that should be taken into account when deploying anti-malarial interventions.
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Affiliation(s)
| | | | | | | | | | | | | | - Xavier C Ding
- Département Environnement et Santé, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303 Abidjan 01, Côte d'Ivoire.
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Ogouyèmi-Hounto A, Gazard DK, Ndam N, Topanou E, Garba O, Elegbe P, Hountohotegbe T, Massougbodji A. Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum isolates from children in South of Benin. ACTA ACUST UNITED AC 2013; 20:37. [PMID: 24135216 PMCID: PMC3798888 DOI: 10.1051/parasite/2013039] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/06/2013] [Indexed: 01/22/2023]
Abstract
The aim of this study was to determine the genetic diversity of Plasmodium falciparum by analyzing the polymorphism of the msp-1 and msp-2 genes and the multiplicity of infection in children with uncomplicated malaria in southern Benin. Blood samples of children with fever or history of fever with thick smear positive P. falciparum were collected on filter paper. After extraction of DNA by Chelex®, the samples underwent nested PCR. 93 isolates from children were genotyped. For the msp-1 gene, the K1 and R033 sequences were the most represented in the study population with 85.2% and 83% prevalence, respectively. Regarding the msp-2 gene, the FC27 family was more highly represented with 99% prevalence against 81.5% for 3D7. Mixed infections accounted for 80.4% of the samples. Twenty-five alleles were identified for msp-1 and 28 for msp-2. Fourteen and ten alleles belonged to the K1 (100-500 bp) and MAD20 (100-500 bp) families, respectively. The RO33 sequence did not show any polymorphism, with only one variant (160 bp) detected. The msp-2 gene was present as 16 FC27 family fragments (250-800 bp) and 12 of the 3D7 family (350-700 bp). The multiplicity of infection was estimated at 3.8 for msp-1 and 3.9 for msp-2 with 77 (87.5%) and 84 (91.3%) samples harboring more than one parasite genotype for msp-1 and msp-2, respectively. The multiplicity of infection (MOI) was influenced neither by age nor by parasite density. This study shows a significant diversity of P. falciparum in southern Benin with an MOI unaffected by age or by parasite density.
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Affiliation(s)
- Aurore Ogouyèmi-Hounto
- Unité d'Enseignement et de Recherche en Parasitologie-Mycologie de la Faculté des Sciences de la Santé, 01BP188 Cotonou, Bénin - Laboratoire du Centre de Lutte Intégrée contre le Paludisme, 01BP188 Cotonou, Bénin
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Koepfli C, Colborn KL, Kiniboro B, Lin E, Speed TP, Siba PM, Felger I, Mueller I. A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children. PLoS Negl Trop Dis 2013; 7:e2403. [PMID: 24040428 PMCID: PMC3764149 DOI: 10.1371/journal.pntd.0002403] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 07/23/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND When both parasite species are co-endemic, Plasmodium vivax incidence peaks in younger children compared to P. falciparum. To identify differences in the number of blood stage infections of these species and its potential link to acquisition of immunity, we have estimated the molecular force of blood-stage infection of P. vivax ((mol)FOB, i.e. the number of genetically distinct blood-stage infections over time), and compared it to previously reported values for P. falciparum. METHODS P. vivax (mol)FOB was estimated by high resolution genotyping parasites in samples collected over 16 months in a cohort of 264 Papua New Guinean children living in an area highly endemic for P. falciparum and P. vivax. In this cohort, P. vivax episodes decreased three-fold over the age range of 1-4.5 years. RESULTS On average, children acquired 14.0 new P. vivax blood-stage clones/child/year-at-risk. While the incidence of clinical P. vivax illness was strongly associated with mol FOB (incidence rate ratio (IRR) = 1.99, 95% confidence interval (CI95) [1.80, 2.19]), (mol)FOB did not change with age. The incidence of P. vivax showed a faster decrease with age in children with high (IRR = 0.49, CI95 [0.38, 0.64] p<0.001) compared to those with low exposure (IRR = 0.63, CI95[0.43, 0.93] p = 0.02). CONCLUSION P. vivax (mol)FOB is considerably higher than P. falciparum (mol)FOB (5.5 clones/child/year-at-risk). The high number of P. vivax clones that infect children in early childhood contribute to the rapid acquisition of immunity against clinical P. vivax malaria.
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Affiliation(s)
- Cristian Koepfli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Kathryn L. Colborn
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- University of California, Berkeley, Department of Biostatistics, Berkeley, California, United States of America
| | - Benson Kiniboro
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | - Enmoore Lin
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | | | - Peter M. Siba
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highland Province, Papua New Guinea
- Barcelona Centre for International Health Research, Barcelona, Spain
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Jaki T, Parry A, Winter K, Hastings I. Analysing malaria drug trials on a per-individual or per-clone basis: a comparison of methods. Stat Med 2013; 32:3020-38. [PMID: 23258694 DOI: 10.1002/sim.5706] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 11/22/2012] [Indexed: 11/05/2022]
Abstract
There are a variety of methods used to estimate the effectiveness of antimalarial drugs in clinical trials, invariably on a per-person basis. A person, however, may have more than one malaria infection present at the time of treatment. We evaluate currently used methods for analysing malaria trials on a per-individual basis and introduce a novel method to estimate the cure rate on a per-infection (clone) basis. We used simulated and real data to highlight the differences of the various methods. We give special attention to classifying outcomes as cured, recrudescent (infections that never fully cleared) or ambiguous on the basis of genetic markers at three loci. To estimate cure rates on a per-clone basis, we used the genetic information within an individual before treatment to determine the number of clones present. We used the genetic information obtained at the time of treatment failure to classify clones as recrudescence or new infections. On the per-individual level, we find that the most accurate methods of classification label an individual as newly infected if all alleles are different at the beginning and at the time of failure and as a recrudescence if all or some alleles were the same. The most appropriate analysis method is survival analysis or alternatively for complete data/per-protocol analysis a proportion estimate that treats new infections as successes. We show that the analysis of drug effectiveness on a per-clone basis estimates the cure rate accurately and allows more detailed evaluation of the performance of the treatment.
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Affiliation(s)
- Thomas Jaki
- Medical and Pharmaceutical Research Unit, Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
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The suitability of P. falciparum merozoite surface proteins 1 and 2 as genetic markers for in vivo drug trials in Yemen. PLoS One 2013; 8:e67853. [PMID: 23861823 PMCID: PMC3701615 DOI: 10.1371/journal.pone.0067853] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/22/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The accuracy of the conclusions from in vivo efficacy anti-malarial drug trials depends on distinguishing between recrudescences and re-infections which is accomplished by genotyping genes coding P. falciparum merozoite surface 1 (MSP1) and MSP2. However, the reliability of the PCR analysis depends on the genetic markers' allelic diversity and variant frequency. In this study the genetic diversity of the genes coding for MSP1 and MSP2 was obtained for P. falciparum parasites circulating in Yemen. METHODS Blood samples were collected from 511 patients with fever and screened for malaria parasites using Giemsa-stained blood films. A total 74 samples were infected with P. falciparum, and the genetic diversity was assessed by nested PCR targeting Pfmsp1 (Block2) and Pfmsp2 (block 3). RESULTS Overall, 58%, 28% and 54% of the isolates harboured parasites of the Pfmsp1 K1, MAD20 and RO33 allelic families, and 55% and 89% harboured those of the Pfmsp2 FC27 and 3D7 allelic families, respectively. For both genetic makers, the multiplicity of the infection (MOI) was significantly higher in the isolates from the foothills/coastland areas as compared to those from the highland (P<0.05). Pfmsp2 had higher number of distinct allelic variants than Pfmsp1 (20 vs 11). The expected heterozygosity (HE) for Pfmsp1 and Pfmsp2 were 0.82 and 0.94, respectively. Nonetheless, a bias in the frequency distribution of the Pfmsp1 allelic variants was noted from all areas, and of those of Pfmsp2 in the samples collected from the highland areas. CONCLUSIONS Significant differences in the complexity and allelic diversity of Pfmsp1 and Pfmsp2 genes between areas probably reflect differences in the intensity of malaria transmission. The biased distribution of allelic variants suggests that in Yemen Pfmsp1 should not be used for PCR correction of in vivo clinical trials outcomes, and that caution should be exercised when employing Pfmsp2.
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Khaireh BA, Assefa A, Guessod HH, Basco LK, Khaireh MA, Pascual A, Briolant S, Bouh SM, Farah IH, Ali HM, Abdi AIA, Aden MO, Abdillahi Z, Ayeh SN, Darar HY, Koeck JL, Rogier C, Pradines B, Bogreau H. Population genetics analysis during the elimination process of Plasmodium falciparum in Djibouti. Malar J 2013; 12:201. [PMID: 23758989 PMCID: PMC3685531 DOI: 10.1186/1475-2875-12-201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 05/28/2013] [Indexed: 11/26/2022] Open
Abstract
Background Case management of imported malaria within the context of malaria pre-elimination is increasingly considered to be relevant because of the risk of resurgence. The assessment of malaria importation would provide key data i) to select countries with propitious conditions for pre-elimination phase and ii) to predict its feasibility. Recently, a sero-prevalence study in Djibouti indicated low malaria prevalence, which is propitious for the implementation of pre-elimination, but data on the extent of malaria importation remain unknown. Methods Djiboutian plasmodial populations were analysed over an eleven-year period (1998, 1999, 2002 and 2009). The risk of malaria importation was indirectly assessed by using plasmodial population parameters. Based on 5 microsatellite markers, expected heterozygosity (H.e.), multiplicity of infection, pairwise Fst index, multiple correspondence analysis and individual genetic relationship were determined. The prevalence of single nucleotide polymorphisms associated with pyrimethamine resistance was also determined. Results Data indicated a significant decline in genetic diversity (0.51, 0.59, 0.51 and 0 in 1998, 1999, 2002 and 2009, respectively) over the study period, which is inconsistent with the level of malaria importation described in a previous study. This suggested that Djiboutian malaria situation may have benefited from the decline of malaria prevalence that occurred in neighbouring countries, in particular in Ethiopia. The high Fst indices derived from plasmodial populations from one study period to another (0.12 between 1999 and 2002, and 0.43 between 2002 and 2009) suggested a random sampling of parasites, probably imported from neighbouring countries, leading to oligo-clonal expansion of few different strains during each transmission season. Nevertheless, similar genotypes observed during the study period suggested recurrent migrations and imported malaria. Conclusion In the present study, the extent of genetic diversity was used to assess the risk of malaria importation in the low malaria transmission setting of Djibouti. The molecular approach highlights i) the evolution of Djiboutian plasmodial population profiles that are consistent and compatible with Djiboutian pre-elimination goals and ii) the necessity to implement the monitoring of plasmodial populations and interventions at the regional scale in the Horn of Africa to ensure higher efficiency of malaria control and elimination.
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Affiliation(s)
- Bouh Abdi Khaireh
- Unité de Parasitologie, Département d'Infectiologie de Terrain, Institut de Recherche Biomédicale des Armées, Allée du Médecin Colonel E, Jamot, Parc du Pharo, BP 60109, 13262 Marseille Cedex 07, France
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Factors determining the occurrence of submicroscopic malaria infections and their relevance for control. Nat Commun 2013; 3:1237. [PMID: 23212366 PMCID: PMC3535331 DOI: 10.1038/ncomms2241] [Citation(s) in RCA: 435] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/31/2012] [Indexed: 01/05/2023] Open
Abstract
Malaria parasite prevalence in endemic populations is an essential indicator for monitoring the progress of malaria control, and has traditionally been assessed by microscopy. However, surveys increasingly use sensitive molecular methods that detect higher numbers of infected individuals, questioning our understanding of the true infection burden and resources required to reduce it. Here we analyse a series of data sets to characterize the distribution and epidemiological factors associated with low-density, submicroscopic infections. We show that submicroscopic parasite carriage is common in adults, in low-endemic settings and in chronic infections. We find a strong, non-linear relationship between microscopy and PCR prevalence in population surveys (n=106), and provide a tool to relate these measures. When transmission reaches very low levels, submicroscopic carriers are estimated to be the source of 20–50% of all human-to-mosquito transmissions. Our findings challenge the idea that individuals with little previous malaria exposure have insufficient immunity to control parasitaemia and suggest a role for molecular screening. Malaria can persist at levels that escape detection by standard microscopy, but can be detected by PCR. Okell et al. now show that rates of submicroscopic infection can be predicted using more widely available microscopy data, and are most epidemiologically significant in areas with low malaria transmission.
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Natural selection and population genetic structure of domain-I of Plasmodium falciparum apical membrane antigen-1 in India. INFECTION GENETICS AND EVOLUTION 2013; 18:247-56. [PMID: 23747831 DOI: 10.1016/j.meegid.2013.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/16/2013] [Accepted: 05/18/2013] [Indexed: 12/27/2022]
Abstract
Development of a vaccine against Plasmodium falciparum infection is an urgent priority particularly because of widespread resistance to most traditionally used drugs. Multiple evidences point to apical membrane antigen-1(AMA-1) as a prime vaccine candidate directed against P. falciparum asexual blood-stages. To gain understanding of the genetic and demographic forces shaping the parasite sequence diversity in Kolkata, a part of Pfama-1 gene covering domain-I was sequenced from 100 blood samples of malaria patients. Statistical and phylogenetic analyses of the sequences were performed using DnaSP and MEGA. Very high haplotype diversity was detected both at nucleotide (0.998±0.002) and amino-acid (0.996±0.001) levels. An abundance of low frequency polymorphisms (Tajima's D=-1.190, Fu & Li's D(∗) and F(∗)=-3.068 and -2.722), unimodal mismatch distribution and a star-like median-joining network of ama-1 haplotypes indicated a recent population expansion among Kolkata parasites. The high minimum number of recombination events (Rm=26) and a significantly high dN/dS of 3.705 (P<0.0001) in Kolkata suggested recombination and positive selection as major forces in the generation and maintenance of ama-1 allelic diversity. To evaluate the impact of observed non-synonymous substitutions in the context of AMA-1 functionality, PatchDock and FireDock protein-protein interaction solutions were mapped between PfAMA-1-PfRON2 and PfAMA-1-host IgNAR. Alterations in the desolvation and global energies of PfAMA-1-PfRON2 interaction complexes at the hotspot contact residues were observed together with redistribution of surface electrostatic potentials at the variant alleles with respect to referent Pf3D7 sequence. Finally, a comparison of P. falciparum subpopulations in five Indian regional isolates retrieved from GenBank revealed a significant level of genetic differentiation (FST=0.084-0.129) with respect to Kolkata sequences. Collectively, our results indicated a very high allelic and haplotype diversity, a high recombination rate and a signature of natural selection favoring accumulation of non-synonymous substitutions that facilitated PfAMA-1-PfRON2 interaction and hence parasite growth in Kolkata clinical isolates.
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Mehrizi AA, Sepehri M, Karimi F, Djadid ND, Zakeri S. Population genetics, sequence diversity and selection in the gene encoding the Plasmodium falciparum apical membrane antigen 1 in clinical isolates from the south-east of Iran. INFECTION GENETICS AND EVOLUTION 2013; 17:51-61. [PMID: 23557839 DOI: 10.1016/j.meegid.2013.03.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/17/2013] [Accepted: 03/23/2013] [Indexed: 12/26/2022]
Abstract
The Plasmodium falciparum apical membrane antigen1 (AMA1) is a leading malaria vaccine candidate antigen. In the present investigation, for the first time, the almost full length of the ama1 gene covering domain I (DI), DII and DIII was PCR amplified and sequenced in 21 P. falciparum isolates collected from the southeastern parts of Iran. The result showed the low genetic diversity of Iranian PfAMA1 with 11 PfAMA1 haplotypes in which nine out of 11 haplotypes are novel and have been reported for the first time. The Iranian P. falciparum population indicated a moderate level of genetic differentiation. The difference among the rates of non-synonymous and synonymous mutations, Tajima's D and McDonald-Kreitman tests suggested that the diversity at DI is due to positive natural selection. In addition, recombination contributes to the diversity of Iranian PfAMA1 and this is supported by the decline of the linkage disequilibrium index R(2) with increasing the nucleotide distance. The highly polymorphic residues (positions: 187, 197, 200, 230 and 243) were polymorphic; however, most of the SNPs in non-polymorphic residues were conserved except the residue at position 395. Nevertheless, no mutation was found in the DII loop of the Iranian PfAMA1, indicating that it is subjected to purifying selection. In conclusion, the low genetic diversity in PfAMA1 among Iranian isolates supports and provides valuable information for the development of a PfAMA1-based malaria vaccine.
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MESH Headings
- Amino Acid Sequence
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Evolution, Molecular
- Gene Frequency
- Genetic Variation
- Haplotypes
- Humans
- Iran
- Malaria Vaccines/genetics
- Malaria Vaccines/immunology
- Malaria, Falciparum/immunology
- Malaria, Falciparum/prevention & control
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/immunology
- Molecular Sequence Data
- Mutation
- Phylogeny
- Plasmodium falciparum/genetics
- Plasmodium falciparum/immunology
- Plasmodium falciparum/isolation & purification
- Polymorphism, Genetic
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Recombination, Genetic
- Selection, Genetic
- Sequence Analysis, DNA
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Affiliation(s)
- Akram Abouie Mehrizi
- Malaria and Vector Research Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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Barry AE, Schultz L, Senn N, Nale J, Kiniboro B, Siba PM, Mueller I, Reeder JC. High levels of genetic diversity of Plasmodium falciparum populations in Papua New Guinea despite variable infection prevalence. Am J Trop Med Hyg 2013; 88:718-25. [PMID: 23400571 PMCID: PMC3617858 DOI: 10.4269/ajtmh.12-0056] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 11/30/2012] [Indexed: 11/07/2022] Open
Abstract
High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity.
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Affiliation(s)
- Alyssa E Barry
- Centre for Population Health, Burnet Institute, Melbourne, Australia.
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