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Letcher B, Maciuca S, Iqbal Z. Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum. PLoS Biol 2024; 22:e3002507. [PMID: 38451924 PMCID: PMC10919680 DOI: 10.1371/journal.pbio.3002507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/19/2024] [Indexed: 03/09/2024] Open
Abstract
While the malaria parasite Plasmodium falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell-infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical P. falciparum transmission bottleneck.
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Affiliation(s)
- Brice Letcher
- EMBL-EBI, Hinxton, United Kingdom
- Laboratory of Biology and Modelling of the Cell, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
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Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Aniebo I, Aninagyei E, Ansah F, Ansah PO, Apinjoh T, Arnaldo P, Ashley E, Auburn S, Awandare GA, Ba H, Baraka V, Barry A, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Bouyou-Akotet M, Branch O, Bull PC, Cheah H, Chindavongsa K, Chookajorn T, Chotivanich K, Claessens A, Conway DJ, Corredor V, Courtier E, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Dhorda M, Diakite M, Djimde A, Dolecek C, Dondorp A, Doumbia S, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Enosse SMM, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fleharty M, Forbes M, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Harrison GLA, Healy SA, Hendry JA, Hernandez-Koutoucheva A, Hien TT, Hill CA, Hombhanje F, Hott A, Htut Y, Hussein M, Imwong M, Ishengoma D, Jackson SA, Jacob CG, Jeans J, Johnson KJ, Kamaliddin C, Kamau E, Keatley J, Kochakarn T, Konate DS, Konaté A, Kone A, Kwiatkowski DP, Kyaw MP, Kyle D, Lawniczak M, Lee SK, Lemnge M, Lim P, Lon C, Loua KM, Mandara CI, Marfurt J, Marsh K, Maude RJ, Mayxay M, Maïga-Ascofaré O, Miotto O, Mita T, Mobegi V, Mohamed AO, Mokuolu OA, Montgomery J, Morang’a CM, Mueller I, Murie K, Newton PN, Ngo Duc T, Nguyen T, Nguyen TN, Nguyen Thi Kim T, Nguyen Van H, Noedl H, Nosten F, Noviyanti R, Ntui VNN, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Oyibo WA, Pearson R, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Quang HH, Randrianarivelojosia M, Rayner JC, Ringwald P, Rosanas-Urgell A, Rovira-Vallbona E, Ruano-Rubio V, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Sissoko MS, Smith C, Su XZ, Sutherland C, Takala-Harrison S, Talman A, Tavul L, Thanh NV, Thathy V, Thu AM, Toure M, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Whitton G, Yavo W, van der Pluijm RW. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res 2023; 8:22. [PMID: 36864926 PMCID: PMC9971654 DOI: 10.12688/wellcomeopenres.18681.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
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Affiliation(s)
| | | | - Mohamed Hassan Abdelraheem
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Nuclear Applications In Biological Sciences, Sudan Atomic Energy Commission, Khartoum, Sudan
| | - Desmond Omane Acheampong
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ambroise Ahouidi
- Health Research Epidemiological Surveillance and Training Institute (IRESSEF), Université Cheikh Anta Diop, Dakar, Senegal
| | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - Tim Anderson
- Texas Biomedical Research Institute, San Antonio, USA
| | | | | | - Enoch Aninagyei
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health & Allied Sciences, Ho, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Patrick O Ansah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | | | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Maputo, Mozambique
| | - Elizabeth Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Nuffield Department of Medicine, University of Oxford, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Antwerp, Belgium
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Melbourne, Australia
- Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F Boni
- Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marielle Bouyou-Akotet
- Department of Parasitology-Mycology, Université des Sciences de la Santé, Libreville, Gabon
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Huch Cheah
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- WorldWide Antimalarial Resistance Network – Asia Regional Centre, Bangkok, Thailand
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Seydou Doumbia
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Diego F Echeverry
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Caterina A Fanello
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Mark Fleharty
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | | | - Mark Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Sara Anne Healy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason A Hendry
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Tran Tinh Hien
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, USA
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | | | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | - Mazza Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Claire Kamaliddin
- Institute of Research for Development (IRD), Paris, France
- The University of Calgary, Calgary, Canada
| | - Edwin Kamau
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Drissa S Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Aminatou Kone
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Myat P Kyaw
- Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar
- University of Public Health, Yangon, Myanmar
| | - Dennis Kyle
- University of South Florida, Tampa, USA
- University of Georgia, Athens, USA
| | | | - Samuel K Lee
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | - Martha Lemnge
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Kovana M Loua
- University Gamal Abdel Nasser of Conakry, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Celine I Mandara
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Jutta Marfurt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Richard James Maude
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK
| | | | - Victor Mobegi
- Department of Biochemistry and Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | | | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jaqui Montgomery
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
- World Mosquito Program, Monash University, Melbourne, Australia
| | - Collins Misita Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | | | - Paul N Newton
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | | | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | | | - Hong Nguyen Van
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
- Medical University of Vienna, Vienna, Austria
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dhahran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
- Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- Wellcome Sanger Institute, Hinxton, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | | | | | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung P Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Huynh Hong Quang
- Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Quy Nhon, Vietnam
| | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Mahamadou S. Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Arthur Talman
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ngo Viet Thanh
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Mahamoudou Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Yale School of Medicine, New Haven, CT, USA
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason Wendler
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Seattle Children’s Hospital, Seattle, USA
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
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Shah Z, Naung MT, Moser KA, Adams M, Buchwald AG, Dwivedi A, Ouattara A, Seydel KB, Mathanga DP, Barry AE, Serre D, Laufer MK, Silva JC, Takala-Harrison S. Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria. PLoS Genet 2021; 17:e1009576. [PMID: 34033654 PMCID: PMC8184011 DOI: 10.1371/journal.pgen.1009576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/07/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. Immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode possible targets of naturally acquired immunity that should be validated immunologically and further characterized for their potential as vaccine candidates.
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Affiliation(s)
- Zalak Shah
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Myo T. Naung
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Kara A. Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Andrea G. Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Karl B. Seydel
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Don P. Mathanga
- University of Malawi College of Medicine, Malaria Alert Centre, Blantyre, Malawi
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- Disease Elimination and Maternal and Child Health, Burnet Institute, Melbourne, Victoria, Australia
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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4
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Fu H, Yang Y, Mishra V, Zhou Q, Zuzak K, Feindel D, Harding MW, Feng J. Most Plasmodiophora brassicae Populations in Single Canola Root Galls from Alberta Fields are Mixtures of Multiple Strains. PLANT DISEASE 2020; 104:116-120. [PMID: 31644392 DOI: 10.1094/pdis-06-19-1235-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on canola in Alberta, Canada. The pathogen is grouped into pathotypes according to their virulence reaction on differential hosts. Multiple pathotypes or strains are known exist in one field, one plant, or even one gall. This study was conducted with the objective of testing the prevalence of the coexistence of multiple strains in a single gall. In all, 79 canola clubroot galls were collected from 22 fields across Northern Alberta in 2018. Genomic DNA extracted from these single galls was analyzed using RNase H-dependent PCR (rhPCR). The rhPCR primers were designed to amplify a partial sequence of a dimorphic gene, with one primer pair specific to one sequence and the other primer pair specific to the alternative sequence. The amplification of both sequences from DNA obtained from a single gall would indicate that it contains two different P. brassicae strains. The rhPCR analyses indicated that the P. brassicae populations in 50 of the 79 galls consisted of more than one strain. This result emphasizes the need for cautious interpretation of results when a single-gall population is subject to pathotyping or being used as inoculum in plant pathology research. It also confirms that the maintenance of pathotype diversity within single root galls is a common occurrence which has implications for the durability, and stewardship, of single-gene host resistance.
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Affiliation(s)
- Heting Fu
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - Yalong Yang
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - Vachaspati Mishra
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - Qixing Zhou
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - Krista Zuzak
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - David Feindel
- Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
| | - Michael W Harding
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, T1R 1E6, Canada
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Forestry, Edmonton, AB, T5Y 6H3, Canada
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5
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Bahk YY, Kim J, Ahn SK, Na BK, Chai JY, Kim TS. Genetic Diversity of Plasmodium vivax Causing Epidemic Malaria in the Republic of Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:545-552. [PMID: 30630274 PMCID: PMC6327206 DOI: 10.3347/kjp.2018.56.6.545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is more challenging to control and eliminate than P. falciparum due to its more asymptomatic infections with low parasite densities making diagnosis more difficult, in addition to its unique biological characteristics. The potential re-introduction of incidence cases, either through borders or via human migrations, is another major hurdle to sustained control and elimination. The Republic of Korea has experienced re-emergence of vivax malaria in 1993 but is one of the 32 malaria-eliminating countries to-date. Despite achieving successful nationwide control and elimination of vivax malaria, the evolutionary characteristics of vivax malaria isolates in the Republic of Korea have not been fully understood. In this review, we present an overview of the genetic variability of such isolates to increase understanding of the epidemiology, diversity, and dynamics of vivax populations in the Republic of Korea.
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Affiliation(s)
- Young Yil Bahk
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju 27478,
Korea
| | - Jeonga Kim
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, UAB Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294,
USA
| | - Seong Kyu Ahn
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Jong-Yil Chai
- Korea Association of Health Promotion, Seoul 07653,
Korea
| | - Tong-Soo Kim
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
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6
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Oboh MA, Singh US, Antony HA, Ndiaye D, Badiane AS, Ali NA, Bharti PK, Das A. Molecular epidemiology and evolution of drug-resistant genes in the malaria parasite Plasmodium falciparum in southwestern Nigeria. INFECTION GENETICS AND EVOLUTION 2018; 66:222-228. [PMID: 30316883 DOI: 10.1016/j.meegid.2018.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 11/27/2022]
Abstract
Malaria is an age-old disease of human kind living in the tropical and sub-tropical regions of the globe, with Africa contributing the highest incidence of morbidity and mortality. Among many hurdles, evolution and spread of drug-resistant Plasmodium falciparum parasites constitute major challenges to malaria control and elimination. Information on molecular epidemiology and pattern of evolution of genes conferring resistance to different antimalarials are needed to track the route of the spread of resistant parasites and also to inform if the drug-resistant genes are adapted in the population following the Darwinian model of evolution. In the present study, we have followed molecular methods to detect both the known and emerging mutations in three genes (Pfcrt, Pfdhfr and Pfdhps) of P. falciparum conferring resistance to chloroquine and sulfadoxine-pyrimethamine from two different states (Edo: meso-endemic and Lagos: hypo-endemic) in southwestern Nigeria. High diversities in haplotypes and nucleotides in genes responsible for chloroquine (Pfcrt) and sulfadoxine (Pfdhps) resistance are recorded. About 96% of Pfdhfr and Pfdhps gene in both the meso- and hypo- endemic areas were mutant type, followed by 61% in Pfcrt gene. Many unique haplotypes of Pfdhps and Pfcrt were found to be segregated in these two populations. One particular mutant haplotype of Pfdhfr (AIRNI) was found to be in very high frequency in both Lagos and Edo. While the net haplotype diversity was highest in Pfdhps (0.81 in Lagos, 0.87 in Edo), followed by Pfcrt (0.69 in Lagos, 0.65 in Edo); highest number of haplotype was found in Pfdhps with 13 distinct haplotypes, followed by seven in Pfcrt and four in Pfdhfr gene. Moreover, detection of strong linkage among mutations of Pfcrt and Pfdhfr and feeble evidence for balancing selection in Pfdhps are indicative of evolutionary potential of mutation in genes responsible for drug resistance in Nigerian populations of P. falciparum.
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Affiliation(s)
- Mary Aigbiremo Oboh
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Upasana Shyamsunder Singh
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Hiasindh Ashmi Antony
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Daouda Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Aida Sadikh Badiane
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Nazia Anwar Ali
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Praveen Kumar Bharti
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Aparup Das
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India.
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7
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Yasukochi Y, Naka I, Patarapotikul J, Hananantachai H, Ohashi J. Evolution of Fseg/Cseg dimorphism in region III of the Plasmodium falciparum eba-175 gene. INFECTION GENETICS AND EVOLUTION 2017; 49:251-255. [PMID: 28137625 DOI: 10.1016/j.meegid.2017.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/27/2022]
Abstract
The 175-kDa erythrocyte binding antigen (EBA-175) of the malaria parasite Plasmodium falciparum is important for its invasion into human erythrocytes. The primary structure of eba-175 is divided into seven regions, namely I to VII. Region III contains highly divergent dimorphic segments, termed Fseg and Cseg. The allele frequencies of segmental dimorphism within a P. falciparum population have been extensively examined; however, the molecular evolution of segmental dimorphism is not well understood. A comprehensive comparison of nucleotide sequences among 32 P. falciparum eba-175 alleles identified in our previous study, two Plasmodium reichenowi, and one P. gaboni orthologous alleles obtained from the GenBank database was conducted to uncover the origin and evolutionary processes of segmental dimorphism in P. falciparum eba-175. In the eba-175 nucleotide sequence derived from a P. reichenowi CDC strain, both Fseg and Cseg were found in region III, which implies that the original eba-175 gene had both segments, and deletions of F- and C-segments generated Cseg and Fseg alleles, respectively. We also confirmed the presence of allele with Fseg and Cseg in another P. reichenowi strain (SY57), by re-mapping short reads obtained from the GenBank database. On the other hand, the segmental sequence of eba-175 ortholog in P. gaboni was quite diverged from those of the other species, suggesting that the original eba-175 dimorphism of P. falciparum can be traced back to the stem linage of P. falciparum and P. reichenowi. Our findings suggest that Fseg and Cseg alleles are derived from a single eba-175 allele containing both segments in the ancestral population of P. falciparum and P. reichenowi, and that the allelic dimorphism of eba-175 was shaped by the independent emergence of similar dimorphic lineage in different species that has never been observed in any evolutionary mode of allelic dimorphism at other loci in malaria genomes.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Jintana Patarapotikul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Hathairad Hananantachai
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
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8
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Miles A, Iqbal Z, Vauterin P, Pearson R, Campino S, Theron M, Gould K, Mead D, Drury E, O'Brien J, Ruano Rubio V, MacInnis B, Mwangi J, Samarakoon U, Ranford-Cartwright L, Ferdig M, Hayton K, Su XZ, Wellems T, Rayner J, McVean G, Kwiatkowski D. Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. Genome Res 2016; 26:1288-99. [PMID: 27531718 PMCID: PMC5052046 DOI: 10.1101/gr.203711.115] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/28/2016] [Indexed: 12/14/2022]
Abstract
The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.
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Affiliation(s)
- Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Paul Vauterin
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Richard Pearson
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Susana Campino
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Michel Theron
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Kelda Gould
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Daniel Mead
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Eleanor Drury
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jonathan Mwangi
- Department of Biochemistry, Medical School, Mount Kenya University, 01000 Thika, Kenya; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Upeka Samarakoon
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lisa Ranford-Cartwright
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Karen Hayton
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Thomas Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Julian Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom; Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Dominic Kwiatkowski
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
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9
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Loy DE, Liu W, Li Y, Learn GH, Plenderleith LJ, Sundararaman SA, Sharp PM, Hahn BH. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int J Parasitol 2016; 47:87-97. [PMID: 27381764 DOI: 10.1016/j.ijpara.2016.05.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque. However, the discovery of a multitude of Plasmodium spp. in chimpanzees and gorillas has refuted these theories and instead revealed that both P. falciparum and P. vivax evolved from parasites infecting wild-living African apes. It is now clear that P. falciparum resulted from a recent cross-species transmission of a parasite from a gorilla, whilst P. vivax emerged from an ancestral stock of parasites that infected chimpanzees, gorillas and humans in Africa, until the spread of the protective Duffy-negative mutation eliminated P. vivax from human populations there. Although many questions remain concerning the biology and zoonotic potential of the P. falciparum- and P. vivax-like parasites infecting apes, comparative genomics, coupled with functional parasite and vector studies, are likely to yield new insights into ape Plasmodium transmission and pathogenesis that are relevant to the treatment and prevention of human malaria.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Guimarães LO, Wunderlich G, Alves JMP, Bueno MG, Röhe F, Catão-Dias JL, Neves A, Malafronte RS, Curado I, Domingues W, Kirchgatter K. Merozoite surface protein-1 genetic diversity in Plasmodium malariae and Plasmodium brasilianum from Brazil. BMC Infect Dis 2015; 15:529. [PMID: 26572971 PMCID: PMC4647813 DOI: 10.1186/s12879-015-1238-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/20/2015] [Indexed: 01/23/2023] Open
Abstract
Background The merozoite surface protein 1 (MSP1) gene encodes the major surface antigen of invasive forms of the Plasmodium erythrocytic stages and is considered a candidate vaccine antigen against malaria. Due to its polymorphisms, MSP1 is also useful for strain discrimination and consists of a good genetic marker. Sequence diversity in MSP1 has been analyzed in field isolates of three human parasites: P. falciparum, P. vivax, and P. ovale. However, the extent of variation in another human parasite, P. malariae, remains unknown. This parasite shows widespread, uneven distribution in tropical and subtropical regions throughout South America, Asia, and Africa. Interestingly, it is genetically indistinguishable from P. brasilianum, a parasite known to infect New World monkeys in Central and South America. Methods Specific fragments (1 to 5) covering 60 % of the MSP1 gene (mainly the putatively polymorphic regions), were amplified by PCR in isolates of P. malariae and P. brasilianum from different geographic origin and hosts. Sequencing of the PCR-amplified products or cloned PCR fragments was performed and the sequences were used to construct a phylogenetic tree by the maximum likelihood method. Data were computed to give insights into the evolutionary and phylogenetic relationships of these parasites. Results Except for fragment 4, sequences from all other fragments consisted of unpublished sequences. The most polymorphic gene region was fragment 2, and in samples where this region lacks polymorphism, all other regions are also identical. The low variability of the P. malariae msp1 sequences of these isolates and the identification of the same haplotype in those collected many years apart at different locations is compatible with a low transmission rate. We also found greater diversity among P. brasilianum isolates compared with P. malariae ones. Lastly, the sequences were segregated according to their geographic origins and hosts, showing a strong genetic and geographic structure. Conclusions Our data show that there is a low level of sequence diversity and a possible absence of allelic dimorphism of MSP1 in these parasites as opposed to other Plasmodium species. P. brasilianum strains apparently show greater divergence in comparison to P. malariae, thus P. malariae could derive from P. brasilianum, as it has been proposed. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1238-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lilian O Guimarães
- Núcleo de Estudos em Malária, Superintendência de Controle de Endemias/Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Gerhard Wunderlich
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - João M P Alves
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - Marina G Bueno
- Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, 05508-270, Brazil.
| | - Fabio Röhe
- Wildlife Conservation Society, Rio de Janeiro, RJ, 22461-000, Brazil.
| | - José L Catão-Dias
- Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, 05508-270, Brazil.
| | - Amanda Neves
- Laboratório de Protozoologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Rosely S Malafronte
- Laboratório de Protozoologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil. .,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, 01246-903, Brazil.
| | - Izilda Curado
- Laboratório de Imunoepidemiologia, Superintendência de Controle de Endemias, São Paulo, SP, 01027-000, Brazil.
| | - Wilson Domingues
- Laboratório de Soroepidemiologia e Imunobiologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Karin Kirchgatter
- Núcleo de Estudos em Malária, Superintendência de Controle de Endemias/Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
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11
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Roy SW. The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum. INFECTION GENETICS AND EVOLUTION 2015; 36:441-449. [PMID: 26296605 DOI: 10.1016/j.meegid.2015.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 12/27/2022]
Abstract
In the deadly human malaria parasite Plasmodium falciparum, several major merozoite surface proteins (MSPs) show a striking pattern of allelic diversity called allelic dimorphism (AD). In AD, the vast majority of observed alleles fall into two highly divergent allelic classes, with recombinant alleles being rare or not observed, presumably due to repression by natural selection (recombination suppression, or RS). The three AD loci, merozoite surface proteins (MSPs) 1, 2, and 6, along with MSP3, which also exhibits RS among four allelic classes, can be collectively called AD/RS. The causes of AD/RS and the evolutionary history of allelic diversity at these loci remain mysterious. The few available sequences from a single closely related chimpanzee parasite, P. reichenowi, have suggested that for 3/4 loci, AD/RS is an ancient state that has been retained in P. falciparum since well before the P. falciparum-P. reichenowi ancestor. On the other hand, based on comparative sequence analysis, we recently suggested that (i) AD/RS P. falciparum loci have undergone interallelic recombination over longer evolutionary times (on the timescale of recent speciation events), and thus (ii) AD/RS may be a recent phenomenon. The recent publication of genomic sequencing efforts for P. gaboni, an outgroup to P. falciparum and P. reichenowi, allows for improved reconstruction of the evolutionary history of these loci. In this work, I report genic sequence for P. gaboni for all four AD/RS P. falciparum loci (MSP1, 2, 3, and 6). Comparison of these sequences with available P. falciparum and P. reichenowi data strengthens the evidence for interallelic recombination over the evolutionary history of these species and also strengthens the case that AD/RS at these loci is ancient. Combined with previous results, these data provide evidence that AD/RS at different loci has evolved at several different times in the evolutionary history of P. falciparum: (i) before the P. gaboni-P. falciparum divergence, for much of MSP1 and MSP3; (ii) between the P. gaboni-P. falciparum and P. reichenowi-P. falciparum divergences, for the 5' end of the AD region of MSP6 and block 3 of MSP1; (iii) near the P. reichenowi-P. falciparum divergence, for the 3' end of the AD region of MSP6; and (iv) after the P. reichenowi-P. falciparum divergence, for MSP2. Based on these results, I suggest a new hypothesis for long-term evolutionary maintenance of AD/RS by recombination within allelic groups.
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Affiliation(s)
- Scott William Roy
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA.
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12
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Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, Krishna S, Rayner JC, Cox-Singh J. Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS One 2015; 10:e0121303. [PMID: 25830531 PMCID: PMC4382175 DOI: 10.1371/journal.pone.0121303] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/30/2015] [Indexed: 11/21/2022] Open
Abstract
Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology.
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Affiliation(s)
- Miguel M. Pinheiro
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
| | - Md Atique Ahmed
- Malaria Research Centre, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - Scott B. Millar
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
| | - Theo Sanderson
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Thomas D. Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Woon Chan Lu
- Sarikei Hospital, Sarikei, Sarawak, 96100, Malaysia
| | - Sanjeev Krishna
- Division of Clinical Sciences, St. George’s, University of London, London, United Kingdom
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Janet Cox-Singh
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
- * E-mail:
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Roy SW, Ferreira MU. A new model for the origins of allelic dimorphism in Plasmodium falciparum. Parasitol Int 2014; 64:229-37. [PMID: 25251164 DOI: 10.1016/j.parint.2014.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/11/2014] [Accepted: 09/12/2014] [Indexed: 11/17/2022]
Abstract
In his landmark 1987 study of the merozoite surface protein-1 locus in Plasmodium falciparum, Kazuyuki Tanabe and coauthors introduced the phenomenon of allelic dimorphism, in which antigenic diversity is arranged into two maximally diverged haplotypes. Further work has extended this finding to other loci in P. falciparum. Each of the loci at which allelic dimorphism is observed encodes major surface antigens of blood-stage malaria parasites, and is consequently a major vaccine target, thus understanding the origins and implications of allelic dimorphism is of crucial importance. Here we examine the essential features of allelic dimorphism in dimorphic malarial surface antigens. From sequence analysis, we conclude that the ancestral population may have been recombining/multimorphic rather than dimorphic. We hypothesize a pathway to allelic dimorphism in which an ancestral allele-rich recombining population could have undergone a severe population bottleneck, putatively caused by the lateral transfer of P. falciparum from apes to humans. This bottleneck produced a reduction in allelic diversity, favoring the survival of the most divergent alleles, which in turn led to recombination suppression by strong natural selection against recombinants.
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Affiliation(s)
- Scott W Roy
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, 05508-900 São Paulo, SP, Brazil.
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Thompson PC, Rosenthal BM, Hare MP. Hybridization between previously isolated ancestors may explain the persistence of exactly two ancient lineages in the genome of the oyster parasite Perkinsus marinus. INFECTION GENETICS AND EVOLUTION 2014; 24:167-76. [PMID: 24681265 DOI: 10.1016/j.meegid.2014.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 02/18/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
Theory predicts that neutral genetic variation accumulates within populations to a level determined by gains through mutation and losses by genetic drift. This balance results in a characteristic distribution of allelic variation with the maximum allelic difference determined by effective population size. Here, we report a striking departure from these expectations in the form of allelic dimorphism, observed at the majority of seven loci examined in Perkinsus marinus, an important oyster parasite that causes Dermo disease. DNA sequences were collected from five loci flanking microsatellite repeats and two loci coding for superoxide dismutase enzymes that may mediate the parasite's interaction with its host. Based on 474 sequences, sampled across 5000 km of the eastern United States coastline, no more than two alleles were observed at each locus (discounting singletons). Depending on the locus, the common allele ranged in overall frequency from 72% to 92%. At each locus the two alleles differed substantially (3.8% sequence difference, on average), and the among-locus variance in divergences was not sufficient to reject a simultaneous origin for all dimorphisms using approximate Bayesian methods. Dimorphic alleles were estimated to have diverged from a common ancestral allele at least 0.9 million years ago. Across these seven loci, only five other alleles were ever observed, always as singletons and differing from the dimorphic alleles by no more than two nucleotides. Free recombination could potentially have shuffled these dimorphisms into as many as 243 multilocus combinations, but the existence of only ten combinations among all samples strongly supports low recombination frequencies and is consistent with the observed absence of intragenic recombination. We consider several demographic and evolutionary hypotheses to explain these patterns. Few can be conclusively rejected with the present data, but we advance a recent hybridization of ancient divergent lineages scenario as the most parsimonious.
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Affiliation(s)
- Peter C Thompson
- University of Maryland, Department of Biology, 1210 Biology-Psychology Bldg, College Park, MD 20742, USA.
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Lab, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Matthew P Hare
- University of Maryland, Department of Biology, 1210 Biology-Psychology Bldg, College Park, MD 20742, USA
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15
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Zilversmit MM, Chase EK, Chen DS, Awadalla P, Day KP, McVean G. Hypervariable antigen genes in malaria have ancient roots. BMC Evol Biol 2013; 13:110. [PMID: 23725540 PMCID: PMC3680017 DOI: 10.1186/1471-2148-13-110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 05/06/2013] [Indexed: 01/07/2023] Open
Abstract
Background The var genes of the human malaria parasite Plasmodium falciparum are highly polymorphic loci coding for the erythrocyte membrane proteins 1 (PfEMP1), which are responsible for the cytoaherence of P. falciparum infected red blood cells to the human vasculature. Cytoadhesion, coupled with differential expression of var genes, contributes to virulence and allows the parasite to establish chronic infections by evading detection from the host’s immune system. Although studying genetic diversity is a major focus of recent work on the var genes, little is known about the gene family's origin and evolutionary history. Results Using a novel hidden Markov model-based approach and var sequences assembled from additional isolates and species, we are able to reveal elements of both the early evolution of the var genes as well as recent diversifying events. We compare sequences of the var gene DBLα domains from divergent isolates of P. falciparum (3D7 and HB3), and a closely-related species, Plasmodium reichenowi. We find that the gene family is equally large in P. reichenowi and P. falciparum -- with a minimum of 51 var genes in the P. reichenowi genome (compared to 61 in 3D7 and a minimum of 48 in HB3). In addition, we are able to define large, continuous blocks of homologous sequence among P. falciparum and P. reichenowi var gene DBLα domains. These results reveal that the contemporary structure of the var gene family was present before the divergence of P. falciparum and P. reichenowi, estimated to be between 2.5 to 6 million years ago. We also reveal that recombination has played an important and traceable role in both the establishment, and the maintenance, of diversity in the sequences. Conclusions Despite the remarkable diversity and rapid evolution found in these loci within and among P. falciparum populations, the basic structure of these domains and the gene family is surprisingly old and stable. Revealing a common structure as well as conserved sequence among two species also has implications for developing new primate-parasite models for studying the pathology and immunology of falciparum malaria, and for studying the population genetics of var genes and associated virulence phenotypes.
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Affiliation(s)
- Martine M Zilversmit
- National Institute of Allergy of Infectious Disease, National Institutes of Health, 12735 Twinbrook Parkway, Rockville, MD 20852, USA.
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Brito CFAD, Ferreira MU. Molecular markers and genetic diversity of Plasmodium vivax. Mem Inst Oswaldo Cruz 2012; 106 Suppl 1:12-26. [PMID: 21881753 DOI: 10.1590/s0074-02762011000900003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/08/2011] [Indexed: 11/22/2022] Open
Abstract
Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.
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Kamau L, Skilton RA, Odongo DO, Mwaura S, Githaka N, Kanduma E, Obura M, Kabiru E, Orago A, Musoke A, Bishop RP. Differential transcription of two highly divergent gut-expressed Bm86 antigen gene homologues in the tick Rhipicephalus appendiculatus (Acari: Ixodida). INSECT MOLECULAR BIOLOGY 2011; 20:105-114. [PMID: 20854482 DOI: 10.1111/j.1365-2583.2010.01043.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The transcriptional control of gene expression is not well documented in the Arthropoda. We describe transcriptional analysis of two exceptionally divergent homologues (Ra86) of the Bm86 gut antigen from Rhipicephalus appendiculatus. Bm86 forms the basis of a commercial vaccine for the control of Rhipicephalus (Boophilus) microplus. The R. appendiculatus Ra86 proteins contain 654 and 693 amino acids, with only 80% amino acid sequence identity. Reverse-transcription PCR of gut cDNA showed transcription of only one genotype in individual female ticks. PCR amplification of 3' untranslated sequences from genomic DNA indicated that both variants could be encoded within a single genome. When both variants were present, one of the two Ra86 genotypes was transcriptionally dominant.
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Affiliation(s)
- L Kamau
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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18
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Neal AT, Jordan SJ, Oliveira AL, Hernandez JN, Branch OH, Rayner JC. Limited variation in vaccine candidate Plasmodium falciparum Merozoite Surface Protein-6 over multiple transmission seasons. Malar J 2010; 9:138. [PMID: 20497564 PMCID: PMC2881939 DOI: 10.1186/1475-2875-9-138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 05/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum Merozoite Surface Protein-6 (PfMSP6) is a component of the complex proteinacious coat that surrounds P. falciparum merozoites. This location, and the presence of anti-PfMSP6 antibodies in P. falciparum-exposed individuals, makes PfMSP6 a potential blood stage vaccine target. However, genetic diversity has proven to be a major hurdle for vaccines targeting other blood stage P. falciparum antigens, and few endemic field studies assessing PfMSP6 gene diversity have been conducted. This study follows PfMSP6 diversity in the Peruvian Amazon from 2003 to 2006 and is the first longitudinal assessment of PfMSP6 sequence dynamics. METHODS Parasite DNA was extracted from 506 distinct P. falciparum infections spanning the transmission seasons from 2003 to 2006 as part of the Malaria Immunology and Genetics in the Amazon (MIGIA) cohort study near Iquitos, Peru. PfMSP6 was amplified from each sample using a nested PCR protocol, genotyped for allele class by agarose gel electrophoresis, and sequenced to detect diversity. Allele frequencies were analysed using JMP v.8.0.1.0 and correlated with clinical and epidemiological data collected as part of the MIGIA project. RESULTS Both PfMSP6 allele classes, K1-like and 3D7-like, were detected at the study site, confirming that both are globally distributed. Allele frequencies varied significantly between transmission seasons, with 3D7-class alleles dominating and K1-class alleles nearly disappearing in 2005 and 2006. There was a significant association between allele class and village location (p-value = 0.0008), but no statistically significant association between allele class and age, sex, or symptom status. No intra-allele class sequence diversity was detected. CONCLUSIONS Both PfMSP6 allele classes are globally distributed, and this study shows that allele frequencies can fluctuate significantly between communities separated by only a few kilometres, and over time in the same community. By contrast, PfMSP6 was highly stable at the sequence level, with no SNPs detected in the 506 samples analysed. This limited diversity supports further investigation of PfMSP6 as a blood stage vaccine candidate, with the clear caveat that any such vaccine must either contain both alleles or generate cross-protective responses that react against both allele classes. Detailed immunoepidemiology studies are needed to establish the viability of these approaches before PfMSP6 advances further down the vaccine development pipeline.
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Affiliation(s)
- Aaron T Neal
- William C Gorgas Center for Geographic Medicine, Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens. INFECTION GENETICS AND EVOLUTION 2009; 10:200-6. [PMID: 19931645 DOI: 10.1016/j.meegid.2009.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 11/06/2009] [Accepted: 11/11/2009] [Indexed: 11/24/2022]
Abstract
Plasmodium falciparum, the causative agent of human malaria, invades host erythrocytes using several proteins on the surface of the invasive merozoite, which have been proposed as potential vaccine candidates. Members of the multi-gene PfRh family are surface antigens that have been shown to play a central role in directing merozoites to alternative erythrocyte receptors for invasion. Recently, we identified a large structural polymorphism, a 0.58Kb deletion, in the C-terminal region of the PfRh2b gene, present at a high frequency in parasite populations from Senegal. We hypothesize that this region is a target of humoral immunity. Here, by analyzing 371 P. falciparum isolates we show that this major allele is present at varying frequencies in different populations within Senegal, Africa, and throughout the world. For allelic dimorphisms in the asexual stage antigens, Msp-2 and EBA-175, we find minimal geographic differentiation among parasite populations from Senegal and other African localities, suggesting extensive gene flow among these populations and/or immune-mediated frequency-dependent balancing selection. In contrast, we observe a higher level of inter-population divergence (as measured by F(st)) for the PfRh2b deletion, similar to that observed for SNPs from the sexual stage Pfs45/48 loci, which is postulated to be under directional selection. We confirm that the region containing the PfRh2b polymorphism is a target of humoral immune responses by demonstrating antibody reactivity of endemic sera. Our analysis of inter-population divergence suggests that in contrast to the large allelic dimorphisms in EBA-175 and Msp-2, the presence or absence of the large PfRh2b deletion may not elicit frequency-dependent immune selection, but may be under positive immune selection, having important implications for the development of these proteins as vaccine candidates.
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Sander AF, Salanti A, Lavstsen T, Nielsen MA, Magistrado P, Lusingu J, Ndam NT, Arnot DE. Multiple var2csa-type PfEMP1 genes located at different chromosomal loci occur in many Plasmodium falciparum isolates. PLoS One 2009; 4:e6667. [PMID: 19690615 PMCID: PMC2723927 DOI: 10.1371/journal.pone.0006667] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/13/2009] [Indexed: 12/03/2022] Open
Abstract
Background The var2csa gene encodes a Plasmodium falciparum adhesion receptor which binds chondroitin sulfate A (CSA). This var gene is more conserved than other PfEMP1/var genes and is found in all P. falciparum isolates. In isolates 3D7, FCR3/It4 and HB3, var2csa is transcribed from a sub-telomeric position on the left arm of chromosome 12, but it is not known if this location is conserved in all parasites. Genome sequencing indicates that the var2csa gene is duplicated in HB3, but whether this is true in natural populations is uncertain. Methodology/Principal Findings To assess global variation in the VAR2CSA protein, sequence variation in the DBL2X region of var2csa genes in 54 P.falciparum samples was analyzed. Chromosome mapping of var2csa loci was carried out and a quantitative PCR assay was developed to estimate the number of var2csa genes in P.falciparum isolates from the placenta of pregnant women and from the peripheral circulation of other malaria patients. Sequence analysis, gene mapping and copy number quantitation in P.falciparum isolates indicate that there are at least two loci and that both var2csa-like genes can be transcribed. All VAR2CSA DBL2X domains fall into one of two distinct phylogenetic groups possessing one or the other variant of a large (∼26 amino acid) dimorphic motif, but whether either motif variant is linked to a specific locus is not known. Conclusions/Significance Two or more related but distinct var2csa-type PfEMP1/var genes exist in many P. falciparum isolates. One gene is on chromosome 12 but additional var2csa-type genes are on different chromosomes in different isolates. Multiplicity of var2csa genes appears more common in infected placentae than in samples from non-pregnant donors indicating a possible advantage of this genotype in pregnancy associated malaria.
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Affiliation(s)
- Adam F. Sander
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Ali Salanti
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Thomas Lavstsen
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Morten A. Nielsen
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Pamela Magistrado
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
- JMP-ENRICA Project, National Institute for Medical Research, Korogwe Laboratory, Tanga, Tanzania
| | - John Lusingu
- JMP-ENRICA Project, National Institute for Medical Research, Korogwe Laboratory, Tanga, Tanzania
| | - Nicaise Tuikue Ndam
- Institut de Recherche pour le Developpment, UR010, Universite Paris Descartes, Paris, France
| | - David E. Arnot
- Centre for Medical Parasitology, Department of International Health, Immunology & Microbiology, Faculty of Health Sciences, University of Copenhagen & Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
- Institute of Immunology & Infection Research, School of Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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Roy SW, Weedall GD, da Silva RL, Polley SD, Ferreira MU. Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum. Gene 2009; 443:12-21. [PMID: 19463923 DOI: 10.1016/j.gene.2009.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 04/30/2009] [Accepted: 05/11/2009] [Indexed: 11/30/2022]
Abstract
Immune evasion by Plasmodium falciparum is favored by extensive allelic diversity of surface antigens. Some of them, most notably the vaccine-candidate merozoite surface protein (MSP)-1, exhibit a poorly understood pattern of allelic dimorphism, in which all observed alleles group into two highly diverged allelic families with few or no inter-family recombinants. Here we describe contrasting levels and patterns of sequence diversity in genes encoding three MSP-1-associated surface antigens of P. falciparum, ranging from an ancient allelic dimorphism in the Msp-6 gene to a near lack of allelic divergence in Msp-9 to a more classical multi-allele polymorphism in Msp-7. Other members of the Msp-7 gene family exhibit very little polymorphism in non-repetitive regions. A comparison of P. falciparum Msp-6 sequences to an orthologous sequence from P. reichenowi provided evidence for distinct evolutionary histories of the 5' and 3' segments of the dimorphic region in PfMsp-6, consistent with one dimorphic lineage having arisen from recombination between now-extinct ancestral alleles. In addition, we uncovered two surprising patterns of evolution in repetitive sequence. First, in Msp-6, large deletions are associated with (nearly) identical sequence motifs at their borders. Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi.
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Affiliation(s)
- Scott W Roy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA.
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Differential selective pressures on the merozoite surface protein 2 locus of Plasmodium falciparum in a low endemic area. Gene 2008; 427:51-7. [PMID: 18840512 DOI: 10.1016/j.gene.2008.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 08/14/2008] [Accepted: 09/05/2008] [Indexed: 11/22/2022]
Abstract
195 Plasmodium falciparum merozoite surface protein-2 alleles collected in Tak Province, Thailand, in 1996 and 2006 revealed extremely limited sequence polymorphism except in the variable (V) region, which defines the two allelic families 3D7 and FC27. This pattern is most easily explained by repeated inter-allelic gene conversion events homogenizing alleles outside the V region. Comparison of synonymous and nonsynonymous differences in V regions within allelic families supported the hypothesis that amino acid sequence polymorphism in this region is selectively favored. The pattern of sequence differentiation supported the hypothesis that repeats in the V region have evolved by concerted evolution in the 3D7 family but not in the FC27 family. In the FC27 family two alleles of relatively high frequency were the most common V-region alleles in both 1996 and 2006, while 3D7 alleles constituted a significantly greater proportion of the sequences collected in 2006 (56.1%) than of those collected in 1996 (28.9%). These changes in the frequencies of 3D7 alleles may reflect increased intensity of selection on the P. falciparum population in Thailand as a result of effective control measures that have sharply reduced the incidence of malaria infection.
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Iriko H, Kaneko O, Otsuki H, Tsuboi T, Su XZ, Tanabe K, Torii M. Diversity and evolution of the rhoph1/clag multigene family of Plasmodium falciparum. Mol Biochem Parasitol 2007; 158:11-21. [PMID: 18155305 DOI: 10.1016/j.molbiopara.2007.11.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 11/05/2007] [Accepted: 11/06/2007] [Indexed: 11/19/2022]
Abstract
A complex of high-molecular-mass proteins (PfRhopH) of the human malaria parasite Plasmodium falciparum induces host protective immunity and therefore is a candidate for vaccine development. Understanding the level of polymorphism and the evolutionary processes is important for advancements in both vaccine design and knowledge of the evolution of cell invasion in this parasite. In the present study, we sequenced the entire open reading frames of seven genes encoding the proteins of the PfRhopH complex (rhoph2, rhoph3, and five rhoph1/clag gene paralogs). We found that four rhoph1/clag genes (clag2, 3.1, 3.2, and 8) were highly polymorphic. Amino acid substitutions and indels are predominantly clustered around amino acid positions 1000-1200 of these four rhoph1/clag genes. An excess of nonsynonymous substitutions over synonymous substitutions was detected for clag8 and 9, indicating positive selection. The McDonald-Kreitman test with a Plasmodium reichenowi orthologous sequence also supports positive selection on clag8. Based on the ratio of interspecific genetic distance to intraspecific distance, the time to the most recent common ancestor of the clag2 and 8 polymorphisms was estimated to be 1.89 and 0.87 million years ago, respectively, assuming divergence of P. falciparum and P. reichenowi 6 million years ago. In addition to a copy number polymorphism, gene conversion events were detected for the rhoph1/clag genes on chromosome 3, which likely play a role in increasing the diversity of each locus. Our results indicate that a high diversity of the PfRhopH1/Clag multigene family is maintained by diversifying selection forces over a considerably long period.
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Affiliation(s)
- Hideyuki Iriko
- Department of Molecular Parasitology, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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