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5. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

Author

Jacob, Christopher G, Thuy-Nhien, Nguyen, Mayxay, Mayfong, Maude, Richard J, Quang, Huynh Hong, Hongvanthong, Bouasy, Vanisaveth, Viengxay, Ngo Duc, Thang, Rekol, Huy, van der Pluijm, Rob, von Seidlein, Lorenz, Fairhurst, Rick, Nosten, François, Hossain, Md Amir, Park, Naomi, Goodwin, Scott, Ringwald, Pascal, Chindavongsa, Keobouphaphone, Newton, Paul, Ashley, Elizabeth, Phalivong, Sonexay, Maude, Rapeephan, Leang, Rithea, Huch, Cheah, Dong, Le Thanh, Nguyen, Kim-Tuyen, Nhat, Tran Minh, Hien, Tran Tinh, Nguyen, Hoa, Zdrojewski, Nicole, Canavati, Sara, Sayeed, Abdullah Abu, Uddin, Didar, Buckee, Caroline, Fanello, Caterina I, Onyamboko, Marie, Peto, Thomas, Tripura, Rupam, Amaratunga, Chanaki, Myint Thu, Aung, Delmas, Gilles, Landier, Jordi, Parker, Daniel M, Chau, Nguyen Hoang, Lek, Dysoley, Suon, Seila, Callery, James, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Phyo, Aung Pyae, Smithuis, Frank, Lin, Khin, Thant, Myo, Hlaing, Tin Maung, Satpathi, Parthasarathi, Satpathi, Sanghamitra, Behera, Prativa K, Tripura, Amar, Baidya, Subrata, Valecha, Neena, Anvikar, Anupkumar R, Ul Islam, Akhter, Faiz, Abul, Kunasol, Chanon, Drury, Eleanor, Kekre, Mihir, Ali, Mozam, Love, Katie, Rajatileka, Shavanthi, Jeffreys, Anna E, Rowlands, Kate, Hubbart, Christina S, Dhorda, Mehul, Vongpromek, Ranitha, Kotanan, Namfon, Wongnak, Phrutsamon, Almagro Garcia, Jacob, Pearson, Richard D, Ariani, Cristina V, Chookajorn, Thanat, Malangone, Cinzia, Nguyen, T, Stalker, Jim, Jeffery, Ben, Keatley, Jonathan, Johnson, Kimberly J, Muddyman, Dawn, Chan, Xin Hui S, Sillitoe, John, Amato, Roberto, Simpson, Victoria, Gonçalves, Sonia, Rockett, Kirk, Day, Nicholas P, Dondorp, Arjen M, Kwiatkowski, Dominic P, and Miotto, Olivo

Subjects
asia, drug resistance, epidemiology, genetic surveillance, global health, infectious disease, malaria, microbiology, Biochemistry and Cell Biology
Abstract

BackgroundNational Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.MethodsSamples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs.ResultsGenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs.ConclusionsGenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community.FundingThe GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.

Published
2021

6. Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response

Author

Zhu, Lei, van der Pluijm, Rob W., Kucharski, Michal, Nayak, Sourav, Tripathi, Jaishree, White, Nicholas J., Day, Nicholas P. J., Faiz, Abul, Phyo, Aung Pyae, Amaratunga, Chanaki, Lek, Dysoley, Ashley, Elizabeth A., Nosten, François, Smithuis, Frank, Ginsburg, Hagai, von Seidlein, Lorenz, Lin, Khin, Imwong, Mallika, Chotivanich, Kesinee, Mayxay, Mayfong, Dhorda, Mehul, Nguyen, Hoang Chau, Nguyen, Thuy Nhien Thanh, Miotto, Olivo, Newton, Paul N., Jittamala, Podjanee, Tripura, Rupam, Pukrittayakamee, Sasithon, Peto, Thomas J., Hien, Tran Tinh, Dondorp, Arjen M., and Bozdech, Zbynek

Published
2022
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8. The PAGODAS protocol: pediatric assessment group of dengue and Aedes saliva protocol to investigate vector-borne determinants of Aedes-transmitted arboviral infections in Cambodia.

Author

Manning, Jessica E, Oliveira, Fabiano, Parker, Daniel M, Amaratunga, Chanaki, Kong, Dara, Man, Somnang, Sreng, Sokunthea, Lay, Sreyngim, Nang, Kimsour, Kimsan, Soun, Sokha, Ly, Kamhawi, Shaden, Fay, Michael P, Suon, Seila, Ruhl, Parker, Ackerman, Hans, Huy, Rekol, Wellems, Thomas E, Valenzuela, Jesus G, and Leang, Rithea

Subjects
Saliva, Animals, Humans, Aedes, Dengue Virus, Chikungunya virus, Arbovirus Infections, Dengue, Antibodies, Viral, Longitudinal Studies, Follow-Up Studies, Prospective Studies, Seroepidemiologic Studies, Pediatrics, Seasons, Child, Child, Preschool, Cambodia, Female, Male, Zika Virus, Mosquito Vectors, Arbovirus, Cohort, Mosquito, Seroprevalence, Vaccines, Vector, Tropical Medicine, Mycology & Parasitology, Medical Microbiology, Public Health and Health Services
Abstract

BackgroundMosquito-borne arboviruses, like dengue virus, continue to cause significant global morbidity and mortality, particularly in Southeast Asia. When the infectious mosquitoes probe into human skin for a blood meal, they deposit saliva containing a myriad of pharmacologically active compounds, some of which alter the immune response and influence host receptivity to infection, and consequently, the establishment of the virus. Previous reports have highlighted the complexity of mosquito vector-derived factors and immunity in the success of infection. Cumulative evidence from animal models and limited data from humans have identified various vector-derived components, including salivary components, that are co-delivered with the pathogen and play an important role in the dissemination of infection. Much about the roles and effects of these vector-derived factors remain to be discovered.Methods/designWe describe a longitudinal, pagoda (community)-based pediatric cohort study to evaluate the burden of dengue virus infection and document the immune responses to salivary proteins of Aedes aegypti, the mosquito vector of dengue, Zika, and chikungunya viruses. The study includes community-based seroprevalence assessments in the peri-urban town of Chbar Mon in Kampong Speu Province, Cambodia. The study aims to recruit 771 children between the ages of 2 and 9 years for a three year period of longitudinal follow-up, including twice per year (rainy and dry season) serosurveillance for dengue seroconversion and Ae. aegypti salivary gland homogenate antibody intensity determinations by ELISA assays. Diagnostic tests for acute dengue, Zika and chikungunya viral infections will be performed by RT-PCR.DiscussionThis study will serve as a foundation for further understanding of mosquito saliva immunity and its impact on Aedes-transmitted arboviral diseases endemic to Cambodia.Trial registrationNCT03534245 registered on 23 May 2018.

Published
2018

9. Triple therapy with artemether–lumefantrine plus amodiaquine versus artemether–lumefantrine alone for artemisinin-resistant, uncomplicated falciparum malaria: an open-label, randomised, multicentre trial

Author

Peto, Thomas J, Tripura, Rupam, Callery, James J, Lek, Dysoley, Nghia, Ho Dang Trung, Nguon, Chea, Thuong, Nguyen Thi Huyen, van der Pluijm, Rob W, Dung, Nguyen Thi Phuong, Sokha, Meas, Van Luong, Vo, Long, Le Thanh, Sovann, Yok, Duanguppama, Jureeporn, Waithira, Naomi, Hoglund, Richard M, Chotsiri, Palang, Chau, Nguyen Hoang, Ruecker, Andrea, Amaratunga, Chanaki, Dhorda, Mehul, Miotto, Olivo, Maude, Richard J, Rekol, Huy, Chotivanich, Kesinee, Tarning, Joel, von Seidlein, Lorenz, Imwong, Mallika, Mukaka, Mavuto, Day, Nicholas P J, Hien, Tran Tinh, White, Nicholas J, and Dondorp, Arjen M

Published
2022
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14. Artemisinin-resistant malaria in Africa demands urgent action.

Author

Dhorda, Mehul, Akira Kaneko, Ryuichi Komatsu, K. C., Achyut, Mshamu, Salum, Gesase, Samwel, Kapologwe, Ntuli, Assefa, Ashenafi, Opigo, Jimmy, Adoke, Yeka, Ebong, Chris, Karema, Corine, Uwimana, Aline, Mangara, Jean-Louis Ndikumana, Amaratunga, Chanaki, Peto, Thomas J., Tripura, Rupam, Callery, James J., Adhikari, Bipin, and Mukaka, Mavuto

Published
2024
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15. Artemisinin resistance phenotypes and K13 inheritance in a Plasmodium falciparum cross and Aotus model

Author

Sá, Juliana M., Kaslow, Sarah R., Krause, Michael A., Melendez-Muniz, Viviana A., Salzman, Rebecca E., Kite, Whitney A., Zhang, Min, Barros, Roberto R. Moraes, Mu, Jianbing, Han, Paul K., Mershon, J. Patrick, Figan, Christine E., Caleon, Ramoncito L., Rahman, Rifat S., Gibson, Tyler J., Amaratunga, Chanaki, Nishiguchi, Erika P., Breglio, Kimberly F., Engels, Theresa M., Velmurugan, Soundarapandian, Ricklefs, Stacy, Straimer, Judith, Gnädig, Nina F., Deng, Bingbing, Liu, Anna, Diouf, Ababacar, Miura, Kazutoyo, Tullo, Gregory S., Eastman, Richard T., Chakravarty, Sumana, James, Eric R., Udenze, Kenneth, Li, Suzanne, Sturdevant, Daniel E., Gwadz, Robert W., Porcella, Stephen F., Long, Carole A., Fidock, David A., Thomas, Marvin L., Fay, Michael P., Sim, B. Kim Lee, Hoffman, Stephen L., Adams, John H., Fairhurst, Rick M., Su, Xin-zhuan, and Wellems, Thomas E.

Published
2018

16. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study

Author

van der Pluijm, Rob W, Imwong, Mallika, Chau, Nguyen Hoang, Hoa, Nhu Thi, Thuy-Nhien, Nguyen Thanh, Thanh, Ngo Viet, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Chutasmit, Kitipumi, Saelow, Chalermpon, Runjarern, Ratchadaporn, Kaewmok, Weerayuth, Tripura, Rupam, Peto, Thomas J, Yok, Sovann, Suon, Seila, Sreng, Sokunthea, Mao, Sivanna, Oun, Savuth, Yen, Sovannary, Amaratunga, Chanaki, Lek, Dysoley, Huy, Rekol, Dhorda, Mehul, Chotivanich, Kesinee, Ashley, Elizabeth A, Mukaka, Mavuto, Waithira, Naomi, Cheah, Phaik Yeong, Maude, Richard J, Amato, Roberto, Pearson, Richard D, Gonçalves, Sónia, Jacob, Christopher G, Hamilton, William L, Fairhurst, Rick M, Tarning, Joel, Winterberg, Markus, Kwiatkowski, Dominic P, Pukrittayakamee, Sasithon, Hien, Tran Tinh, Day, Nicholas PJ, Miotto, Olivo, White, Nicholas J, and Dondorp, Arjen M

Published
2019
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17. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study

Author

Hamilton, William L, Amato, Roberto, van der Pluijm, Rob W, Jacob, Christopher G, Quang, Huynh Hong, Thuy-Nhien, Nguyen Thanh, Hien, Tran Tinh, Hongvanthong, Bouasy, Chindavongsa, Keobouphaphone, Mayxay, Mayfong, Huy, Rekol, Leang, Rithea, Huch, Cheah, Dysoley, Lek, Amaratunga, Chanaki, Suon, Seila, Fairhurst, Rick M, Tripura, Rupam, Peto, Thomas J, Sovann, Yok, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Chau, Nguyen Hoang, Imwong, Mallika, Dhorda, Mehul, Vongpromek, Ranitha, Chan, Xin Hui S, Maude, Richard J, Pearson, Richard D, Nguyen, T, Rockett, Kirk, Drury, Eleanor, Gonçalves, Sónia, White, Nicholas J, Day, Nicholas P, Kwiatkowski, Dominic P, Dondorp, Arjen M, and Miotto, Olivo

Published
2019
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19. A framework for stakeholder engagement in the adoption of new antimalarial treatments in Africa: a case study of Nigeria

Author

Mokuolu, Olugbenga, primary, Bolarinwa, Oladimeji Akeem, additional, Opadiran, Oluwatumobi Racheal, additional, Ameen, Hafsat Abolore, additional, Tindana, Paulina, additional, Haan, Freek de, additional, Dhorda, Mehul, additional, Cheah, Phaik Yeong, additional, Amaratunga, Chanaki, additional, and Dondorp, Arjen M., additional

Published
2023
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22. Host immunity to Plasmodium falciparum and the assessment of emerging artemisinin resistance in a multinational cohort

Author

Ataide, Ricardo, Ashley, Elizabeth A., Powell, Rosanna, Chan, Jo-Anne, Malloy, Michael J., O’Flaherty, Katherine, Takashima, Eizo, Langer, Christine, Tsuboi, Takafumi, Dondorp, Arjen M., Day, Nicholas P., Dhorda, Mehul, Fairhurst, Rick M., Lim, Pharath, Amaratunga, Chanaki, Pukrittayakamee, Sasithon, Hien, Tran Tinh, Htut, Ye, Mayxay, Mayfong, Faiz, M. Abul, Beeson, James G., Nosten, Francois, Simpson, Julie A., White, Nicholas J., and Fowkes, Freya J. I.

Published
2017

23. Raising awareness of antimicrobial resistance: development of an ‘antibiotic footprint calculator’

Author

Prapharsavat, Ravikanya, primary, Kittikongnapang, Rattanasiri, additional, Smithkittipol, Chokdee, additional, Udomrat, Warute, additional, Numsawat, Sukanya, additional, Hernandez-Koutoucheva, Anastasia, additional, Naemiratch, Bhensri, additional, Chomkatekaew, Chalita, additional, Amaratunga, Chanaki, additional, Bleho, John, additional, Mathee, Kalai, additional, Schneiders, Mira Leonie, additional, Khirikoekkong, Napat, additional, Kanthawang, Nipaphan, additional, Sumpradit, Nithima, additional, Suveeranont, Rapee, additional, Asarath, Supa-at, additional, Poomchaichote, Tassawan, additional, Schilling, William, additional, Chan, Xin Hui S, additional, Osterrieder, Anne, additional, Cheah, Phaik Yeong, additional, and Limmathurotsakul, Direk, additional

Published
2023
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24. Immunological characterization of a VIR protein family member (VIR-14) in Plasmodium vivax-infected subjects from different epidemiological regions in Africa and South America

Author

Fantin, Raianna F., primary, Coelho, Camila H., additional, Berhe, Anne D., additional, Magalhães, Luisa M. D., additional, Pereira, Dhélio B., additional, Salinas, Nichole D., additional, Tolia, Niraj H., additional, Amaratunga, Chanaki, additional, Suon, Seila, additional, Sagara, Issaka, additional, Narum, David L., additional, Fujiwara, Ricardo T., additional, Abejon, Claudia, additional, Campos-Neto, Antonio, additional, Duffy, Patrick E., additional, and Bueno, Lilian L., additional

Published
2023
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27. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Author

Abdel Hamid, Muzamil Mahdi, Abdelraheem, Mohamed Hassan, Acheampong, Desmond Omane, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim, Andrianaranjaka, Voahangy, Aniebo, Ifeyinwa, Aninagyei, Enoch, Ansah, Felix, Ansah, Patrick, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys, Boni, Maciej, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, Corredor, Vladimir, Courtier, Erin, Craig, Alister, d'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas, Denis, Brigitte, Dhorda, Mehul, Diakite, Mahamadou, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen, Doumbia, Seydou, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego, Egwang, Thomas, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick, Faiz, Abdul, Fanello, Caterina, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, G, Healy, Sara Anne, Hendry, Jason, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott, Jacob, Chris, Jeans, Julia, Johnson, Kimberly, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic, Kyaw, Myat, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana, Mandara, Celine, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga, Montgomery, Jaqui, Morang'A, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, François, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung, Plowe, Christopher, Price, Ric, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria, Sissoko, Mahamadou, Smith, Christen, Su, Xin-Zhuan, Sutherland, Colin, Takala-Harrison, Shannon, Talman, Arthur, Tavul, Livingstone, Thanh, Ngo Viet, Thathy, Vandana, Thu, Aung Myint, Toure, Mahamoudou, Tshefu, Antoinette, Verra, Federica, Vinetz, Joseph, Wellems, Thomas, Wendler, Jason, White, Nicholas, Whitton, Georgia, Yavo, William, van der Pluijm, Rob, MalariaGEN, University of Khartoum, University of Cape Coast [Ghana], Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine [Fajara, Gambia], London School of Hygiene and Tropical Medicine (LSHTM), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), West African Centre for Cell Biology of Infectious Pathogens [Legon, Ghana] (WACCBIP), University of Ghana, Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), Kenya Medical Research Institute (KEMRI), Texas Biomedical Research Institute [San Antonio, TX], Université d'Antananarivo, University of Buéa, Instituto Nacional de Saude [Maputo, Mozambique] (INS), Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford-University of Oxford, Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, Menzies School of Health Research [Australia], Charles Darwin University [Australia], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, Institut de Recherche pour le Développement (IRD), Laboratory of Pathogen and Host Immunity [Montpellier] (LPHI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)

Subjects
data resource, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], plasmodium falciparum, genomics, malaria, Medicine (miscellaneous), genomic epidemiology, General Biochemistry, Genetics and Molecular Biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Contains fulltext : 291985.pdf (Publisher’s version ) (Open Access) 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.

Published
2023

28. A framework for stakeholder engagement in the adoption of new antimalarial treatments in Africa: a case study of Nigeria

Author

Mokuolu, Olugbenga Ayodeji, primary, Bolarinwa, Oladimeji Akeem, additional, Opadiran, Oluwatumobi Racheal, additional, Ameen, Hafsat Abolore, additional, Dhorda, Mehul, additional, Cheah, Phaik Yeong, additional, Amaratunga, Chanaki, additional, Haan, Freek, additional, Tindana, Paulina, additional, and Dondorp, Arjen M., additional

Published
2022
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29. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Author

MalariaGEN, Abdel Hamid, Muzamil Mahdi, Abdelraheem, Mohamed Hassan, Acheampong, Desmond Omane, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim, Andrianaranjaka, Voahangy, Aniebo, Ifeyinwa, Aninagyei, Enoch, Ansah, Felix, Ansah, Patrick O, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon A, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter C, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David J, Corredor, Vladimir, Courtier, Erin, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas, Denis, Brigitte, Dhorda, Mehul, Diakite, Mahamadou, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen, Doumbia, Seydou, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, GL Abby, Healy, Sara Anne, Hendry, Jason A, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine A, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott A, Jacob, Chris G, Jeans, Julia, Johnson, Kimberly J, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa S, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic P, Kyaw, Myat P, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel K, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Mandara, Celine I, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga A, Montgomery, Jaqui, Morang'a, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul N, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie A, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung P, Plowe, Christopher V, Price, Ric N, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian C, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria J, Sissoko, Mahamadou S, Smith, Christen, Su, Xin-Zhuan, Sutherland, Colin, Takala-Harrison, Shannon, Talman, Arthur, Tavul, Livingstone, Thanh, Ngo Viet, Thathy, Vandana, Thu, Aung Myint, Toure, Mahamoudou, Tshefu, Antoinette, Verra, Federica, Vinetz, Joseph, Wellems, Thomas E, Wendler, Jason, White, Nicholas J, Whitton, Georgia, Yavo, William, Van Der Pluijm, Rob W, Amenga-Etego, Lucas [0000-0003-4468-0506], Anderson, Tim [0000-0002-0191-0204], Ansah, Patrick O [0000-0002-3214-5621], Ashley, Elizabeth [0000-0002-7620-4822], Ba, Hampate [0000-0002-9299-5775], Baraka, Vito [0000-0001-9694-9293], Bejon, Philip [0000-0002-2135-7549], Bertin, Gwladys I [0000-0002-2218-9591], Boni, Maciej F [0000-0002-0830-9630], Bousema, Teun [0000-0003-2666-094X], Chookajorn, Thanat [0000-0003-2876-6203], Claessens, Antoine [0000-0002-4277-0914], Conway, David J [0000-0002-8711-3037], Craig, Alister [0000-0003-0914-6164], D'Alessandro, Umberto [0000-0001-6341-5009], Day, Nicholas [0000-0003-2309-1171], Diakite, Mahamadou [0000-0002-4268-8857], Djimde, Abdoulaye [0000-0003-0062-2283], Dondorp, Arjen [0000-0001-5190-2395], Drakeley, Chris [0000-0003-4863-075X], Echeverry, Diego F [0000-0003-0301-4478], Erko, Berhanu [0000-0003-1685-752X], Faiz, Abdul [0000-0002-3460-7535], Fanello, Caterina A [0000-0003-1932-9562], Gamboa, Dionicia [0000-0002-1420-7729], Golassa, Lemu [0000-0002-1216-8711], Healy, Sara Anne [0000-0003-3078-6094], Ishengoma, Deus [0000-0003-2040-3416], Jackson, Scott A [0000-0002-3172-1607], Kamaliddin, Claire [0000-0001-8198-6235], Kamau, Edwin [0000-0002-5761-7883], Konate, Drissa S [0000-0002-4177-9642], Kwiatkowski, Dominic P [0000-0002-5023-0176], Kyle, Dennis [0000-0002-0238-965X], Lawniczak, Mara [0000-0002-3006-2080], Loua, Kovana M [0000-0003-0571-0944], Marsh, Kevin [0000-0001-8377-5466], Mayxay, Mayfong [0000-0002-6056-4516], Miotto, Olivo [0000-0001-8060-6771], Mita, Toshihiro [0000-0001-8180-2344], Mobegi, Victor [0000-0002-1962-5583], Morang'a, Collins Misita [0000-0002-6988-150X], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Ntui, Vincent Ntui-Njock [0000-0002-7532-9930], Oduro, Abraham [0000-0002-4191-7419], Onyamboko, Marie A [0000-0002-7501-5931], Ouedraogo, Jean-Bosco [0000-0003-0412-8733], Oyebola, Kolapo [0000-0002-1003-2570], Pearson, Richard [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Rosanas-Urgell, Anna [0000-0002-0432-5203], Shayo, Alex [0000-0002-7099-8537], Su, Xin-Zhuan [0000-0003-3246-3248], Vinetz, Joseph [0000-0001-8344-2004], Wellems, Thomas E [0000-0003-3899-8454], and Apollo - University of Cambridge Repository

Subjects
data resource, plasmodium falciparum, genomics, malaria, genomic epidemiology
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.

Published
2023

30. The risk of Plasmodium vivax parasitaemia after P. falciparum malaria: An individual patient data meta-analysis from the WorldWide Antimalarial Resistance Network

Author

Hossain, Mohammad S., Commons, Robert J., Douglas, Nicholas M., Thriemer, Kamala, Alemayehu, Bereket H., Amaratunga, Chanaki, Anvikar, Anupkumar R., Ashley, Elizabeth A., Asih, Puji B. S., Carrara, Verena I., Lon, Chanthap, D'Alessandro, Umberto, Davis, Timothy M. E., Dondorp, Arjen M., Edstein, Michael D., Fairhurst, Rick M., Ferreira, Marcelo U., Hwang, Jimee, Janssens, Bart, Karunajeewa, Harin, Kiechel, Jean R., Ladeia-Andrade, Simone, Laman, Moses, Mayxay, Mayfong, McGready, Rose, Moore, Brioni R., Mueller, Ivo, Newton, Paul N., Thuy-Nhien, Nguyen T., Noedl, Harald, Nosten, Francois, Phyo, Aung P., Poespoprodjo, Jeanne R., Saunders, David L., Smithuis, Frank, Spring, Michele D., Stepniewska, Kasia, Suon, Seila, Suputtamongkol, Yupin, Syafruddin, Din, Tran, Hien T., Valecha, Neena, Van Herp, Michel, Van Vugt, Michele, White, Nicholas J., Guerin, Philippe J., Simpson, Julie A., and Price, Ric N.

Subjects
Malaria -- Drug therapy -- Complications and side effects, Protozoan diseases -- Risk factors, Biological sciences
Abstract

Background There is a high risk of Plasmodium vivax parasitaemia following treatment of falciparum malaria. Our study aimed to quantify this risk and the associated determinants using an individual patient data meta-analysis in order to identify populations in which a policy of universal radical cure, combining artemisinin-based combination therapy (ACT) with a hypnozoitocidal antimalarial drug, would be beneficial. Methods and findings A systematic review of Medline, Embase, Web of Science, and the Cochrane Database of Systematic Reviews identified efficacy studies of uncomplicated falciparum malaria treated with ACT that were undertaken in regions coendemic for P. vivax between 1 January 1960 and 5 January 2018. Data from eligible studies were pooled using standardised methodology. The risk of P. vivax parasitaemia at days 42 and 63 and associated risk factors were investigated by multivariable Cox regression analyses. Study quality was assessed using a tool developed by the Joanna Briggs Institute. The study was registered in the International Prospective Register of Systematic Reviews (PROSPERO: CRD42018097400). In total, 42 studies enrolling 15,341 patients were included in the analysis, including 30 randomised controlled trials and 12 cohort studies. Overall, 14,146 (92.2%) patients had P. falciparum monoinfection and 1,195 (7.8%) mixed infection with P. falciparum and P. vivax. The median age was 17.0 years (interquartile range [IQR] = 9.0-29.0 years; range = 0-80 years), with 1,584 (10.3%) patients younger than 5 years. 2,711 (17.7%) patients were treated with artemether-lumefantrine (AL, 13 studies), 651 (4.2%) with artesunate-amodiaquine (AA, 6 studies), 7,340 (47.8%) with artesunate-mefloquine (AM, 25 studies), and 4,639 (30.2%) with dihydroartemisinin-piperaquine (DP, 16 studies). 14,537 patients (94.8%) were enrolled from the Asia-Pacific region, 684 (4.5%) from the Americas, and 120 (0.8%) from Africa. At day 42, the cumulative risk of vivax parasitaemia following treatment of P. falciparum was 31.1% (95% CI 28.9-33.4) after AL, 14.1% (95% CI 10.8-18.3) after AA, 7.4% (95% CI 6.7-8.1) after AM, and 4.5% (95% CI 3.9-5.3) after DP. By day 63, the risks had risen to 39.9% (95% CI 36.6-43.3), 42.4% (95% CI 34.7-51.2), 22.8% (95% CI 21.2-24.4), and 12.8% (95% CI 11.4-14.5), respectively. In multivariable analyses, the highest rate of P. vivax parasitaemia over 42 days of follow-up was in patients residing in areas of short relapse periodicity (adjusted hazard ratio [AHR] = 6.2, 95% CI 2.0-19.5; p = 0.002); patients treated with AL (AHR = 6.2, 95% CI 4.6-8.5; p < 0.001), AA (AHR = 2.3, 95% CI 1.4-3.7; p = 0.001), or AM (AHR = 1.4, 95% CI 1.0-1.9; p = 0.028) compared with DP; and patients who did not clear their initial parasitaemia within 2 days (AHR = 1.8, 95% CI 1.4-2.3; p < 0.001). The analysis was limited by heterogeneity between study populations and lack of data from very low transmission settings. Study quality was high. Conclusions In this meta-analysis, we found a high risk of P. vivax parasitaemia after treatment of P. falciparum malaria that varied significantly between studies. These P. vivax infections are likely attributable to relapses that could be prevented with radical cure including a hypnozoitocidal agent; however, the benefits of such a novel strategy will vary considerably between geographical areas., Author(s): Mohammad S. Hossain 1,2,3,4, Robert J. Commons 1,2,5, Nicholas M. Douglas 2,3, Kamala Thriemer 2, Bereket H. Alemayehu 6, Chanaki Amaratunga 7, Anupkumar R. Anvikar 8, Elizabeth A. Ashley [...]

Published
2020
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31. A framework for stakeholder engagement in the adoption of new anti-malarial treatments in Africa: a case study of Nigeria.

Author

Mokuolu, Olugbenga Ayodeji, Bolarinwa, Oladimeji Akeem, Opadiran, Oluwatumobi Racheal, Ameen, Hafsat Abolore, Dhorda, Mehul, Cheah, Phaik Yeong, Amaratunga, Chanaki, de Haan, Freek, Tindana, Paulina, and Dondorp, Arjen M.

Subjects
STAKEHOLDER analysis, DRUG efficacy, PRENATAL care, ARTEMISININ, COMMUNITIES
Abstract

Background: Recent reports of artemisinin partial resistance from Rwanda and Uganda are worrisome and suggest a future policy change to adopt new anti-malarials. This is a case study on the evolution, adoption, and implementation of new anti-malarial treatment policies in Nigeria. The main objective is to provide perspectives to enhance the future uptake of new anti-malarials, with an emphasis on stakeholder engagement strategies. Methods: This case study is based on an analysis of policy documents and stakeholders' perspectives drawn from an empirical study conducted in Nigeria, 2019–2020. A mixed methods approach was adopted, including historical accounts, review of programme and policy documents, and 33 qualitative in-depth interviews and 6 focus group discussions. Results: Based on policy documents reviewed, the adoption of artemisinin-based combination therapy (ACT) in Nigeria was swift due to political will, funding and support from global developmental partners. However, the implementation of ACT was met with resistance from suppliers, distributors, prescribers, and end-users, attributed to market dynamics, costs and inadequate stakeholder engagement. Deployment of ACT in Nigeria witnessed increased developmental partner support, robust data generation, ACT case-management strengthening and evidence on anti-malarial use in severe malaria and antenatal care management. A framework for effective stakeholder engagement for the future adoption of new anti-malarial treatment strategies was proposed. The framework covers the pathway from generating evidence on drug efficacy, safety and uptake; to making treatment accessible and affordable to end-users. It addresses which stakeholders to engage with and the content of engagement strategies with key stakeholders at different levels of the transition process. Conclusion: Early and staged engagement of stakeholders from global bodies to community level end-users is critical to the successful adoption and uptake of new anti-malarial treatment policies. A framework for these engagements was proposed as a contribution to enhancing the uptake of future anti-malarial strategies. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Ethical considerations in deploying triple artemisinin-based combination therapies for malaria: An analysis of stakeholders’ perspectives in Burkina Faso and Nigeria

Author

Tindana, Paulina, primary, Guissou, Rosemonde, additional, Bolarinwa, Oladimeji Akeem, additional, Tou, Fatoumata, additional, de Haan, Freek, additional, Dhorda, Mehul, additional, Dondorp, Arjen M., additional, Amaratunga, Chanaki, additional, Mokuolu, Olugbenga Ayodeji, additional, Ouedraogo, Jean Bosco, additional, and Cheah, Phaik Yeong, additional

Published
2022
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34. Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance

Author

Mok, Sachel, Ashley, Elizabeth A., Ferreira, Pedro E., Zhu, Lei, Lin, Zhaoting, Yeo, Tomas, Chotivanich, Kesinee, Imwong, Mallika, Pukrittayakamee, Sasithon, Dhorda, Mehul, Nguon, Chea, Lim, Pharath, Amaratunga, Chanaki, Suon, Seila, Hien, Tran Tinh, Htut, Ye, Faiz, M. Abul, Onyamboko, Marie A., Mayxay, Mayfong, Newton, Paul N., Tripura, Rupam, Woodrow, Charles J., Miotto, Olivo, Kwiatkowski, Dominic P., Nosten, François, Day, Nichoals P. J., Preiser, Peter R., White, Nicholas J., Dondorp, Arjen M., Fairhurst, Rick M., and Bozdech, Zbynek

Published
2015

36. Comparison of Antibody Responses and Parasite Clearance in Artemisinin Therapeutic Efficacy Studies in the Democratic Republic of Congo and Asia

Author

Cutts, Julia C, primary, O’Flaherty, Katherine, additional, Zaloumis, Sophie G, additional, Ashley, Elizabeth A, additional, Chan, Jo Anne, additional, Onyamboko, Marie A, additional, Fanello, Caterina, additional, Dondorp, Arjen M, additional, Day, Nicholas P, additional, Phyo, Aung Pyae, additional, Dhorda, Mehul, additional, Imwong, Mallika, additional, Fairhurst, Rick M, additional, Lim, Pharath, additional, Amaratunga, Chanaki, additional, Pukrittayakamee, Sasithon, additional, Hien, Tran Tinh, additional, Htut, Ye, additional, Mayxay, Mayfong, additional, Faiz, M Abdul, additional, Takashima, Eizo, additional, Tsuboi, Takafumi, additional, Beeson, James G, additional, Nosten, Francois, additional, Simpson, Julie A, additional, White, Nicholas J, additional, and Fowkes, Freya J I, additional

Published
2022
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37. Novel phenotypic assays for the detection of artemisinin-resistant Plasmodium falciparum malaria in Cambodia: in-vitro and ex-vivo drug-response studies

Author

Witkowski, Benoit, Amaratunga, Chanaki, Khim, Nimol, Sreng, Sokunthea, Chim, Pheaktra, Kim, Saorin, Lim, Pharath, Mao, Sivanna, Sopha, Chantha, Sam, Baramey, Anderson, Jennifer M, Duong, Socheat, Chuor, Char Meng, Taylor, Walter R J, Suon, Seila, Mercereau-Puijalon, Odile, Fairhurst, Rick M, and Menard, Didier

Published
2013
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38. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Author

Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Grigg, Matthew J [0000-0001-9914-8352], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository

Subjects
parasitic diseases, Genomics, Genomic Epidemiology, Plasmodium vivax, Malaria, Data Resource
Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Published
2022

39. Anti-Gametocyte Antigen Humoral Immunity and Gametocytemia During Treatment of Uncomplicated Falciparum Malaria: A Multi-National Study

Author

O’Flaherty, Katherine, primary, Chan, Jo-Anne, additional, Cutts, Julia C., additional, Zaloumis, Sophie G., additional, Ashley, Elizabeth A., additional, Phyo, Aung Pyae, additional, Drew, Damien R., additional, Dondorp, Arjen M., additional, Day, Nicholas P., additional, Dhorda, Mehul, additional, Fairhurst, Rick M., additional, Lim, Pharath, additional, Amaratunga, Chanaki, additional, Pukrittayakamee, Sasithon, additional, Hien, Tran Tinh, additional, Htut, Ye, additional, Mayxay, Mayfong, additional, Faiz, M. Abul, additional, Mokuolu, Olugbenga A., additional, Onyamboko, Marie A., additional, Fanello, Caterina, additional, Takashima, Eizo, additional, Tsuboi, Takafumi, additional, Theisen, Michael, additional, Nosten, Francois, additional, Beeson, James G., additional, Simpson, Julie A., additional, White, Nicholas J., additional, and Fowkes, Freya J. I., additional

Published
2022
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40. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Author

MalariaGEN, Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, AII - Infectious diseases, Intensive Care Medicine, MalariaGEN, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository

Subjects
Data resource, parasitic diseases, Medicine (miscellaneous), Genomics, Genomic epidemiology, Plasmodium vivax, General Biochemistry, Genetics and Molecular Biology, Malaria
Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Published
2022

41. Artemisinin-resistant Plasmodium falciparum in Pursat province, western Cambodia: a parasite clearance rate study

Author

Amaratunga, Chanaki, Sreng, Sokunthea, Suon, Seila, Phelps, Erika S, Stepniewska, Kasia, Lim, Pharath, Zhou, Chongjun, Mao, Sivanna, Anderson, Jennifer M, Lindegardh, Niklas, Jiang, Hongying, Song, Jianping, Su, Xin-zhuan, White, Nicholas J, Dondorp, Arjen M, Anderson, Tim JC, Fay, Michael P, Mu, Jianbing, Duong, Socheat, and Fairhurst, Rick M

Published
2012
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42. Genetic architecture of artemisinin-resistant Plasmodium falciparum

Author

Miotto, Olivo, Amato, Roberto, Ashley, Elizabeth A, MacInnis, Bronwyn, Almagro-Garcia, Jacob, Amaratunga, Chanaki, Lim, Pharath, Mead, Daniel, Oyola, Samuel O, Dhorda, Mehul, Imwong, Mallika, Woodrow, Charles, Manske, Magnus, Stalker, Jim, Drury, Eleanor, Campino, Susana, Amenga-Etego, Lucas, Thanh, Thuy-Nhien Nguyen, Tran, Hien Tinh, Ringwald, Pascal, Bethell, Delia, Nosten, Francois, Phyo, Aung Pyae, Pukrittayakamee, Sasithon, Chotivanich, Kesinee, Chuor, Char Meng, Nguon, Chea, Suon, Seila, Sreng, Sokunthea, Newton, Paul N, Mayxay, Mayfong, Khanthavong, Maniphone, Hongvanthong, Bouasy, Htut, Ye, Han, Kay Thwe, Kyaw, Myat Phone, Faiz, Md Abul, Fanello, Caterina I, Onyamboko, Marie, Mokuolu, Olugbenga A, Jacob, Christopher G, Takala-Harrison, Shannon, Plowe, Christopher V, Day, Nicholas P, Dondorp, Arjen M, Spencer, Chris C A, McVean, Gilean, Fairhurst, Rick M, White, Nicholas J, and Kwiatkowski, Dominic P

Published
2015
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44. Evolution of Multidrug Resistance in Plasmodium falciparum: a Longitudinal Study of Genetic Resistance Markers in the Greater Mekong Subregion

Author

Imwong, Mallika, primary, Suwannasin, Kanokon, additional, Srisutham, Suttipat, additional, Vongpromek, Ranitha, additional, Promnarate, Cholrawee, additional, Saejeng, Aungkana, additional, Phyo, Aung Pyae, additional, Proux, Stephane, additional, Pongvongsa, Tiengkham, additional, Chea, Nguon, additional, Miotto, Olivo, additional, Tripura, Rupam, additional, Nguyen Hoang, Chau, additional, Dysoley, Lek, additional, Ho Dang Trung, Nghia, additional, Peto, Thomas J., additional, Callery, James J., additional, van der Pluijm, Rob W., additional, Amaratunga, Chanaki, additional, Mukaka, Mavuto, additional, von Seidlein, Lorenz, additional, Mayxay, Mayfong, additional, Thuy-Nhien, Nguyen Thanh, additional, Newton, Paul N., additional, Day, Nicholas P. J., additional, Ashley, Elizabeth A., additional, Nosten, Francois H., additional, Smithuis, Frank M., additional, Dhorda, Mehul, additional, White, Nicholas J., additional, and Dondorp, Arjen M., additional

Published
2021
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45. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

Author

Aney, Frederic, Witkowski, Benoit, Amaratunga, Chanaki, Beghain, Johann, Langlois, Anne-Claire, Khim, Nimol, Kim, Saorin, Duru, Valentine, Bouchier, Christiane, Ma, Laurence, Lim, Pharath, Leang, Rithea, Duong, Socheat, Sreng, Sokunthea, Suon, Seila, Chuor, Char Meng, Bout, Denis Mey, Menard, Sandie, Rogers, William O., Genton, Blaise, Fandeur, Thierry, Miotto, Olivo, Ringwald, Pascal, Bras, Jacques Le, Berry, Antoine, Barale, Jean-Christophe, Fairhurst, Rick M., Benoit-Vical, Francoise, Mercereau-Puijalon, Odile, and Menard, Didier

Subjects
Drug resistance in microorganisms -- Research, Molecular biology -- Research, Plasmodium falciparum -- Physiological aspects -- Health aspects, Microbiological research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread., The emergence of Plasmodium falciparum resistance to artemisinin derivatives (ART) in Cambodia threatens the world's malaria control and elimination efforts (1,2). The risk of ART-resistant parasites spreading from western Cambodia [...]

Published
2014
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46. To what extent are the antimalarial markets in African countries ready for a transition to triple artemisinin-based combination therapies?

Author

de Haan, Freek, primary, Bolarinwa, Oladimeji Akeem, additional, Guissou, Rosemonde, additional, Tou, Fatoumata, additional, Tindana, Paulina, additional, Boon, Wouter P. C., additional, Moors, Ellen H. M., additional, Cheah, Phaik Yeong, additional, Dhorda, Mehul, additional, Dondorp, Arjen M., additional, Ouedraogo, Jean Bosco, additional, Mokuolu, Olugbenga A., additional, and Amaratunga, Chanaki, additional

Published
2021
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47. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

Author

Jacob, Christopher G, primary, Thuy-Nhien, Nguyen, additional, Mayxay, Mayfong, additional, Maude, Richard J, additional, Quang, Huynh Hong, additional, Hongvanthong, Bouasy, additional, Vanisaveth, Viengxay, additional, Ngo Duc, Thang, additional, Rekol, Huy, additional, van der Pluijm, Rob, additional, von Seidlein, Lorenz, additional, Fairhurst, Rick, additional, Nosten, François, additional, Hossain, Md Amir, additional, Park, Naomi, additional, Goodwin, Scott, additional, Ringwald, Pascal, additional, Chindavongsa, Keobouphaphone, additional, Newton, Paul, additional, Ashley, Elizabeth, additional, Phalivong, Sonexay, additional, Maude, Rapeephan, additional, Leang, Rithea, additional, Huch, Cheah, additional, Dong, Le Thanh, additional, Nguyen, Kim-Tuyen, additional, Nhat, Tran Minh, additional, Hien, Tran Tinh, additional, Nguyen, Hoa, additional, Zdrojewski, Nicole, additional, Canavati, Sara, additional, Sayeed, Abdullah Abu, additional, Uddin, Didar, additional, Buckee, Caroline, additional, Fanello, Caterina I, additional, Onyamboko, Marie, additional, Peto, Thomas, additional, Tripura, Rupam, additional, Amaratunga, Chanaki, additional, Myint Thu, Aung, additional, Delmas, Gilles, additional, Landier, Jordi, additional, Parker, Daniel M, additional, Chau, Nguyen Hoang, additional, Lek, Dysoley, additional, Suon, Seila, additional, Callery, James, additional, Jittamala, Podjanee, additional, Hanboonkunupakarn, Borimas, additional, Pukrittayakamee, Sasithon, additional, Phyo, Aung Pyae, additional, Smithuis, Frank, additional, Lin, Khin, additional, Thant, Myo, additional, Hlaing, Tin Maung, additional, Satpathi, Parthasarathi, additional, Satpathi, Sanghamitra, additional, Behera, Prativa K, additional, Tripura, Amar, additional, Baidya, Subrata, additional, Valecha, Neena, additional, Anvikar, Anupkumar R, additional, Ul Islam, Akhter, additional, Faiz, Abul, additional, Kunasol, Chanon, additional, Drury, Eleanor, additional, Kekre, Mihir, additional, Ali, Mozam, additional, Love, Katie, additional, Rajatileka, Shavanthi, additional, Jeffreys, Anna E, additional, Rowlands, Kate, additional, Hubbart, Christina S, additional, Dhorda, Mehul, additional, Vongpromek, Ranitha, additional, Kotanan, Namfon, additional, Wongnak, Phrutsamon, additional, Almagro Garcia, Jacob, additional, Pearson, Richard D, additional, Ariani, Cristina V, additional, Chookajorn, Thanat, additional, Malangone, Cinzia, additional, Nguyen, T, additional, Stalker, Jim, additional, Jeffery, Ben, additional, Keatley, Jonathan, additional, Johnson, Kimberly J, additional, Muddyman, Dawn, additional, Chan, Xin Hui S, additional, Sillitoe, John, additional, Amato, Roberto, additional, Simpson, Victoria, additional, Gonçalves, Sonia, additional, Rockett, Kirk, additional, Day, Nicholas P, additional, Dondorp, Arjen M, additional, Kwiatkowski, Dominic P, additional, and Miotto, Olivo, additional

Published
2021
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49. Author response: Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

Author

Jacob, Christopher G, primary, Thuy-Nhien, Nguyen, additional, Mayxay, Mayfong, additional, Maude, Richard J, additional, Quang, Huynh Hong, additional, Hongvanthong, Bouasy, additional, Vanisaveth, Viengxay, additional, Ngo Duc, Thang, additional, Rekol, Huy, additional, van der Pluijm, Rob, additional, von Seidlein, Lorenz, additional, Fairhurst, Rick, additional, Nosten, François, additional, Hossain, Md Amir, additional, Park, Naomi, additional, Goodwin, Scott, additional, Ringwald, Pascal, additional, Chindavongsa, Keobouphaphone, additional, Newton, Paul, additional, Ashley, Elizabeth, additional, Phalivong, Sonexay, additional, Maude, Rapeephan, additional, Leang, Rithea, additional, Huch, Cheah, additional, Dong, Le Thanh, additional, Nguyen, Kim-Tuyen, additional, Nhat, Tran Minh, additional, Hien, Tran Tinh, additional, Nguyen, Hoa, additional, Zdrojewski, Nicole, additional, Canavati, Sara, additional, Sayeed, Abdullah Abu, additional, Uddin, Didar, additional, Buckee, Caroline, additional, Fanello, Caterina I, additional, Onyamboko, Marie, additional, Peto, Thomas, additional, Tripura, Rupam, additional, Amaratunga, Chanaki, additional, Myint Thu, Aung, additional, Delmas, Gilles, additional, Landier, Jordi, additional, Parker, Daniel M, additional, Chau, Nguyen Hoang, additional, Lek, Dysoley, additional, Suon, Seila, additional, Callery, James, additional, Jittamala, Podjanee, additional, Hanboonkunupakarn, Borimas, additional, Pukrittayakamee, Sasithon, additional, Phyo, Aung Pyae, additional, Smithuis, Frank, additional, Lin, Khin, additional, Thant, Myo, additional, Hlaing, Tin Maung, additional, Satpathi, Parthasarathi, additional, Satpathi, Sanghamitra, additional, Behera, Prativa K, additional, Tripura, Amar, additional, Baidya, Subrata, additional, Valecha, Neena, additional, Anvikar, Anupkumar R, additional, Ul Islam, Akhter, additional, Faiz, Abul, additional, Kunasol, Chanon, additional, Drury, Eleanor, additional, Kekre, Mihir, additional, Ali, Mozam, additional, Love, Katie, additional, Rajatileka, Shavanthi, additional, Jeffreys, Anna E, additional, Rowlands, Kate, additional, Hubbart, Christina S, additional, Dhorda, Mehul, additional, Vongpromek, Ranitha, additional, Kotanan, Namfon, additional, Wongnak, Phrutsamon, additional, Almagro Garcia, Jacob, additional, Pearson, Richard D, additional, Ariani, Cristina V, additional, Chookajorn, Thanat, additional, Malangone, Cinzia, additional, Nguyen, T, additional, Stalker, Jim, additional, Jeffery, Ben, additional, Keatley, Jonathan, additional, Johnson, Kimberly J, additional, Muddyman, Dawn, additional, Chan, Xin Hui S, additional, Sillitoe, John, additional, Amato, Roberto, additional, Simpson, Victoria, additional, Gonçalves, Sonia, additional, Rockett, Kirk, additional, Day, Nicholas P, additional, Dondorp, Arjen M, additional, Kwiatkowski, Dominic P, additional, and Miotto, Olivo, additional

Published
2021
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