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