Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination
Authors: 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 , Miotto Olivo 
Published: August 2021

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.