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Abstract
Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
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1 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, USA
2 Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
3 National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Beijing, PR China
4 Center for Geospatial Information Science, University of Maryland, College Park, MD, USA
5 Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, USA; Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
6 Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
7 Armed Forces Research Institute of Medical Sciences, Phnom Penh, Cambodia
8 Global Malaria Programme, World Health Organization, Geneva, Switzerland
9 Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
10 Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
11 Defence Services Medical Research Centre, Naypyitaw, Myanmar
12 Duke Global Health Institute, Duke University, Durham, NC, USA
13 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
14 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
15 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
16 Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
17 Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
18 International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
19 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Laos
20 Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
21 Asia Regional Centre & EQA Programme, Worldwide Antimalarial Resistance Network, Oxford, UK
22 Malaria Research Group and Dev Care Foundation, Dhaka, Bangladesh
23 Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
24 Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Laos; Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Laos
25 Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Bangkok, Thailand
26 Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Bangkok, Thailand
27 Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
28 Centre for Tropical Medicine Oxford University Clinical Research Unit Vietnam (OUCRU), Ho Chi Minh City, Vietnam
29 Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria