Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States.|Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States.|Makerere University School of Public Health, College of Health Sciences, Kampala, Uganda.|Infectious Disease Research Collaboration, Kampala, Uganda.|Infectious Disease Research Collaboration, Kampala, Uganda.|London School of Hygiene and Tropical Medicine, London, United Kingdom.|Department of Medicine, University of California, San Francisco, San Francisco, California, United States.|Department of Medicine, University of California, San Francisco, San Francisco, California, United States.|Genome Sequencing and Analysis Program, Broad Institute, Cambridge, Massachusetts, United States.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.|Wellcome Trust Sanger Institute, Cambridge, United Kingdom.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.|Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States.|Department of Medicine, University of California, San Francisco, San Francisco, California, United States.