Author information: (1)Africa Health Research Institute, Durban, South Africa. (2)School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa. (3)KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa. (4)Division of Infection and Immunity, University College London, London, United Kingdom. (5)HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa. (6)Max Planck Institute for Infection Biology, Berlin, Germany. (7)Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa. (8)Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa. (9)Department of Cardiothoracic Surgery, University of KwaZulu-Natal, Durban, South Africa. (10)Africa Health Research Institute and Department of Paediatrics, University of Oxford, Oxford, United Kingdom. (11)Africa Health Research Institute and the Institute for Global Health, University College London, London, United Kingdom. (12)Department of Neurosurgery, University of KwaZulu-Natal, Durban, South Africa. (13)Africa Health Research Institute and the South African Population Research Infrastructure Network, Durban, South Africa. (14)Africa Health Research Institute and the Institute of Child Health, University College London, London, United Kingdom. (15)Africa Health Research Institute and Division of Infection and Immunity, University College London, London, United Kingdom. (16)College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa. (17)Centre for the AIDS Programme of Research in South Africa, Durban, South Africa. (18)Africa Health Research Institute and the Ragon Institute of MGH, MIT and Harvard, Cambridge, United States. (19)Department of Pulmonology and Critical Care, University of KwaZulu-Natal, Durban, South Africa. (20)Department of Neurology, University of KwaZulu-Natal, Durban, South Africa. (21)Africa Health Research Institute and Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, United States. (22)Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, United States. (23)Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. (24)Department of Global Health, University of Washington, Seattle, United States. (25)Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.