Stellenbosch University, Stellenbosch University - Tygerberg Academic Hospital, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, Stellenbosch University - Faculty of Medicine and Health Sciences, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, 4Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu–Natal, National Health Laboratory Services (NHLS), University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences and Division of Medical Virology

University of Cape Town (UCT) - Desmond Tutu HIV Foundation, Centre for the AIDS Programme of Research in Africa (CAPRISA), University of KwaZulu- Natal, University of Pretoria, University of Cape Town (UCT), South African Medical Research Council - Biostatistics Research Unit, Independent, University of Cape Town (UCT) - Centre for Infectious Disease Epidemiology and Research, School of Public Health, Discovery Health - Strategic Risk Management and Data Science Unit, University of the Witwatersrand - Clinical HIV Research Unit, Western Cape Government - Health Intelligence, South African Medical Research Council, Independent, Western Cape Government - Health Intelligence, Discovery Health - Strategic Risk Management and Data Science Unit, Discovery Health - Strategic Risk Management and Data Science Unit, Medscheme, Independent, Independent, National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis, National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases, National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases, University of the Witwatersrand - Department of Clinical Microbiology and Infectious Diseases, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Harvard Medical School - Beth Israel Deaconess Medical Center - Center for Virology and Vaccine Research, Independent, South African Government - National Department of Health, Independent, South African Medical Research Council - Burden of Disease Research Unit, Independent, National Health Laboratory Services (NHLS), University of Cape Town, University of the Witwatersrand, Independent, University of Cape Town (UCT), Fred Hutchinson Cancer Research Center, Independent, University of the Witwatersrand, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division and South African Medical Research Council

Africa Health Research Institute, Africa Health Research Institute, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, National Institute for Communicable Diseases of the National Health Laboratory Service, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, Africa Health Research Institute, Africa Health Research Institute, Africa Health Research Institute, Africa Health Research Institute, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, University of Washington, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, Africa Health Research Institute, Africa Health Research Institute, Africa Health Research Institute, University of KwaZulu-Natal - Department of Infectious Diseases, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of Cape Town (UCT) - South African Tuberculosis Vaccine Initiative, University of Washington, Africa Health Research Institute, affiliation not provided to SSRN, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, University of the Witwatersrand, University of KwaZulu-Natal - Department of Infectious Diseases, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences and Africa Health Research Institute