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

Centre for the AIDS Programme of Research in Africa (CAPRISA), University of KwaZulu- Natal, University of Washington, Fred Hutchinson Cancer Research Center, Johns Hopkins Bloomberg School of Public Health, Malawi, Fred Hutchinson Cancer Research Center, University of Zimbabwe, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Duke University - Department of Surgery, Fred Hutchinson Cancer Research Center, Chris Hani Baragwanath Academic Hospital, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, University of KwaZulu-Natal, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, Fred Hutchinson Cancer Research Center, Fred Hutchinson Cancer Research Center, National Institutes of Health, National Institutes of Health, COVID-19 Prevention Network, University of Zimbabwe - Faculty of Medicine and Health Sciences, Baylor College of Medicine, Botswana Harvard AIDS Institute Partnership (BHP), Centre for Infectious Disease Research in Zambia, Columbia University - ICAP, Wits University - Clinical HIV Research Unit, Aurum Institute, Synexus Helderberg, University of Cape Town Lung Institute, University of the Witwatersrand - Reproductive Health and HIV Research Unit (RHRU), TASK, FAMCRU Family Clinical Research Unit, University of Cape Town (UCT), Aurum Institute, University of North Carolina (UNC) at Chapel Hill - UNC-Project Malawi, Center for Family Health Research Zambia (CFHRZ), The Aurum Institute, Aurum Institute, South African Medical Research Council, UNC Global Projects, Soweto Clinical Trials Centre, Blantyre District Council, Center for Family Health Research Zambia (CFHRZ), Wits Health Consortium - Perinatal HIV Research Unit (PHRU), Synergy Biomed Research Institute, MERC Middelburg, Kisumu Clinical Research Site, TASK, TASK, Tembisa Clinic 4, Nelson Mandela Academic Clinical Research Unit Clinical Research Site, University of the Witwatersrand - Perinatal HIV Research Unit, Joint Clinical Research Centre, University of KwaZulu-Natal, South African Medical Research Council, Soweto Clinical Trials Centre, UVRI-IAVI HIV Vaccine Program, MeCRU Clinical Research Site, Maseno University, Synexus Stanza Clinical Research Centre Clinical Research Site, University of KwaZulu-Natal, PHOENIX Pharma (Pty) Ltd, Moi University, University of Cape Town (UCT), MERC Kempton, MERC Welkom, MU-JHU Care Ltd - MUJHU Research Collaboration, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Cape Town (UCT) - Desmond Tutu HIV Foundation, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division, South African Medical Research Council, Fred Hutchinson Cancer Research Center - Vaccine and Infectious Disease Division, Qhakaza Mbokodo Research Clinic and Independent

University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), FIND, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, University of KwaZulu-Natal, KwaZulu-Natal Research Innovation and Sequencing Platform - KRISP, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa, Epicentre Health Research, University of KwaZulu-Natal - School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA), the global alliance for diagnostics - FIND, University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA)University of the Witwatersrand - South African Medical Research Council and University of KwaZulu-Natal - Centre for the AIDS Programme of Research in South Africa (CAPRISA)

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