1. Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa;
2. South African MRC Centre for the Study of Antimicrobial Resistance,
3. Division of Anatomical Pathology, Department of Pathology, and
4. Division of Anatomical Pathology,
5. South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
6. Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;
7. Division of Medical Virology,
8. Africa Health Research Institute, Durban, South Africa; and
9. Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa;
10. Centre of Excellence in Respiratory Pathogens, Hospices Civils de Lyon and Centre International de Recherche en Infectiologie, Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses, Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard – Lyon 1, Lyon, France
11. Institute of Infectious Disease and Molecular Medicine,
12. Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom;