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Jaumdally S, Tomasicchio M, Pooran A, Esmail A, Kotze A, Meier S, Wilson L, Oelofse S, van der Merwe C, Roomaney A, Davids M, Suliman T, Joseph R, Perumal T, Scott A, Shaw M, Preiser W, Williamson C, Goga A, Mayne E, Gray G, Moore P, Sigal A, Limberis J, Metcalfe J, Dheda K. Frequency, kinetics and determinants of viable SARS-CoV-2 in bioaerosols from ambulatory COVID-19 patients infected with the Beta, Delta or Omicron variants. Nat Commun 2024; 15:2003. [PMID: 38443359 PMCID: PMC10914788 DOI: 10.1038/s41467-024-45400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/22/2024] [Indexed: 03/07/2024] Open
Abstract
Airborne transmission of SARS-CoV-2 aerosol remains contentious. Importantly, whether cough or breath-generated bioaerosols can harbor viable and replicating virus remains largely unclarified. We performed size-fractionated aerosol sampling (Andersen cascade impactor) and evaluated viral culturability in human cell lines (infectiousness), viral genetics, and host immunity in ambulatory participants with COVID-19. Sixty-one percent (27/44) and 50% (22/44) of participants emitted variant-specific culture-positive aerosols <10μm and <5μm, respectively, for up to 9 days after symptom onset. Aerosol culturability is significantly associated with lower neutralizing antibody titers, and suppression of transcriptomic pathways related to innate immunity and the humoral response. A nasopharyngeal Ct <17 rules-in ~40% of aerosol culture-positives and identifies those who are probably highly infectious. A parsimonious three transcript blood-based biosignature is highly predictive of infectious aerosol generation (PPV > 95%). There is considerable heterogeneity in potential infectiousness i.e., only 29% of participants were probably highly infectious (produced culture-positive aerosols <5μm at ~6 days after symptom onset). These data, which comprehensively confirm variant-specific culturable SARS-CoV-2 in aerosol, inform the targeting of transmission-related interventions and public health containment strategies emphasizing improved ventilation.
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Affiliation(s)
- S Jaumdally
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - M Tomasicchio
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - A Pooran
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - A Esmail
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - A Kotze
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - S Meier
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - L Wilson
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - S Oelofse
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - C van der Merwe
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - A Roomaney
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - M Davids
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - T Suliman
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - R Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - T Perumal
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - A Scott
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa
| | - M Shaw
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - W Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch Tygerberg Campus; Medical Virology, National Health Laboratory Service Tygerberg, Parow, Cape Town, South Africa
| | - C Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | - A Goga
- HIV and Other Infectious Diseases Research Unit, South African Medical Research Council, Pretoria, South Africa
- Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa
| | - E Mayne
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - G Gray
- South African Medical Research Council, Cape Town, South Africa
| | - P Moore
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - J Limberis
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California, San Francisco, San Francisco, CA, USA
| | - J Metcalfe
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California, San Francisco, San Francisco, CA, USA
| | - K Dheda
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.
- Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa.
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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