Frequency, kinetics and determinants of viable SARS-CoV-2 in bioaerosols from ambulatory COVID-19 patients infected with the Beta, Delta or Omicron variants
Shameem Z. Jaumdally, Michele Tomasicchio, Anil Pooran, Aliasgar Esmail, Alwyn Kotzé, Stuart Meier, Lindsay Wilson, Suzette Oelofse, Celia van der Merwe, Aqeedah Roomaney, Mogamat Razeen Davids, Tasnim Suliman, R Joseph, Tahlia Perumal, Alex Scott, Megan L. Shaw, Wolfgang Preiser, Carolyn Williamson, Ameena Goga, Elizabeth Mayne, Glenda Gray, Penny L. Moore, Alex Sigal, Jason Limberis, John Metcalfe, Keertan Dheda
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.