Fig. 1: Study overview and scientific experiments.

A Participants (n = 59) were screened at COVID-19 testing facilities and the next day underwent evaluation using the cough aerosol sampling system (CAS) if the PCR and/or rapid antigen test was positive and within 7 days of symptom onset (visit 1; n = 44). A follow-up visit was scheduled 48–72 h thereafter (visit 2; n = 38). B CAS was undertaken using a six-stage Anderson cascade impactor connected to cough tubing leading to a mouthpiece. A settle plate was included for collection of airborne SARS-CoV-2 in the cough cubicle (participant asked to count from 1–100 as loud as possible prior to cough sampling). Upper respiratory samples (nasopharyngeal swab, saliva) were also collected. C Venous blood to evaluate host transcriptomics and soluble biomarkers such as neutralizing antibodies were collected over a 48-hour period (visit 1 and 2). D, E All respiratory samples were assessed for SARS-CoV-2 by quantitative RT PCR and positive samples were further investigated for potential infectiousness by viral culture. Culture positivity was ascertained using a combination of cytopathic effect visualised using a light microscope (D) in tandem with confirmation of longitudinally increasing viral load determined by PCR (E). Representative micrographs are shown for baseline respiratory samples collected from participant CAS013, displaying cells at 24 h and 72 h post-infection. Samples showing the cytopathic effect (denoted by red arrow) have been highlighted by the bordered micrographs (clearing of the cellular monolayer). The viral supernatant was collected at 1, 3, 6 and 9-days post-infection and tested by qRT PCR. Viral culture positivity was defined as an increase, of at least 100-fold, in viral copy number over the 9-day duration of culture. Viral culture experiments were duplicated for 10% of all samples to assess reproducibility of the technique.