Symptom scores
Symptom scores were measured three times per day for experimental cases
and once per day for natural cases during a research clinic visit where
exhaled breath was collected. Scores taken closest in time to exhaled
breath collection were selected for analysis. The upper respiratory
score was sum of runny nose, stuffy nose, sneezing, sore throat, earache
symptom scores (range 0-15). The lower respiratory score was the sum of
shortness of breath, and cough scores (range 0-6). The systemic symptom
score was the sum of malaise, headache, muscle/join ache scores (range
0-9). The tympanic temperature for experimental and oral for naturally
infected cases was recorded. Observed cough counts were recorded during
half-hour breath collections.
Adjustment for qRT-PCR
detection limit
Tobit regression was used to impute fine aerosol RNA copy number for
qRT-PCR replicates below detection limit where one or more replicates
for a sample had detectable RNA. Imputation of RNA copies was not done
for samples without any replicates above detection limit, differing from
the approach used by Yan and colleagues, where there were a minority of
fine aerosol samples below detection limit (14%).15It is less reasonable to do the same for the experimentally infected
population where 72% of the observations would be imputed. Tobit
regression imputed values for samples with qRT-PCR detectable RNA in ≥1
replicate. For both experimentally and naturally infected populations,
Tobit models consisted of fixed effects of cough and study day with
random effect of person. Fixed effects for these models were selected
based on a priori evidence of an association with fine aerosol
shedding.15