Results
Patient Demographics
A total of 44 participants were enrolled. The mean age at enrollment was 12·8 years; mean FEV1 percent predicted was 94·2% (Table 1). An upper airway sample was collected at each of 359 visits during the study period, for an average of 8·2 samples per participant (SD 2·4, range 5–14). Most nasal samples were collected by nasal swab rather than nasal wash because of participant preference.
A paired sputum specimen was collected simultaneously with the upper airway sample from 21 participants who were able to expectorate at one or more visits during the study. This sub-cohort of expectorating patients was similar to the total cohort in terms of demographics, but had lower BMI percentiles and worse lung function at enrollment than observed for the full cohort (Table 1). Paired sputum samples were collected at 98 visits; however, samples from six visits could not be assayed (four because of failure to amplify and two were missing). Thus, paired sputum samples were available from 92 visits (23% of which were characterized by pulmonary exacerbation).
Viral Detection in Upper Airway Samples
Among the 359 upper airway samples tested by PCR, at least one respiratory virus was detected in 108 samples (30·1%), with two or more respiratory viruses detected in six specimens. The average number of positive upper airway samples per participant was 2·5 (SD, 1·9; range, 0–9). Rhinovirus was the most commonly detected virus, found in 83 samples (23·1%), with results for additional viruses summarized in Table 2. Among the 44 study participants, 41 (93·2%) had at least one positive upper airway sample during the 2-year follow-up. Thirty-nine participants (88·6%) had rhinovirus detected at one or more visits, including 10 participants with rhinovirus detected twice and 11 with rhinovirus detected at three or more visits (up to a total of eight visits). The proportion of visits with rhinovirus detection was highest during the fourth quarter of the year (37·5% versus 14·6%, 23·9%, and 19·0% for first through third quarters, respectively).
Viral Detection in Paired Upper Airway and Sputum Samples
Among the 92 visits with paired sputum samples also collected, rhinoviruses were the most commonly detected virus, with the same detection rate for both sample types (21·7% each, Table 2). For all other virus types, the number of positive samples was low, including 56 of 92 pairs (60·9%) with both sample types negative for all viruses tested. For rhinoviruses, there were 80 concordant pairs (14 positive/positive; 66 negative/negative) and 12 discordant pairs (six upper positive/sputum negative; six upper negative/sputum positive). For other virus types, there were 85 concordant pairs (seven positive/positive; 78 negative/negative) and seven discordant pairs (four upper positive/sputum negative; three upper negative/sputum positive). There was no evidence of a significant difference in the types of discordant pairs for rhinoviruses or for other virus types combined (P = 1·0 and P = 0·67, respectively). We estimated the sensitivity and specificity of sputum sampling for rhinovirus detection relative to detection by upper airway sampling; the observed sensitivity was 70·0% (95% CI 48·0, 85·5) and specificity was 91·7% (95% CI 83·7, 95·9). Estimates of sensitivity and specificity were not calculated for other virus types because of their low relative frequency.
Clinical Features Associated With Upper Airway Rhinovirus Detection
As rhinovirus was the most prevalent virus type detected in our study, further analyses examined rhinovirus detection in association with clinical parameters. These analyses were restricted to the subset of 329 upper airway samples with rhinovirus as the only virus detected (n = 78) or with no viruses detected (n = 251); samples with isolation of other virus types (n = 25) or with co-isolation of rhinovirus and another virus type (n = 5) were excluded. Among the 329 visits giving rise to these samples, 130 (39·5%) visits were characterized by respiratory illness requiring antibiotic treatment (intravenous or inhaled antibiotics for pulmonary exacerbation or other antibiotic treatment for respiratory-related illness). Rhinovirus was detected in 35 of 130 respiratory illness visits (26·9%) and in 43 of 199 non-illness visits (21·6%). Findings from a logistic regression model were not significant for an association between respiratory illness and concurrent detection of rhinovirus (OR, 1·4; 95% CI 0·9, 2·1; P = 0·17). When respiratory illnesses requiring antibiotic treatment up to 30 days prior to the study visit were included, the association with the detection of rhinovirus was slightly stronger (OR 1·6; 95% CI 0·95, 2·7; P = 0·07).
Among respiratory signs recorded at each visit, rhinorrhea (OR 2·0; 95% CI 1·2, 3·2; P = 0·004) and abnormal chest exam (OR 2·3; 95% CI 1·2, 4·4; P = 0·01) were positively associated with upper airway detection of rhinovirus. Among concurrent respiratory symptoms collected by participant self-report, increased cough, increased nasal congestion, increased sputum production, and wheezing were significant predictors of rhinovirus detection ( Table 3 ). Increased cough and increased sputum production were most predictive of rhinovirus detection among symptoms reported for the 30 days preceding the clinic visit, with results similar to those observed for concurrent symptoms.
Bacterial culture results were also evaluated to determine whether concurrent culture positivity for Pseudomonas aeruginosa or Staphylococcus aureus was associated with upper airway rhinovirus detection. Among 265 visits with concurrent culture data available, S. aureus positive cultures were associated with rhinovirus detection (OR, 2·8; 95% CI 1·0, 7·3; P = 0·04); however, P. aeruginosa positive cultures were not (OR 0·8; 95% CI 0·4, 1·4; P = 0·36).