Viral respiratory infections (VRI) are common in children with cystic fibrosis (CF) and are associated with significant clinical deterioration. Little previous research has been conducted on VRI in adults with CF. This thesis describes a prospective study to determine the epidemiology and clinical impact of VRI among 100 adults with CF.The incidence of identifiable VRI was 1.66 cases/patient-year. Rhinovirus accounted for 72.5% of viruses. Identifiable VRI was associated with increased risk of pulmonary exacerbation, increased respiratory symptoms and higher C-reactive protein levels. Changes in the climate and seasons affected the incidence of identifiable VRI. Rhinovirus was most common in autumn and other viruses predominated during winter. Warmer ambient temperatures were associated with increased risk of rhinovirus infection while other viruses were more common in colder temperatures. Genetic sequencing of a subset of 42 rhinoviruses identified during the study showed that rhinovirus A accounted for 69% of cases and was associated with more severe respiratory symptoms and higher C-reactive protein levels than rhinovirus B.The impact of identifiable VRI on changes to bacterial communities within the lungs of patients with CF was investigated. Ribosomal intergenic spacer analysis (RISA) was developed as a tool to profile the bacterial diversity of CF sputum and was compared with standard culture and 16S rRNA gene pyrosequencing. No consistent effect of identifiable VRI on the microbial diversity of CF sputum was detected with any of these methods in longitudinal analysis of a subset of 18 patients.

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