**3. Detection of respiratory viruses**

days of intravenous antibiotics, showed less response to treatment and had a shorter time to

Flight et al. [35] followed up 100 adult CF patients prospectively for 12 months. Sputum, nose swabs and throat swabs were collected every 2 months and at the onset of pulmonary exacerbation for virus detection. PCR assays for *adenovirus, influenza A&B, human metapneu‐ movirus, parainfluenza 1-3, respiratory syncytial virus* and *human rhinovirus* were performed on each sample. Symptom scores, spirometry and inflammatory markers were measured at each visit. Overall, virology results were available for 626 of 649 completed study visits. Of these, 191 (30.5%) were positive for a respiratory virus including 9 episodes of dual viral infection. Human *rhinovirus* accounted for 72.5% of viruses. Overall incidence of viral respiratory infection (VRI) was 1.66 (95% CI 1.39 to 1.92) cases/patient-year. VRI was associated with increased risk of pulmonary exacerbation (OR=2.19; 95% CI 1.56 to 3.08; p<0.001) and pre‐ scription of antibiotics (OR=2.26; 95% CI 1.63 to 3.13; p<0.001). Virus-positive visits were associated with higher respiratory symptom scores and greater C-reactive protein levels. Virus-positive exacerbations had a lower acute fall in FEV1 than virus-negative exacerbations (12.7% vs. 15.6%; p=0.040). The incidence of exacerbations, but not VRI, was associated with greater lung function decline over 12 months (-1.79% per pulmonary exacerbation/year; 95%

Experimental data on the effects of viral infections in CF are limited. Toll-like receptors (TLRs) have recently been identified as key mediators of the innate response and they recognise pathogens through detection of conserved microbial structures that are absent from the host. Kurt-Jones et al. [49] found that *RSV* persisted longer in the lungs of infected TLR4-deficient mice compared to normal mice. Haynes et al. [50] also demonstrated that TLR4-deficient mice when challenged with *RSV* exhibited impaired natural killer cell trafficking and impaired virus clearance compared to normal ones. Limited human studies have demonstrated the important role of TLRs in host response against many major groups of mammalian pathogens [51]. The relationship between TLR and respiratory virus including *RSV* in humans will require further

Some studies have suggested a higher viral replication when there is an impairment of the innate host defence in CF. *Influenza* titres were significantly increased in a mouse model which were chronically infected with *P. aeruginosa* compared to control model [52]. This in turn led to an increase in susceptibility to fatal streptococcus pneumonia infection. Increased virus replication was also found after *PIV* infection of CF human airway epithelial cells, compared to controls [53]. One of the possible causes of increased virus replication and of virus persis‐ tence might be a reduced production of respiratory nitric oxide (NO), which is a vital part of innate antiviral defence mechanism [54]. Increased production of NO protects against viral infections. In CF patients, expression of the NO producing enzyme NO synthase type 2 (NOS2)

Xu et al. [55] showed that CF cells that were infected with influenza A had less IFN-related antiviral gene induction at 24 h but more significant inflammatory cytokine gene induction at 1 h after infection. Therefore, the lesser antiviral and greater early inflammatory response may explain the severe respiratory illness of CF patients with viral infections. Sutanto and co-

next pulmonary exacerbation compared to matched controls.

CI -3.4 to -0.23; p=0.025).

150 Cystic Fibrosis in the Light of New Research

studies before it can be established.

is considerably reduced.

The diagnostic accuracy and sensitivity of respiratory viral detection is determined by several factors:


mation to public health authorities such that public health policies can be adjusted accordingly, e.g. the outbreak of SARS and influenza H5N1 virus.

**4.** Utilisation of real-time multiplex amplification technique allows multiple viruses being quantified even if the copy number of the viral target is low.

More recently, Virochip has been shown to be a pan-virus microarray platform that is capable of detection of known as well as novel viruses in a single assay simultaneously [59]. Probes chosen for Virochip can identify nodes in the viral taxonomy at the family, genus and species levels. As the Virochip probes are updated regularly, the extent of probes that can be covered are ever increasing, up to 36,000. It has a diagnostic sensitivity comparable to PCR for detecting respiratory genomes at levels as low as 100 genome copies. At the present time, Virochip is very much a research tool, and several issues must be addressed before it can be used as a routine test for virus detection in the clinical setting, including cost, diagnostic accuracy, repeatability, and sensitivity/specificity for virus detection. In addition, the clinical implication of novel viruses in the human respiratory tract is not yet defined. Therefore, the accurate interpretation of Virochip in the clinical setting remains a formidable task. For example, where specimens are polymicrobial or viral material are present at low levels, clinical and epidemio‐ logical information might be required to draw clinically meaningful conclusions.
