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A total of 500 nasopharyngeal aspirates collected from community based patients in Manchester, UK (North West) with respiratory symptoms between October 2006 and February 2007 were evaluated for the presence of respiratory viruses. Molecular assays used were developed, optimized and evaluated initially using 100 NPA specimens obtained from paediatric patients. The relative frequencies and seasonal distribution of specific viruses were assessed, and virus type was correlated with specific clinical signs and symptoms.

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Acute respiratory illness represents a large proportion of adult patients admitted to secondary care. Many of these patients have respiratory virus infection but the exact burden of disease in defined clinical groups is unknown. Rhino-enteroviruses are increasingly implicated in severe acute respiratory illness in adults and advances in molecular diagnostics have led the recognition of high strain diversity and to the discovery of a new species (HRV-C). Biomarkers such as procalcitonin and C reactive protein may be able to identify patients with acute respiratory illness without bacterial infection, in whom antibiotics can be safely withheld, and so reduce unnecessary antibiotic prescribing. Patients with acute respiratory illness were recruited from two acute hospital sites in Leicester between 2005 and 2008 and nasopharyngeal swabs were collected and tested for the presence of respiratory viruses using a newly developed comprehensive, multiplex real-time RT-PCR assay. Gene sequencing was performed on samples positive for rhinovirus RNA. Levels of the biomarkers CRP and Procalcitonin were measured on serum samples. A high incidence of viral infection was identified among adults hospitalised with acute respiratory illness (44%) with rhino-enteroviruses accounting for around half of all viruses isolated. The rate of viral infection amongst non-respiratory control patients was low (7%). Rhinovirus gene sequencing demonstrated that around a quarter of all rhinovirus infections were caused by HRV-C and that there was a high level of diversity of strains circulating during the study period. The biomarkers procalcitonin and CRP were both highly accurate in distinguishing patients with pneumonia from exacerbations of airways disease. The results of this work have implications for hospital infection control practices, rationalisation of antibiotic use and in certain circumstances the use of directed antiviral agents. Procalcitonin and CRP could both potentially be used to reduce inappropriate antibiotic prescribing in patients hospitalised with acute respiratory illness.