Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011-2012

Abstract

Few studies have examined the epidemiology of respiratory viral infections in large tertiary centres over more than one season in the era of molecular diagnosis. Respiratory clinical specimens received between 1 January 2011 and 31 December 2012 were analysed. Respiratory virus testing was performed using a large panel of real-time PCR or RT-PCR. Results were analysed according to sample type (upper versus lower respiratory tract) and age group. In all, 2996 (2469 (82.4%) upper; 527 (17.6%) lower) specimens were analysed. Overall positivity rate was 47.4% and 23.7% for upper and lower respiratory samples, respectively. The highest positivity rate was observed in patients under 18 years old (p <0.001); picornaviruses were the most frequent viruses detected over the year. Influenza virus, respiratory syncytial virus, human metapneumovirus and coronaviruses showed a seasonal peak during the winter season, while picornaviruses and adenoviruses were less frequently detected in these periods. Multiple viral infections were identified in 12% of positive cases and were significantly more frequent in children (p <0.001). In conclusion, we observed significant differences in viral infection rates and virus types among age groups, clinical sample types and seasons. Follow-up of viral detection over several seasons allows a better understanding of respiratory viral epidemiology.

Keywords: Adenovirus; coronavirus; epidemiology; influenza; picornavirus; respiratory syncytial virus; respiratory virus; seasonality.

Figure 1

Clinical respiratory specimens analysed during the study period (1 January 2011 to 31 December 2012). ^aNasopharyngeal swabs and nasopharyngeal aspirates. ^bTracheal and/or bronchial aspirates and bronchoalveolar lavages *In 69 cases there were paired upper and lower respiratory specimens for the same episode.

Figure 2

Viral prevalences according to age group (<18, 18–65 and >65 years old) in all respiratory specimens collected during the study period. hMPV, human metapneumovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus.

Figure 3

(a) Number of positive and negative respiratory clinical specimens received and analysed at the Laboratory of Virology of the University of Geneva Hospitals during the study. (b) Positivity rate for each group of viruses from clinical specimens analysed at the Laboratory of Virology of the University of Geneva Hospitals during the study period. hMPV, human metapneumovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus.