Prevalence of respiratory viruses among adults, by season, age, respiratory tract region and type of medical unit in Paris, France, from 2011 to 2016

<div><p>Background</p><p>Multiplex PCR tests have improved our understanding of respiratory viruses’ epidemiology by allowing their wide range detection. We describe here the burden of these viruses in hospital settings over a five-year period.</p><p>Methods</p><p>All respiratory samples from adult patients (>20 years old) tested by multiplex-PCR at the request of physicians, from May 1 2011 to April 30 2016, were included retrospectively. Viral findings are reported by season, patient age group, respiratory tract region (upper or lower) and type of clinical unit (intensive care unit, pneumology unit, lung transplantation unit and other medical units).</p><p>Results</p><p>In total, 7196 samples (4958 patients) were included; 29.2% tested positive, with viral co-infections detected in 1.6% of samples. Overall, two viral groups accounted for 60.2% of all viruses identified: picornaviruses (rhinovirus or enterovirus, 34.3%) and influenza (26.6%). Influenza viruses constituted the group most frequently identified in winter (34.4%), in the upper respiratory tract (32%) and in patients over the age of 70 years (36.4%). Picornavirus was the second most frequently identified viral group in these populations and in all other groups, including lower respiratory tract infections (41.3%) or patients in intensive care units (37.6%).</p><p>Conclusion</p><p>This study, the largest to date in Europe, provides a broad picture of the distribution of viruses over seasons, age groups, types of clinical unit and respiratory tract regions in the hospital setting. It highlights the burden associated with the neglected picornavirus group. These data have important implications for the future development of vaccines and antiviral drugs.</p></div

Seasonality of respiratory viruses.

<p>For each group of viruses, the monthly number of identifications is shown for the entire study period.</p

Distribution of viruses by season, part of the respiratory tract sampled, type of medical unit and age group.

<p>Distribution of viruses by season, part of the respiratory tract sampled, type of medical unit and age group.</p

Number of samples tested, positivity rates and viral findings by season, area of the respiratory tract sampled, type of medical unit and age group.

<p>Number of samples tested, positivity rates and viral findings by season, area of the respiratory tract sampled, type of medical unit and age group.</p

Monthly cumulative number of samples and seasonal distribution of the respiratory viruses detected by multiplex PCR over the five-year study period.

<p>Monthly cumulative number of samples and seasonal distribution of the respiratory viruses detected by multiplex PCR over the five-year study period.</p

Additional file 1: Table S1. of Viral-bacterial coinfection affects the presentation and alters the prognosis of severe community-acquired pneumonia

Microbiological investigations performed in 174 patients with severe CAP. Table S2. Initial biological findings and radiological patterns of 174 patients with severe CAP, according to the microbiological diagnosis. Table S3. Multivariate analysis of the risk factors for hospital death in 174 patients with severe CAP. Table S4. Multivariate analysis of the risk factors for mechanical ventilation for more than 7 days in survivors at day 28. Table S5. Baseline characteristics, behavior during ICU stay, and outcome of 45 patients with mixed infection, according to the viral diagnosis. Table S6. Baseline characteristics, initial biological findings and radiological patterns, ICU course and outcome in bacteria-matched patients with severe CAP. (DOCX 39 kb