Date Published: July 14, 2017
Publisher: Public Library of Science
Author(s): Benoit Visseaux, Charles Burdet, Guillaume Voiriot, François-Xavier Lescure, Taous Chougar, Olivier Brugière, Bruno Crestani, Enrique Casalino, Charlotte Charpentier, Diane Descamps, Jean-François Timsit, Yazdan Yazdanpanah, Nadhira Houhou-Fidouh, Dena L. Schanzer.
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.
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).
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%).
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.
Interest in respiratory viruses has increased recently, due to the identification of several new viruses  and the threat posed by others able to cross the interspecies barriers, as for severe respiratory acute syndrome (SRAS) , avian influenza A H5N1, H7N9, H1N1v2009 [3,4] and MersCoV .
During the study period, 7196 samples from 4958 patients were included in the analysis. In accordance with our definition and exclusion of repeat samples, no sample obtained, within 30 days, from the same area of the respiratory tract of a given patient as the initial sample was included. The median interval between two included samples from the same respiratory tract area of the same patient was 133 days (interquartile range [IQR] = 63–223). Median patient age was 59.9 years [IQR = 48.0–70.0] and 40.0% [IC95 = 38.2–41.4%] of the patients were female. Overall, 2098 (29.2%, [IC95 = 28.1–30.2]) samples tested positive for a respiratory virus and there were 118 viral co-infections (1.6%, [IC95 = 1.3–2.0%]). The groups of viruses identified were, in descending order of prevalence: picornavirus (n = 762, 34.3% [IC95 = 32.2–36.3%]), influenza (n = 592, 26.6% [IC95 = 24.8–28.5%]), coronavirus (n = 260, 11.7% [IC95 = 10.4–13.1%]), respiratory syncytial virus (RSV) (n = 215, 9.7% [IC95 = 8.5–11.0%]), parainfluenza (n = 179, 8.1% [IC95 = 7.0–9.3%]), metapneumovirus (n = 126, 5.7% IC95 = 4.7–6.7%]), adenovirus (n = 61, 2.7% [IC95 = 2.1–3.5%]) and bocavirus (n = 28, 1.3% [IC95 = 0.8–1.8%]).
The burden of respiratory viruses is well established in children. For example, we recently described the global epidemiology of respiratory viruses in children treated in our hospital group . We found that the broad-range detection provided by multiplex PCR greatly improved the detection of respiratory viruses, and, thus our understanding of their epidemiology. We also found differences between children and adults, as also reported by other groups, especially for influenza . Interest in respiratory viruses present in adult populations is also increasing. However, many previous studies have focused exclusively on the winter period or influenza detection and may have underestimated the potential role of other respiratory viruses. A Canadian study performed with Canada’s national hospitalization database showed that influenza and other respiratory viruses are associated with morbidity requiring hospitalization, in both children and adult populations . Other studies have also described the high frequency of non-influenza viruses in adults hospitalized in China [17,28], Spain  and France . However, due to differences in populations, age groups, climate conditions, sampling or laboratory methods, the incidence and seasonality of respiratory viruses may differ slightly between countries and studies. Moreover, only limited data are available for the distribution of respiratory viruses in the lower respiratory tract.