Abstract
In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify HRV, and the HRV-positive samples were used for sequencing analysis and to reconstruct the phylogenetic tree. HRV was identified in 198 samples (42.2%), and the VP4/VP2 region was successfully amplified in 151 (76.3%). HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%) and HRV-C in 59 (39.1%). Forty-seven (31.1%) of the children with HRV infection were aged <1 year, 71 (47.0%) were aged 1-3 years, and 33 (21.9%) were aged ≥4 years. Blast and phylogenetic analyses showed that the HRV strains were closely related to a total of 66 reference genotypes, corresponding to 29 HRV-A, 9 HRV-B and 28 HRV-C strains. Nucleotide variability was 37% between HRV-A and HRV-B, 37.3% between HRV-A and HRV-C, and 39.9% between HRV-B and HRV-C. A number of sequences clustered with known serotypes and, within these clusters, there were strains circulating during several seasons. The most frequently detected genotypes were HRV-A78 (n=17), HRV-A12 (n=9) and HRV-C2 (n=5). This study shows that, although it is mainly associated with HRV-A, pediatric CAP can also be diagnosed in subjects infected by HRV-C and, more rarely, by HRV-B. Moreover, a large number of genotypes may be involved in causing pediatric CAP and can be different from year to year. Although the prolonged circulation of the same genotypes can sometimes be associated with a number of CAP episodes in different years.
Highlights
The use of molecular methods of respiratory viral screening has recently made it possible to establish that human rhinoviruses (HRVs) are the main cause of the common cold, and common etiologic agents of lower respiratory tract infections (LRTIs) such as bronchiolitis and community-acquired pneumonia (CAP) [1,2,3,4,5,6]
It has been generally found that various HRV genotypes simultaneously circulated in a given period of time in a specific geographic area, most of which belonged to the A and C species; the genotypes belonging to species A were mainly associated with CAP and those belonging to species C were mainly associated with wheezing
All three HRV types were circulating in the study population: type HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%), and HRV-C in 59 (39.1%)
Summary
The use of molecular methods of respiratory viral screening has recently made it possible to establish that human rhinoviruses (HRVs) are the main cause of the common cold (as thought since they were first identified several decades ago), and common etiologic agents of lower respiratory tract infections (LRTIs) such as bronchiolitis and community-acquired pneumonia (CAP) [1,2,3,4,5,6]. It has been generally found that various HRV genotypes simultaneously circulated in a given period of time in a specific geographic area, most of which belonged to the A and C species; the genotypes belonging to species A were mainly associated with CAP and those belonging to species C were mainly associated with wheezing Most of these studies were carried out in a single year and involved a relatively small number of patients, and only a few analysed specific LRTIs. there are few data concerning the circulation of HRVs over a long period of time or the real role of the different species and genotypes in causing LRTIs
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