Methods
Study Population
In this retrospective cohort study, 67 nasopharyngeal lavage (NPL) and bronchoalveolar lavage (BAL) samples were collected from IPF patients referred to hospitals of the Kermanshah University of Medical Sciences (KUMS) between June 2017 and September 2018. All acute exacerbated patients were hospitalized. Inclusion criteria were: radiological, spirometry, therapeutic, and biological data, which are considered for IPF patients by the clinical team of KUMS hospitals.[2] Exclusion criteria were: Patients with chronic hypersensitivity pneumonitis, connective tissue disease or asbestosis. The Ethical Committee of KUMS approved this study.
Nucleic Acid Extraction
DNA and RNA extraction were performed using 200 ml of NPL and/or BAL specimens by QIAamp MinElute Virus Spin Kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions. Extracted genomic DNA/RNA was stored at − 80 °C before use.
DNA Array Assay for Detection of Viruses and Bacteria
The CLART® Pneumovir DNA array assay (Genomica, Coslada, Madrid, Spain) was used to detect a number of viruses in this study (RSV, influenza viruses, HPIV, rhinovirus, adenovirus and coronavirus) according to manufacturer's instructions and as described by us previously.[4] Detection of S. pneumonia, S. aureus and H. influenza was also carried out using this method.
