The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

• Published in: PloS one Vol. 14; no. 10; p. e0223952
• Main Authors: van Rijn, Anneloes L, van Boheemen, Sander, Sidorov, Igor, Carbo, Ellen C, Pappas, Nikos, Mei, Hailiang, Feltkamp, Mariet, Aanerud, Marianne, Bakke, Per, Claas, Eric C J, Eagan, Tomas M, Hiemstra, Pieter S, Kroes, Aloys C M, de Vries, Jutte J C
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24.10.2019; Public Library of Science (PLoS)
• Subjects: Adaptations; Aged; Biology and Life Sciences; Chronic obstructive lung disease; Chronic obstructive pulmonary disease; Clinical decision making; Coronaviridae; Coronaviruses; Correlation; Decision making; Deoxyribonucleic acid; Diagnosis; Diagnostic systems; DNA; DNA viruses; Female; Genetic aspects; Genomics; Herpes simplex; Herpes simplex virus; Herpesvirus infections; High-Throughput Nucleotide Sequencing; High-throughput screening (Biochemical assaying); Hospitals; Humans; Incidence; Infection; Infections; Infectious diseases; Influenza; Lung diseases; Male; Medical research; Medicine and Health Sciences; Metagenomics; Middle Aged; Morbidity; Mortality; Nasopharynx - pathology; Nasopharynx - virology; Netherlands - epidemiology; Next-generation sequencing; Nucleotide sequence; Obstructive lung disease; Pathogenic microorganisms; Pathogens; Patient outcomes; Phages; Pulmonary Disease, Chronic Obstructive - complications; Pulmonary Disease, Chronic Obstructive - virology; Research and Analysis Methods; Respiratory syncytial virus; Respiratory tract diseases; Respiratory Tract Infections - epidemiology; Respiratory Tract Infections - pathology; Respiratory Tract Infections - virology; Ribonucleic acid; RNA; RNA viruses; Studies; Virology; Virus Diseases - epidemiology; Virus Diseases - pathology; Virus Diseases - virology; Viruses; Viruses - classification; Viruses - genetics; Netherlands; Norway
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0223952

Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006-2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection.