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

Abstract

IntroductionExacerbations 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.ObjectivesTo study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS.Study design88 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.ResultsBy 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.ConclusionsThe 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.

An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection

“…Results presented in pharyngeal clinical samples showed that the greatest amounts of viral sequences from mammalian viruses were present in the families Coronaviridae, Anelloviridae, and Paramyxoviridae, Coronaviridae and Anelloviridae comprising the major part of the composition. Both Coronaviridae and Anelloviridae were detected in the same sample in the present research ( Figure 4B), which was inconsistent with previous studies where Anelloviridae were not detected in the Coronaviridaepositive samples and Coronaviridae were not detected in the Anelloviridae-positive samples (van Rijn et al, 2019). We also observed that the M3 did not detecte Herpesviridae, which were thought to have possibly integrated into the human genome.…”

“…Common human respiratory tract viruses have been summarized for the period from 2009 to 2016, including Rhinoviruses, Paramyxoviruses, Orthomyxoviruses, Coronaviruses, Adenoviruses, Parvoviruses, Herpesviruses, Anelloviruses, Papillomaviruses, and Polyomaviruses (Wylie, 2017). To date, only one study characterized respiratory virome in the areas of COPD in 63 patients with acute COPD exacerbation from Norway, in which an obtained median of 11 million sequence reads per sample contained ∼93% of human reads, 3% of bacterial, 0.1% of viral, and 3% of unknown reads, as identified using NGS without any viral enrichment steps (van Rijn et al, 2019). In this study, we aimed to optimize the pretreatment method to enrich viral particles for NGS sequencing to investigate the virome in pharyngeal clinical samples from hospitalized patients with acute COPD exacerbation.…”

“…Among all 12 subsamples, the majority of the viral reads (average: ∼57%) aligned to a crucial respiratory virus (Coronaviridae, HCov-OC43) (Wylie, 2017;van Rijn et al, 2019). To explore the effects of the different methods on the efficiency of genome recovery, we compared the corresponding HCov-OC43 reference (MG197719) genome site sequencing depth profiles (see Figure 4).…”

Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination

“…For quantification of viral reads 8,14,17 , reads were normalized according to the number of preprocessed reads (adaptor-trimmed reads with exclusion of low-quality and low-complexity sequences) and expressed in reads per million (RPM). RPM values corresponding to presumptive viral laboratory, reagent, and/or cross-contaminants in the negative control samples were subtracted from clinical stool samples in the same sequencing batch, with negative RPM values after subtraction set to 0.…”

Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium

“…The development of chronic airway inflammatory diseases is usually linked to specific bacterial species in the microbiome which may thrive in the inflamed airway environment (Diver et al, 2019). In the event of a viral infection such as RV infection, the effect induced by the virus may destabilize the equilibrium of the microbiome present (Molyneaux et al, 2013;Kloepfer et al, 2014;Kloepfer et al, 2017;Jubinville et al, 2018;van Rijn et al, 2019). In addition, viral infection may disrupt biofilm colonies in the upper airway (e.g., Streptococcus pneumoniae) microbiome to be release into the lower airway and worsening the inflammation (Marks et al, 2013;Chao et al, 2014).…”