Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Abstract

BackgroundRespiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections.ResultsWe found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11. We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11-high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling.ConclusionsRespiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1140-8) contains supplementary material, which is available to authorized users.

Episodic viral wheeze and multiple‐trigger wheeze in preschool children are neither distinct nor constant patterns. A prospective multicenter cohort study in secondary care

“…Wesolowska‐Andersen et al recently detected a respiratory virus in 13% of symptom‐free asthmatic children and healthy controls using quantitative PCR, which is considerably lower than the percentage we found in symptom‐free children. This difference is likely explained by the age difference between the studies: 1‐to‐4‐year‐olds in our study, compared to 10‐to‐21‐year‐olds in the previous study.…”

Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection

“…Biomarkernegative, virus-positive samples could represent infections that are not currently part of an active disease process. Recent studies show that while host antiviral responses can be detected in the respiratory tract of asymptomatic virus-infected subjects, the magnitude of transcriptional response (and possibly the presence of a response at the protein level) is greater in symptomatic than asymptomatic subjects [13,[33][34][35]. Consistently, analysis of rhinovirus-positive samples in Study 2 showed a clear correlation between low [CXCL11] and low viral load (Supplementary Figure S4).…”

The Role of Mnk-1, Eukaryotic Translation Initiation Factors and Translation Control in the Pathogenesis of Asthma

“…LiCl is known to regulate C/EBP-α expression [76], and thereby links the action of eIF2B to the lack of C/EBP-α in asthma patients described earlier [75]. Signalling via eIF2 was indicated to be affected by viral infection of the respiratory duct in children based on transcriptomic assessment [77]. Such a signalling pathway is supported by an animal model of allergen induced asthma in mice [78].…”