Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis

Abstract

Rationale: Rhinoviruses (RVs) are a major cause of symptomatic respiratory tract infection in all age groups. However, RVs can frequently be detected in asymptomatic individuals.Objectives: To evaluate the ability of host transcriptional profiling to differentiate between symptomatic RV infection and incidental detection in children.Methods: Previously healthy children younger than 2 years old (n = 151) were enrolled at four study sites and classified into four clinical groups: RV2 healthy control subjects (n = 37), RV1 asymptomatic subjects (n = 14), RV1 outpatients (n = 30), and RV1 inpatients (n = 70). Host responses were analyzed using whole-blood RNA transcriptional profiles.Measurements and Main Results: RV infection induced a robust transcriptional signature, which was validated in three independent cohorts and by quantitative real-time polymerase chain reaction with high prediction accuracy. The immune profile of symptomatic RV infection was characterized by overexpression of innate immunity and underexpression of adaptive immunity genes, whereas negligible changes were observed in asymptomatic RV1 subjects. Unsupervised hierarchical clustering identified two main clusters of subjects. The first included 93% of healthy control subjects and 100% of asymptomatic RV1 subjects, and the second comprised 98% of RV1 inpatients and 88% of RV1 outpatients. Genomic scores of healthy control subjects and asymptomatic RV1 children were similar and significantly lower than those of RV1 inpatients and outpatients (P , 0.0001).Conclusions: Symptomatic RV infection induced a robust and reproducible transcriptional signature, whereas identification of RV in asymptomatic children was not associated with significant systemic transcriptional immune responses. Transcriptional profiling represents a useful tool to discriminate between active infection and incidental virus detection.

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

“…To test this idea, we evaluated a priori-selected gene sets related to innate and adaptive immune responses from the Molecular Signatures Database and found significantly increased expression in patients with confirmed LRTI pathogens versus those without (median, 94.9 [IQR, 93.8-105.6] vs. 33.1 [IQR, 20.7-75.1], Wilcoxon rank sum P = 0.022) (4,10). We observed that two of the three HRV-A-positive subjects demonstrated the lowest expression of this immune response metric, whereas the remaining subject, who was coinfected with HRV-A and Stenotrophomonas maltophilia, had one of the highest values, consistent with prior reports demonstrating that HRV can induce a broad range of disease severity and that viral-bacterial coinfection can increase the severity of disease (8).…”

“…gov/geo/query/acc.cgi?acc=GSE89953). Principal component analysis was performed on the basis of whole-genome gene expression variability between paired AM and PBM samples (8). Differential gene expression between the two cell populations was determined by a Bayesian implementation of the t test (http://cybert.microarray.ics.uci.edu) on log 2 -transformed probe intensities, using a sliding window size of 101 and a Bayesian confidence estimate value of 10.…”

“…Corynebacterium species associated with LRTI (7 Because asymptomatic carriage of respiratory pathogens is well described (8), establishing biomarkers of genuine infection is critical for determining the significance of a given microbiologic finding. Loss of diversity within respiratory tract microbial communities has been proposed as an ecological marker of infection (9), and we thus evaluated alpha diversity of microbes identified by RNA sequencing and found that subjects with confirmed pathogens had a significantly lower Simpson's diversity index than patients with microbes of unlikely or uncertain pathogenicity (median, 0.34 [interquartile range (IQR), 0.15-0.64] vs. 0.92 [IQR, 0.86-0.93], Wilcoxon rank sum P = 0.017; Figure 1) (4).…”

Respiratory viral infections

“…Asymptomatic HRV infection is quite common and its role in asthma pathogenesis has been questioned. Interestingly, Heinonen et al did not find a difference in the blood transcriptome of asymptomatic HRV infected children compared to non-infected controls [91]. Whereas, Wesolowska-Anderson and colleagues demonstrated over 100 differentially expressed genes in the nasal epithelium of asymptomatic infected HRV patients [90].…”

New Molecular Diagnostic Approaches to Bacterial Infections and Antibacterial Resistance

“…In 2007, Ramilo et al first described host gene expression signatures discriminating bacterial and viral infection. 26 Since that time, additional studies have focused on adult and pediatric cohorts 27,28 ; discriminated different types of viral infection 29 ; distinguished infection from colonization 30 ; identified pre-symptomatic disease states 31 ; added non-infectious illness as more appropriate controls 28 ; and showed superiority to existing biomarkers (i.e., PCT) 28,32 . As important as each of these (and many more) studies have been, they all occurred at the pre-clinical stage of development.…”