A Host-Based RT-PCR Gene Expression Signature to Identify Acute Respiratory Viral Infection

Abstract

Improved ways to diagnose acute respiratory viral infections could decrease inappropriate antibacterial use and serve as a vital triage mechanism in the event of a potential viral pandemic. Measurement of the host response to infection is an alternative to pathogen-based diagnostic testing and may improve diagnostic accuracy. We have developed a host-based assay with a reverse transcription polymerase chain reaction (RT-PCR) TaqMan low-density array (TLDA) platform for classifying respiratory viral infection. We developed the assay using two cohorts experimentally infected with influenza A H3N2/Wisconsin or influenza A H1N1/Brisbane, and validated the assay in a sample of adults presenting to the emergency department with fever (n = 102) and in healthy volunteers (n = 41). Peripheral blood RNA samples were obtained from individuals who underwent experimental viral challenge or who presented to the emergency department and had microbiologically proven viral respiratory infection or systemic bacterial infection. The selected gene set on the RT-PCR TLDA assay classified participants with experimentally induced influenza H3N2 and H1N1 infection with 100 and 87% accuracy, respectively. We validated this host gene expression signature in a cohort of 102 individuals arriving at the emergency department. The sensitivity of the RT-PCR test was 89% [95% confidence interval (CI), 72 to 98%], and the specificity was 94% (95% CI, 86 to 99%). These results show that RT-PCR–based detection of a host gene expression signature can classify individuals with respiratory viral infection and sets the stage for prospective evaluation of this diagnostic approach in a clinical setting.

Multiplex DNA Biosensor for Viral Infection Diagnosis Using SERS Molecular Sentinel-on-Chip

“…These two genes have been demonstrated to play a critical role in host immune response to viral infection [26]. By profiling gene expression in peripheral blood in response to respiratory viral infection, a recent study showed that these two genes are among a set of host genes differentially expressed upon viral infection [27][28][29]. It is noteworthy that before our work, various SERSbased multiplex DNA detection techniques have been reported [30][31][32][33][34][35][36].…”

Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients

“…Instead, a more effective diagnostic would detect early disease, when clinical symptoms might be mild and when treatment would be most effective. Examples include viral respiratory infection (40), VAP (41,42), post-trauma infection (43), and sepsis (44,45). Although none of these particular gene-expression signatures has advanced to clinical use, they exemplify Non-ventilated Ventilated Figure 5.…”

Host-Based Peripheral Blood Gene Expression Analysis for Diagnosis of Infectious Diseases

“…Disease classifiers can be thought of as patterns of biomarker perturbations capable of categorizing individuals into defined clinical groups (10). The process for the development of a gene expression-based disease classifier can be visualized through several broad steps, including a discovery phase to evaluate gene expression changes in the disease state of interest, a classifier generation step, and a platform development step that incorporates the classifier into a clinically usable diagnostic test.…”

“…This step has historically represented a major barrier, as technologies capable of rapidly and quantitatively measuring large, complex, gene-based biomarker classifiers have not been available. PCR-based platforms are the current gold standard for mRNA analysis of targeted gene expression (10) (Fig. 2).…”