A blood-based gene expression assay was successfully used to identify viral respiratory disease in patients presenting to hospital emergency departments with fever of unknown origin, researchers reported.
The sensitivity of the reverse transcription polymerase chain reaction (RT-PCR) host-based assay for distinguishing between viral and bacterial infections was 89% (95% CI 72-98%), the specificity was 94% (95% CI 86-99%), and the positive and negative predictive values were 84% (95% CI 65-94%) and 96% (95% CI89-99%), respectively, with an area under the curve (AUC) of 0.92.
The assay could one day be useful for identifying previously unknown or emerging diseases, Geoffrey Ginsburg, MD, PhD, of Duke University, and colleagues wrote in the Sept. 18 online issue of Science Translational Medicine.
"The broad viral sensitivity of this assay may be a distinct advantage over pathogen-based antigen or PC testing should a new influenza virus, or potentially other viral type, begin to circulate in the community," the researchers wrote.
They added that such a test could have proved useful in the 2009 H1N1 pandemic when traditional antigen-based influenza A testing failed to detect most of the adults infected with the new H1N1 influenza virus, or in the more recent 2012 H3N2 outbreak.
The new study represented the "proof of concept" that host expression of a relatively small set of genes, as measured by RT-PCR from blood RNA, can be a useful tool for identifying viral respiratory illness in the emergency department setting, the researchers wrote.
If future prospective studies confirm its clinical utility, the test could help clinicians identify viral infections much more rapidly and reduce the unnecessary use of antibiotics.
"The development of this new assay and its validation in an independent, real-world patient population is an important step on the translational pathway to establishing this platform for diagnostic testing," they wrote.
In earlier studies, Ginsburg and colleagues showed that micro assay profiling of host blood samples can identify several respiratory viral infections, including H3N2 and H1N1, and can distinguish between viral and bacterial respiratory viral infections.
The objective of the current study was to evaluate the performance of an RT-PCR TaqMan low-density array (TLDA) platform developed using two cohorts experimentally infected with either H3N2 or H1N1 influenza.
The researchers initially validated the RT-PCR assay in H2N2- and H1N1-challenged cohorts, finding that the assay was able to distinguish between people with symptomatic and asymptomatic influenza H1N1 or H3N2 with a sensitivity of 87% to 100%, and with cross-validation highly accurate between the influenza subtypes.
In another study that included 102 people treated for fever at a hospital emergency department, the assay accurately classified more than 90% of the patients as having a viral infection or not.
"Many genes in the RT-PCR classifier have low regression coefficients, suggesting that it may be possible to significantly reduce the number of genes represented in the classifier and achieve similar results," the researchers wrote. "Genes selected from the acute respiratory factor comprise the discriminant genes in the assay. Using a smaller set of genes might allow these to be combined with a similar classifier for bacterial infection once that is under development."
They noted that a combined viral/bacterial RT-PCR assay would allow clinicians to classify patients as having a viral or bacterial illness instead of a viral or nonviral illness. Simplifying the test could also make it quicker, cheaper and more clinically useful.
"Ultimately, clinical use of this assay will likely require prospective studies to establish its clinical utility as well as the economic analyses to make the case for reimbursement," the investigators concluded.
This research was supported by grants from the Defense Advanced Research Projects Agency and the National Institute of Allergy and Infectious Diseases.
Ginsburg and several co-authors have filed for a patent on the respiratory viral signature targeted by the assay. Ginsburg and several co-authors also reported links with Novartis.
- Reviewed by F. Perry Wilson, MD, MSCE Instructor of Medicine, Perelman School of Medicine at the University of Pennsylvania and Dorothy Caputo, MA, BSN, RN, Nurse Planner
Science Translational MedicineSource Reference: Zaas, AK "A host-based RT-PCR gene expression signature to identify acute respiratory viral infection"Sci Transl Med 2013; DOI: 10.1126/scitranslmed.3006280.