NEW YORK (GenomeWeb News) – In a study appearing online today in Science Translational Medicine, researchers from Duke University and elsewhere described a gene expression signature assay that's showing promise for distinguishing individuals with viral infections, such as influenza, from those with bacteria-based maladies.
Using a few dozen genes that show differential expression in blood samples from those with acute respiratory viral infections, the team came up with a reverse transcription PCR assay based on a TaqMan low-density array system to detect viral infection.
From their findings so far, those involved believe the approach may eventually yield an alternative or complement to tests designed to pick up the presence of a particular pathogen in infected individuals.
"Current tests require knowledge of the pathogen to confirm infection, because they are strain-specific," co-corresponding author Geoffrey Ginsburg, director of genomic medicine at Duke University, said in a statement. "But our test could be used right away when a new, unknown pathogen emerges."
Ginsburg and his colleagues put together the original version of the assay with the help of data from two influenza A-infected cohorts in the UK. The expression signature subsequently showed 87 percent accuracy for detecting respiratory virus infections in one of the discovery groups and 100 percent accuracy in the other.
When researchers tried out the test on more than 100 feverish individuals from hospital emergency rooms, they found that the RT-PCR TaqMan low-density array, or TLDA, test detected actual respiratory viral infections around 89 percent of the time with 94 percent specificity.
"This is important not only in viral pandemics where infection may be caused by unknown viruses but also in routine care where the decision to treat or not with antibiotics is paramount," the study's first author, Aimee Zaas, an infectious disease researcher at Duke University, said in a statement.
"We were very pleased that the assay could pick out those with viral infection with a high degree of accuracy," Zaas said. "This is perhaps the most important aspect of this effort — the accuracy of the new test in a real-world setting. It is a major step forward in the test becoming a useful diagnostic to help physicians and patients."
The ability to better detect various viral infections is expected to help in identifying new viral threats and in treating more routine infections. Moreover, researchers are keen to find ways of dialing down excessive use of antibiotics, which do not benefit those suffering such infections.
"One of the big global threats at the moment is the emergence of bacterial resistance, and that is largely driven by overuse of antibiotics," co-corresponding author Christopher Woods, a medicine, pathology and global health researcher affiliated with Duke University and the Durham Veterans Affairs Medical Center, said in a statement.
"This is a growing public health threat, creating infections that are increasingly difficult to manage," he said. "A tool that enables us to accurately identify viral infections could curb the indiscriminate use of antibiotics and reduce the development of resistant pathogens."
To that end, the researchers decided to focus on gene expression signatures found in blood samples from those individuals infected with viruses that affect the upper respiratory tract in search of characteristic RNA transcript profiles that can be picked up by RT-PCR.
Through array-based expression profiling of blood samples from UK individuals experimentally infected with influenza A H3N2/Wisconsin or H1N1/Brisbane strains, the group focused in on some 30 genes that appear to be differentially expressed in the blood of those with acute respiratory virus infections.
That transcript set served as the basis for researchers' RT-PCR assay, which they subsequently found to have 100 percent and 87 percent accuracy for detecting viral infection in the H3N2 and H1N1 discovery groups, respectively.
From there, the group took a crack at using the assay to test actual clinical samples, represented by 25 individuals with influenza A infections, three individuals with rhinovirus infections, 39 individuals with bacterial infections, and 35 uninfected controls participating in an unrelated aspirin response study.
There, the blood test detected 25 of the 28 authentic respiratory virus infection cases, while yielding false-positive results for four bacterially infected individuals and one control individual.
"[W]e have established a 'proof of concept' that host expression of a relatively small set of genes, as measured by RT-PCR from blood RNA, can be used to classify viral respiratory illness in unselected individuals presenting at an emergency department for evaluation of fever," the study's authors wrote. "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," they concluded.
Going forward, the group reportedly plans to continue narrowing down the number of genes assessed in the assay, while looking at ways of speeding up the test, which takes around 12 hours in its current form.