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Researchers Find Transcriptional Profiling May Help Diagnose Rhinovirus Infection, Common Cause of Colds, Pneumonia and Other Respiratory Infections

(From the April 2016 issue of Research Now)

Transcriptional profiling, measuring the activity of thousands of genes at once to create a snapshot of cellular function, may make quick work of discriminating between active rhinovirus infection and incidental virus detection — and improve clinical decisions — researchers from Nationwide Children's Hospital and The Ohio State University report.

Rhinovirus (RV) is commonly the cause of colds, pneumonia and other respiratory infections, but with sensitive molecular assays, RV has also been detected at high rates among healthy children and adults who are asymptomatic, meaning that they show no symptoms of the common cold. Whether detection in asymptomatic individuals represents an infection or simply represents the presence of viral RNA in respiratory tract mucosa is not clear.

To tell the difference between the incidental presence of RV - when RV is detected but there are no symptoms of a cold - and true infection, the researchers combined microbiological data with systemic host responses in patients' whole blood samples. They used transcriptional profiling to identify the signatures of severe and mild infection as well as virus “colonization” without symptoms of infection.

"With this study we proved the concept that using this technology (transcriptional profiles or microarray analyses) we can see how host responses are suppressed or activated in response to the infection and really define the stage of the disease," says M. Asuncion Mejias, MD, PhD, a principal investigator in the Center for Vaccines and Immunity in The Research Institute at Nationwide Children's and senior author of the study.

Transcriptomes, which are the full range of all messenger RNA molecules expressed from the genes of an organism, were analyzed for four different groups of children. Specifically, the researchers profiled the transcriptome of children hospitalized with severe infection, children treated as outpatients for mild infection, children who were asymptomatic but tested positive for RV, and healthy children who tested negative. All were younger than 2.

Among those with acute RV infection, they found RV induced activation of innate immunity genes and suppression of adaptive immunity genes. Innate immunity comes into play immediately or within hours of an antigen's (toxic or foreign substance) presence in the body, while adaptive immunity is more complex and is a specific response to a particular antigen. The adaptive immune system creates immune cells specifically designed to attack the antigen and the "memory" to make future responses against that antigen more efficient.

The activation of genes related to interferon, neutrophils (a type of white blood cell), T cells (a sub-type of white blood cells), plasma cells (another type of white blood cell) and apoptosis (cell death) was stronger among patients with severe infection compared to those with mild infection. Interferon is a protein released by cells in response to the entry of a virus, and it has the ability to prevent the virus from replicating. 

In addition, Dr. Mejias' team found negligible changes in the activation or suppression of all these genes in asymptomatic RV+ children, or children who tested positive for the presence of RV but did not show any symptoms. In fact, their genomic scores were similar to those of healthy controls, suggesting a lack of active infection or at least a lack of systemic response. Both group's genomic scores were significantly lower than those of outpatients and inpatients with RV infection.

The signatures were validated using quantitative real time polymerase chain reaction (qRT-PCR) assays, which proved to have high prediction accuracy.

"Once you have identified the signatures, you can develop PCR-based platforms that are about 60 to 100 transcripts, with faster turn-around time," says Octavio Ramilo, MD, chief of the Division of Pediatric Infectious Diseases at Nationwide Children’s and professor of Pediatrics at The Ohio State University College of Medicine. "We're in that phase now."

The researchers estimate that the future PCR-based approach could allow doctors to discern whether a patient has an RV infection or incidental presence of RV in three to six hours.

"That's much more useful for making clinical decisions than waiting five days to culture a virus," says Dr. Mejias, who is also an associate professor of Pediatrics at The Ohio State University College of Medicine.

The faster turnaround could enable a surgeon to decide whether to go forward or delay surgery for a patient who tested positive for RV, the researchers say. Or, in feverish children or those with pneumonia, the results could help determine whether to begin antibiotics or more testing is needed.

If the findings are confirmed in patients with cystic fibrosis or immunodeficiency, signatures could be used to monitor chronic infections, time treatments and assess responses.

Since finding reproducible signatures for RV, the researchers have begun to expand their investigation. They're now looking for transcriptional signatures of other respiratory viruses.

Full Citation:

Heinonen S, Jartti T, Garcia C, Oliva S, Smitherman C, Anguiano E, de Steenhuijsen Piters WA, Vuorinen T, Ruuskanen O, Dimo B, Suarez NM, Pascual V, Ramilo O, Mejias A. Rhinovirus detection in symptomatic and asymptomatic children: Value of host transcriptome analysis. American Journal of Respiratory and Critical Care Medicine.2015 Nov 16.DOI: 10.1164/rccm.201504-0749OC.

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