New test can detect any virus

Scientists have designed a test that can detect not only any known virus type and subtype but also virus outbreaks.

A research team led by the Washington University School of Medicine in St Louis (WUSTL) condensed nearly 1 billion base pairs of viral DNA sequences to create a test that they call ViroCap.

“With this test, you don’t have to know what you’re looking for. It casts a broad net and can efficiently detect viruses that are present at very low levels. We think the test will be especially useful in situations where a diagnosis remains elusive after standard testing or in situations in which the cause of a disease outbreak is unknown,” said research associate Professor Gregory Storch.

To develop the test, the researchers targeted unique stretches of DNA or RNA from every known group of viruses that infects vertebrates – including 2 million unique stretches of genetic material. The stretches of material were used as probes which can pluck out viruses from a sample and find a genetic match. The matched viral material was then analysed by high-throughput genetic sequencing.

The scientists checked the effectiveness of the test by comparing it with standard tests that rely on genome sequencing. The results, published in the journal Genome Research, showed that standard testing failed to detect common viruses such as influenza B, parechovirus, herpes virus 1 and varicella-zoster. The new technology, however, managed to detect the viruses missed by the standard test, and identified the virus adenovirus B type 3A which can cause severe infections in some patients.

Also, the test includes detailed genetic information about various strains of particular viruses allowing it to identify virus subtypes. While standard testing identified a virus as influenza A, which causes seasonal flu, the new test indicated that the virus was a particularly harsh subtype called H3N2.

Research associate Todd Wylie from the WUSTL said: “The test is so sensitive that it also detects variant strains of viruses that are closely related genetically. Slight genetic variations among viruses often can’t be distinguished by currently available tests and complicate physicians’ ability to detect all variants with one test.”

The researchers hope that the new test could be used to detect outbreaks of deadly viruses such as Ebola, Marburg and severe acute respiratory syndrome, as well as more routine viruses, including rotavirus and norovirus, both of which cause severe gastrointestinal infections. They believe the test could be modified to detect pathogens other than viruses, including bacteria, fungi and other microbes, as well as genes that would indicate the pathogen is resistant to treatment.

Paper: http://genome.cshlp.org/content/early/2015/09/22/gr.191049.115.full.pdf+html