A single test could detect almost any virus

A new test that detects virtually any virus that infects people and animals has been developed by researchers at Washington University School of Medicine in St. Louis, according to results published in the journal Genome Research.

The new test can detect a wide range of viruses, including norovirus.

Many thousands of viruses are known to cause illness in people and animals, and diagnosing them correctly can be a long and costly process, involving numerous tests.

Viruses that occur in and on the human body are collectively known as the virome. According to researchers, in a process known as "enhanced virome sequencing," they have developed a way to cast a broad net and "efficiently detect viruses that are present at very low levels."

No test so far has been sensitive enough to detect low levels of viral bugs. Many tests are limited to detecting only those viruses suspected of being responsible for a patient's illness.

The new test could be used to detect outbreaks of deadly viruses such as Ebola, Marburg and severe acute respiratory syndrome (SARS), as well as more commonly occurring viruses, including rotavirus and norovirus, both of which cause severe gastrointestinal infections.

The team expects the test to be useful in cases when standard testing does not reveal a diagnosis, or when it is not known what has caused a disease outbreak.

Test reveals viruses not detected by standard testing

The new test - called ViroCap - has been shown in patient samples to detect viruses not found by standard testing.

The test sequences and detects viruses with the same sensitivity as polymerase chain reaction (PCR) tests, which are used widely in clinical laboratories and considered to be the "gold standard."

However, while PCR tests can screen for up to about 20 similar viruses at one time, it seems that ViroCap could theoretically test for virtually any virus.

To develop the test, researchers targeted unique stretches of DNA or RNA from every known group of viruses that infects humans and animals: 2 million unique stretches of genetic material in all.

These stretches of material are used as probes to pluck out viruses in patient samples that are a genetic match. The matched viral material is then analyzed using high-throughput genetic sequencing.

The team suggests that as completely novel viruses are discovered, their genetic material could easily be added to the test.

Evaluation shows ViroCap to be 52% more effective

The researchers evaluated the new test by taking two sets of biological samples - for example, from blood, stool and nasal secretions - from patients at St. Louis Children's Hospital.

Standard testing detected viruses in 10 of 14 patients, but the new test found viruses in the four children that earlier testing had missed.

Common, everyday viruses not detected by the standard test included influenza B, a cause of seasonal flu, parechovirus, a mild gastrointestinal and respiratory virus, herpes virus-1, responsible for cold sores in the mouth, and varicella-zoster virus, which causes chickenpox.

In a second group of children with unexplained fevers, standard testing detected 8 out of 11 viruses, but the new test found another seven, including a respiratory virus called human adenovirus B type 3A, which is usually harmless but can cause severe infections in some patients.

In all, the number of viruses detected in the two patient groups jumped from 21 from 32 - a 52% increase.

The new test also enables subtypes of viruses to be identified easily, because it includes detailed genetic information about various strains of particular viruses.

For example, 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.

Last flu season, H3N2 contributed to around 36,000 deaths in the US. This information could lead to more effective treatment in patients such as young children, older adults and people with weakened immune systems.

Study author says:

"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 technology developed is being made publicly available to scientists and clinicians worldwide for the benefit of patients and research.

Further research is still needed to validate the accuracy of the test, meaning that it may be several years before it is clinically available, but scientists will be able to use the technology to study viruses in a research setting.

The authors also hope that it could be modified to detect pathogens other than viruses, such as bacteria, fungi and other microbes. It could also show up genes that would indicate that a pathogen is resistant to treatment with antibiotics or other drugs.

The new test will enable a better understanding of such viruses and the role they play in keeping the body healthy.

References:

1.  Enhanced virome sequencing through solution-based capture enrichment, T.N. Wiley et al., Genome Research, doi:10.1101/gr.191049.115, published 29 September 2015.
2.  Washington University School of Medicine news release, accessed 30 September 2015.