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Subspecialties Microbiology and immunology

One-Stop-Shop for Virus Detection

Diagnosing viral infection can be a challenge. Although there are sophisticated tests available, you need to know what you’re looking for; many tests can only detect one, or at best a few, infectious agents. Physician expertise, patient history and clinical symptoms can all provide crucial information, but reaching a diagnosis often still requires some guesswork. What if there was a simple way to check for every known human virus, in one sample? A test developed by researchers at the Center for Infection and Immunity (CII), Colombia University, New York, USA, might be able to do just that, by screening for all viruses that infect vertebrates, including genetic variants and mutations.

The technique involves high throughput sequencing coupled with a probe capture-based system. It required the creation of a library of 1,993,176 oligonucleotide probes in order to capture all viral taxa containing viruses known to infect vertebrates, which can then be targeted for enrichment and sequencing. The developers tested their approach on human lung tissue and whole blood, spiked with varying amounts of viral nucleic acid. When compared with standard high-throughput sequencing processes, they found a 100- to 1,000-fold increase in viral matches, and a reduction of host background matches of 31.5 percent in lung tissue, and over 60 percent in blood. Sequencing coverage also increased, with near full-length sequences being obtained for detected viruses (1).

With comparable sensitivity to targeted real-time PCR, and the added advantage of picking up sequence variants PCR might miss – and in some cases, a variant differing by even a single point mutation can display variations in transmissibility and pathogenicity – the system certainly seems promising. The ability to provide near-complete genome sequences also means the test can provide information on viral diversity and evolution, with obvious applications in epidemiology and public health. And with a cost of US$40 per sample using a multiplex (20 sample) format, the technique is not prohibitively expensive.

But the most important use of the sequencing method, say it’s creators, will be its potential applications in a clinical setting – when viral disease is suspected, or when standard tests are drawing a blank, a test with the potential to identify any virus would be a powerful diagnostic tool.

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  1. T Briese, et al., “Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis”, MBio, 6, e01491–15 (2015). PMID: 26396248.
About the Author
Roisin McGuigan

I have an extensive academic background in the life sciences, having studied forensic biology and human medical genetics in my time at Strathclyde and Glasgow Universities. My research, data presentation and bioinformatics skills plus my ‘wet lab’ experience have been a superb grounding for my role as an Associate Editor at Texere Publishing. The job allows me to utilize my hard-learned academic skills and experience in my current position within an exciting and contemporary publishing company.

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