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Member Research and Reports

Member Research and Reports

Columbia Center for Infection and Immunity’s New Diagnostics Breakthrough Brings Viral Sequencing to Doctors’ Toolkit

Until now, there has not been a fast, efficient way to broadly screen for viral infections. A breakthrough genetic testing method promises to change this situation by giving clinicians a powerful new tool to detect and sequence viruses. Developed by scientists at the Center for Infection and Immunity (CII) at Columbia University’s Mailman School of Public Health, the Virome-Capture-Sequencing platform for Vertebrate viruses (VirCapSeq-VERT) is as sensitive as the gold standard polymerase chain reaction (PCR) assays while enabling simultaneous testing for hundreds of different viruses and providing near complete sequence of their genomes. The system and its capabilities are described for the first time in a paper in the journal mBio.

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[Photo: L to R: Thomas Briese, Nischay Mishra, Arvind Kumar, Amit Kapoor,  and Ian Lipkin]

To use VirCapSeq-VERT, scientists select genetic pieces from among nearly 2 million known viruses, representing all viral taxa known to infect vertebrates. These genetic pieces are used to constitute a probe, which is introduced alongside material taken from the sample being tested. A magnetic process “pulls out” segments from the sample that match the probe; these segments are then analyzed using high-throughput sequencing. In a series of tests detailed in the study, scientists used VirCapSeq-VERT to test for a wide range of viruses in lung tissue, blood, nasal swabs, and feces. In tests of blood or tissue, the method resulted in 100 to 10,000-fold increases in viral matches compared with conventional high-throughput tests.

Dr. Ian Lipkin, CII director and John Snow Professor of Epidemiology, explains that heretofore high-throughput screening lacked the necessary sensitivity for detecting viruses. And PCR lacked the ability to test for multiple viruses simultaneously, making screening viruses time consuming and expensive. By contrast, says Dr. Lipkin, senior author on the paper, “VirCapSeq-VERT is a specific, sensitive, powerful way of characterizing all of the viruses in a sample. This will be an important tool for precision medicine as well as basic and clinical research.”

A major advantage of VirCapSeq-VERT is that it can collect the entire genome of viruses detected in the sample. By contrast, PCR detects a much smaller segment of the viruses’ genome. The method’s ability to detect a broader swath of the genome is especially useful in screening for viruses, which mutate many times faster than bacteria. VirCapSeq-VERT is able to detect and collect genetic information about viruses even if the sample does not exactly match the probe. According to its developers, VirCapSeq-VERT can detect a novel virus when as much as 60 percent of its sequence doesn’t match the probe. When the suspect virus mutates, the technology is still able to catch it.

VirCapSeq-VERT also gives researchers a new tool for efficient viral discovery to help them find all the viruses within a population, or shed light on an emerging infectious disease. CII is already using the tool in its research and is in talks with other labs interested in using it.

But VirCapSeq-VERT’s most important contribution, according to Dr. Thomas Briese, associate professor and first author, will be in the clinical setting. “If you have patients you suspect has a viral disease, you can now for a very reasonable amount of money, definitively characterize all the viruses present in those individuals in order to figure out how they should be treated,” he explains.