When doctors want to identify the virus behind an infection, they usually turn to the polymerase chain reaction (PCR), a method for “amplifying” scattered bits of DNA into a sample large enough to study. To use PCR, however, a physician must know what kind of virus to look for, and that involves guesswork.
This past September a team of Columbia University researchers described a new method that could eliminate that guesswork. The technique, which has the unfortunate name of “virome capture sequencing platform for vertebrate viruses,” or VirCapSeq-VERT, can find every virus in a given drop of saliva, tissue or spinal fluid with near-perfect accuracy. The method makes it possible to simultaneously analyze 21 samples in less than 48 hours at an estimated cost of just $200 per sample. It can also detect novel or mutated viruses, so long as they are at least 40 percent identical to known ones. “When someone goes into an emergency room and winds up having all kinds of tests run, it costs thousands of dollars,” says W. Ian Lipkin, John Snow Professor of Epidemiology at Columbia University's Mailman School of Public Health. “This method is very inexpensive and allows us to personalize medicine by telling you exactly what you have.”
To develop the technique, Lipkin and his colleagues first created a database of more than 1,000 vertebrate viruses. Then they synthesized genetic probes to match every strain of every virus—two million of them, each a strand of DNA 25 to 50 nanometers long. When a probe encounters a matching virus, it binds to it. To extract those viruses, laboratory workers add magnetic beads measuring one to three microns in diameter to the mix; a chemical linker binds the beads to the genetic probes and the viruses they have captured. Researchers then insert a tube containing the mixture into a magnet stand, which pulls the probes to the tube's walls. After researchers isolate and wash the probe-bead-virus combos, they genetically sequence the viruses, eliminating the risk of false positives. Lipkin and his colleagues are now looking to team up with a commercial provider that can distribute the technology to hospitals and clinics around the world. They are also planning on adding probes for all known infectious bacteria and fungi.