Peter Skewes-Cox
PhD student
University of California, San Francisco

Keith, AK, CA

Dr. DeRisi’s Virochip technology lowers the cost of doing business. How does Dr. DeRisi see his tool changing the way viral research is carried out? For example, viral life cycle, demographic virus reserve pool, and many more types of research might now be possible on a wide scale.

Peter Skewes-Cox
HHMI lab associate,
PhD student,
Biological and Medical Informatics,
University of California, San Francisco
This is a great question, but truthfully the Virochip has already changed the way viral research is carried out. When the Virochip first came into widespread use, it was a major upgrade over existing viral detection methods. While nucleic acid–based tests (like PCR) and antibody-based tests (like ELISA) are rapid, inexpensive, and accurate for detecting viruses with known genomic or structural information, these tests fail when a virus of interest differs from its known relatives. The Virochip was a real game changer because the probes on the chip do not require a perfect match to the viruses it can detect; rather, because the detection of viruses with the Virochip depends on hybridization of a longer piece of DNA (70 nucleotides) to the fluorescently labeled DNA in the sample, some mismatching in the base-pairing can be tolerated while still yielding a signal. This robustness to mismatching is an especially valuable trait to have in a viral detection tool, because viruses can mutate on much shorter evolutionary timescales than free-living organisms. The other reason the Virochip gained in popularity was its low cost and rapid turnaround. In fact, when the DeRisi lab got its hands on the SARS sample, it took less than 24 hours to identify a completely novel coronavirus as the culprit!

As you may recall from Dr. DeRisi’s lecture, in recent years, the cost of sequencing has dropped significantly and continues to do so. Because of the plummeting price and the extremely high data quality produced by the new generation of sequencers, many viral discovery projects have begun to use deep sequencing as a rapid, cost-effective way to perform research. It allows researchers to look for viruses in hundreds of samples simultaneously in a completely unbiased fashion; the Virochip can detect only viruses with some similarity to a known virus. But the Virochip still has its place in our lab and others, because, despite all the technological advances in sequencing, there is no sequencer in existence that enables a researcher to screen a sample for tens of thousands of viruses, in a single day, for just a few dollars. In fact, some groups are looking to bring tools like the Virochip to poorer regions of the world where testing for viral infection can have a great impact on quality of life, while others are looking to bring the Virochip into hospitals in the United States as an FDA-approved diagnostic test for viral infection. The cost for setting up a microarray-based virus detection facility is many orders of magnitude cheaper than purchasing a sequencer and enough computer processing power to analyze the data. Don’t be surprised if some day the Virochip ends up being a universal diagnostic tool used by people across the globe.

05/15/11 19:40