New microchip enables quick diagnosis of flu strains

Scientists from the University of Colorado at Boulder and the Centers for Disease Control and Prevention (CDC) have developed a microchip-based test that may allow more labs to diagnose influenza infections and learn more about the viruses causing illness.

The FluChip successfully distinguished among 72 influenza strains - including the H5N1 avian influenza strain - in less than 12 hours. The research was led by University of Colorado scientist Kathy L. Rowlen, Ph.D., and was funded by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH). It appears in the current issue of the Journal of Clinical Microbiology.

Laboratories across the United States can do basic tests to determine the type and subtype of an influenza virus within several hours.

However, only the CDC and a handful of other labs internationally have the high-level biosafety facilities needed to perform specialized tests that reveal critical details about the virus's geographic origin and other features. Because the FluChip technology could be used in lower level biosafety facilities, it could expand influenza diagnostic capacity by allowing more labs to determine the geographic origin of a newly emergent virus and whether its source is human or nonhuman; learn how closely related a new virus is to ones that circulated previously; and detect genetic changes that may signal the virus is becoming more virulent.

"The ability to quickly and accurately identify strains of influenza would be invaluable to international flu surveillance efforts," says NIAID Director Anthony S. Fauci, M.D. "This is an encouraging advance."

"This state-of-the-art research is vital to our efforts to protect the nation's health, and it may provide a new tool in our toolbox in the fight against influenza," says CDC Director Julie Gerberding, M.D. "This is an excellent example of the advances we can achieve when governmental and academic researchers work together, and we look forward to future collaboration."

The FluChip is a type of microarray, commonly called a gene chip. Although there are numerous variations, microarrays can be made by using a robotic arm to drop hundreds or thousands of spots of genetic material - DNA or RNA - of known sequence onto a microscope slide. The spots, called probes, are then exposed to a sample of unknown composition: for instance, material taken from a person with an undiagnosed illness. Probes that match gene sequences of bacteria or viruses present in the sample result in capture of the target gene. By analyzing the pattern of captured targets, doctors can diagnose the cause of infection.

A key challenge in designing a gene chip for flu diagnosis is determining which flu virus gene sequences to use as probes, notes Dr. Rowlen. In a companion paper, the researchers describe a powerful new way to scan vast amounts of flu virus genetic information to find the most informative sequences. "Our goal was to develop an efficient method for mining large databases to identify regions of the flu genome that are largely the same from strain to strain as well as strain-specific sequences," Dr. Rowlen says.