September 1, 2006

Test Enables Quick Diagnosis of Flu Strains

CU-Boulder Professors Robert Kuchta and Kathy Rowlen display a scanner and the Flu Chip CU-Boulder Professors Robert Kuchta and Kathy Rowlen display a scanner and the Flu Chip.University of Colorado at Boulder, Office of News Services

Laboratories across the U.S. can perform some basic tests on an influenza (flu) virus within several hours. However, only the Centers for Disease Control and Prevention (CDC) and a handful of other labs around the world have the high-level biosafety facilities needed to perform specialized tests that can reveal critical details about a virus such as its geographic origin. A new test may change that, allowing labs across the country to diagnose influenza infections and learn more about the viruses causing illness.

The test, called the FluChip, is a type of microarray. Sometimes called gene chips, microarrays are made by using a robotic arm to drop hundreds to 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—for instance, material taken from someone with an undiagnosed illness. Target gene sequences in the sample are “captured” by the probes. By analyzing the pattern of captured targets, doctors can diagnose the cause of infection.

Funded by NIH’s National Institute of Allergy and Infectious Diseases, Dr. Kathy L. Rowlen and her colleagues from the University of Colorado at Boulder, along with researchers from the Centers for Disease Control and Prevention (CDC), scanned vast amounts of flu virus genetic information to find the most informative sequences for use on a gene chip. Beginning with a pool of nearly 5,000 gene sequences, they selected 55 RNA sequences for use as probes. They included probes for two of the most common flu strains in humans, the H1N1 and H3N2 strains, as well as for H5N1, the avian flu. The CDC provided samples for testing from flu strains that infect humans, horses, birds and swine. The researchers worked together in CDC laboratories to process the influenza samples, test the FluChip technology and analyze the results.

The results were published in the August 2006 issue of the Journal of Clinical Microbiology. The researchers showed that the FluChip can successfully distinguish among 72 influenza strains. In less than 12 hours, the chip allowed users to obtain correct information about both type and subtype—considered a full characterization of a strain—from 72% of the samples, the correct type and partially correct subtype information for another 13% and the correct type only for an additional 10%.

“We were surprised and pleased at how well the chip performed in these early tests,” Dr. Rowlen said.

The researchers are now continuing to refine the FluChip. One day, it could potentially be used in lower level biosafety facilities, involving more labs in helping to determine the origin of a newly emergent virus, how it relates to other circulating viruses and whether it harbors genetic changes that may signal the virus is becoming more virulent.

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