FluChip, a microchip device developed by scientists from the University of Colorado at Boulder, and reported by us last year, has shown itself quite reliable in characterizing influenza’s subtypes, according to research from the Centers for Disease Control and Prevention (CDC). Hence the headline: Quick Diagnosis of Flu Strains Possible with New Microchip Test
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.
Beginning with a pool of nearly 5,000 flu gene sequences, the investigators used the data mining process to select 55 flu RNA sequences for use as probes on the FluChip. Among them were probes chosen to enable detection of two of the most common flu strains currently circulating in humans, the H1N1 and H3N2 strains, as well as the avian flu strain H5N1.
The CDC provided flu isolates to the University of Colorado researchers to identify using the FluChip. The samples included flu strains that infect humans, horses, birds and swine. CDC shared its technical expertise on influenza and worked alongside University of Colorado staff in CDC laboratories to process the influenza samples, test the FluChip technology and analyze the results. Combined results after two rounds of tests showed that the FluChip allowed users to obtain correct information about both type and subtype–considered a full characterization of a strain–from 72 percent of the samples. Full information on type–but only partial information on subtype–was obtained for 13 percent of the samples, while 10 percent of the samples could be identified by type only (no information about subtype). It took about 11 hours to conduct the tests and learn the identities of the strains, report the scientists.
“New” test for flu news wire…