Editor's note: We interrupt MDD's series of stories on the recent BioWest 2006 conference to offer another technology development out of Colorado, from the University of Colorado at Boulder. The series continues tomorrow featuring Baxa of Englewood, Colorado.

A test that goes beyond diagnosis of the avian flu – to offer information such as geographic origin or whether a variant of the influenza virus is newly emergent – may soon be made available at laboratories, further enhancing the ability to detect and quickly react to new strains of the virus, including the H5N1 avian influenza strain.

The new microchip-based test, or FluChip, provides results in 12 hours, a feature bannered in national headlines for improving the ability to launch faster therapy. It was developed by scientists from the University of Colorado at Boulder and the Centers for Disease Control and Prevention (CDC; Atlanta), with funds provided by the National Institute of Allergy and Infectious Disease (NIAID; Bethesda, Maryland).

“The FluChip – the advantage of it is that it simultaneously tests for multiple strains, and so can show you if there's a reassortment of them going on or if the virus has picked up genes it doesn't normally have,” Michael Shaw, associate director for laboratory science in the influenza division of the CDC, told Medical Device Daily.

The CDC said that laboratories across the U.S. 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 such specialized tests capable of revealing “critical details” about geographic origin and other features, it said.

Because the FluChip technology could be used in lower-level biosafety facilities, it is expected to expand influenza diagnostic capacity by allowing more labs to determine geographic origin or whether a strain is human or non-human. It is also expected be used to detect any genetic changes that could indicate whether the virus is becoming more virulent, or how closely related a new virus is to ones that have circulated previously, the CDC said.

“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,” said Julie Gerberding, MD, director of the CDC in a statement.

The FluChip is a type of microarray generally referred to as a gene chip.

The CDC said that there are “numerous variations” of microarrays which can be made by using a robotic arm to drop hundreds or thousands of spots, or probes, of genetic material – either DNA or RNA – of known sequence onto a microscope slide. Probes that match gene sequences contained in the sample are said to “capture” the target gene.

By analyzing the pattern of captured targets, doctors can diagnose the cause of infection.

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 staff in CDC laboratories to process the influenza samples, test the FluChip technology and analyze the results.

“They had the basic system, where they knew they could amplify a signal, knew that they could do it on a chip, but what they needed was a specific approach for a particular disease,” Shaw said. “That's where we came in.”

A “key challenge” in designing a gene chip for flu diagnosis is determining which flu virus gene sequences to use as probes, according to the lead author on the paper, Kathy Rowlen, PhD, of the university. In a companion paper, the researchers describe a way to scan “vast amounts” of flu virus genetic information to find the most informative sequences.

The 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,” Rowlen said.

The researchers used this data mining process, beginning with a pool of nearly 5,000 flu gene sequences for use as probes on FluChip. Among those 5,000 sequences were probes chosen to detect two of the most common flu strains now circulating, the H1N1 and H3N2, as well as the avian flu strain H5N1.

Combined results after two rounds of tests showed that the FluChip allowed users to obtain correct information about both type and sub-type from 72% of the samples, the CDC said.

Earlier this year, the CDC reported that the agency had developed a new laboratory test to diagnose H5 strains of influenza in patients suspected to be infected with the avian flu (Medical Device Daily, Feb. 7, 2006). However, the previous test was “basically a yes/no test,” and it required conducting a completely separate test for each strain of influenza, Shaw said. Other commercial tests are available for a so-called “yes/no” diagnosis, but it is thought that none provide the information provided by FluChip.

“If [a test is] for the purpose of a rapid diagnosis to find out if a person has avian flu, then by far the real-time PCR test is the way to go – it's the fastest,” Shaw told MDD.

The “beauty” of the FluChip is that it tests for the strains “all at once,” he said. The disadvantage is that it takes longer.

Whereas results of the real-time PCR test were achieved in about four hours, the full characterization using the FluChip took about 12 hours.

Rowlen said in November in a university news release that the goal is to commercialize the test, and that within a few years the technology potentially could be made small enough to fit into a hand-held portable device to take to remote areas, where the avian flu has been most prevalent to date.

According to the World Health Organization (Geneva, Switzerland) 241 cases of avian flu worldwide have been reported, resulting in 141 deaths as of Aug. 23.