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MChip Identifies Avian, Other Flu Types by Recording Changes in Slow-Mutating Gene

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Researchers at the University of Colorado have developed a new influenza diagnostic that they believe will be cheaper and faster than other devices, and will also require fewer updates for distinguishing the virus’ strains.
 
Like other flu tests, some of which are on the market already, the University of Colorado device recognizes different viral strains by identifying genome-sequence variations.
 
But the test differs from others in that it relies on a small number of variations in the slowly changing influenza M gene rather than the more-traditional HA and NA genes, an innovation that allows a simpler array that requires fewer updates as influenza strains evolve.
 
The MChip also uses an automated artificial neural network to analyze the results.
 
The team is working on a way to use the test to identify antiviral drug-resistant flu strains so that doctors can avoid wasting time and resources with ineffective treatments.
 
But despite its new approach, the device might be too late to overcome diagnostics from competitors such as Combimatrix and Qiagen, which are also planning to develop simpler and cheaper tests.
 
When it’s ready for use, each array for the MChip could cost around $10, according to Kathy Rowlen, the test’s lead developer and a UC professor of biochemistry and chemistry.
 
The chip is the result of a collaboration between the University of Colorado, the US Centers for Disease Control and Prevention, and the private company Indevr, a company Rowlen helped found.
 
According to Rowlen, the MChip may find its first uses in surveillance. “We know that it works for [H5N1, H3N2, and H1N1] strains, and I think right now it could be used in a research setting — say in Southeast Asia — to look at those three strains, and it’ll take a lot more research to know what additional information we can get reliably,” Rowlen said.
 
A timeline for the device’s clinical use depends upon whether a diagnostic partner will agree on a deal to manufacture and distribute it. “The University is currently in negotiations with a company to license the technology, and they’re very excited about it, so once that is done, I think they’ll put a lot of effort into it,” said Rowlen.
 
She declined to disclose the company’s name or the stage of negotiations, but added, “my guess is that the company that [is seeking] a license will get FDA approval.”
 
As the MChip stands now, it will probably be most useful as a pre-pandemic screening tool to rapidly examine sick individuals who have recently entered the US, said Rowlen.
 
Flu-strain surveillance — in which the US Centers of Disease Control and Prevention red-flags specific strains for vaccine manufacturers — may provide another important use for the test, she added.
 
In a small study published Oct. 18 in the online edition of the journal Analytical Chemistry, Rowlen and colleagues used the MChip to identify 21 of 24 different avian flu isolates. The test produced no false-positive results, they said.
 
“The clinical sensitivity was 90 percent, and the clinical specificity was 100 percent,” said Rowlen. The group has another paper under review that attempts to validate the test in a larger sample population.
 
The same University of Colorado research group developed a related Flu Chip that identifies influenza type and subtype using the three flu genes HA, NA, and M [see PGx Reporter 11-10-05]. The MChip, however, is “easier, faster, cheaper, with better performance,” Rowlen said.
 
Rowlen contended that the MChip’s simplified analysis has made it “amazingly robust,” giving it the ability to identify newly emerging strains reported to be spreading through Chinese poultry in the last several months. “We picked up every one of them,” she said.
 
Strain Spotting
 
MChip will have to contend with competitors already occupying the market with strain-typing flu tests, including Combimatrix and Qiagen. However, so far only the CDC’s H5N1 RT-PCR primer and probe set has been cleared by the FDA.
 
Pharmacogenomics Reporter’s sister publication BioCommerce Week reported last week that Qiagen CEO Peer Schatz strongly hinted that the company may seek FDA approval for a flu strain-typing test it acquired in its purchase of Huntsville, Ala.-based Genaco.
 
“That’s one that’s on a high priority due to the number of partners who have shown very aggressive interest in this product,” he said. The test runs on the Luminex platform.
 
Qiagen representatives were unable to respond to questions for this article before deadline. The company already sells a PCR-based flu-detection test and two traditional antibody-based tests for influenza.
 

MChip’s “clinical sensitivity was 90 percent, and the clinical specificity was 100 percent.”

Other players include Celera, which in August received $900,000 from the US National Institutes of Health to develop and commercialize an in vitro diagnostic to detect the A/H5 influenza virus.
 
Celera has said it hopes to sell the test through its alliance with Abbott. The test uses automated real-time PCR technology from Applied Biosystems and will likely run on Abbott’s m2000 system. The m2000 is currently available in Europe with CE Mark certification and is pending 510(k) clearance with the FDA.
 
Combimatrix launched its Influenza A Array in September. And while the company hopes its test will be used in the clinic to guide treatment, it has not yet decided whether to go beyond its CLIA-lab offering to pursue FDA approval, said CEO Amit Kumar.
 
Combimatrix’s test is “much more comprehensive than the MChip” and is already being used in studies of birds in Alaska run by the US Science Applications International Corporation and the US Departments of the Interior and Agriculture, Kumar said.
 
Moreover, Kumar contended that the MChip’s price advantage will probably diminish when the cost of labor and hardware is taken into account. “When you run a test, it’s not just the chip cost … especially in our situation,” he said. “The cost of all the reagents and the labor are usually about 80 percent” of a test’s total cost, he added. Combimatrix’ reader costs about $20,000.
 

Combimatrix has no plans to develop a simplified or easier-to-read version of its test, but Kumar said it’s well suited to field work because the platform is about the size of a toaster. The company continues to update the influenza A array’s strain coverage as sequence information becomes publicly available from the CDC and elsewhere, he added.

Combimatrix has no plans to develop a simplified or easier-to-read version of its test, but Kumar said it’s well suited to field work because the platform is about the size of a toaster. The company continues to update the influenza A array’s strain coverage as sequence information becomes publicly available from the CDC and elsewhere, he added.
 

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