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Some Genomic Shops Could Benefit From Ramp-Up In Gov t Bird Flu Testing Plan

NEW YORK, March 23 (GenomeWeb News) - Federal plans to ratchet up annual testing for avian flu will have national and state labs working overtime, making new H5N1 diagnostic products with high accuracy and low cost all the more welcome, said virologists involved in the effort.

 

"I think we would be remiss by not evaluating the pros and cons of new tests," said Hon Ip of the US Geological Survey's National Wildlife Health Center, where about 11,000 samples from federal parks and wildlife refuge centers will be sent.

 

In particular, commercial technologies enhancing optimization may be needed to contend with the urgency of testing, said Alex Ardans, director of the California Animal Health & Food Safety Laboratory. "We found this during the Newcastle outbreak. We just can't say enough about how gratifying it is when private industry brings their science to the table," he said.

 

According to a new Readiness Plan drafted by the US Departments of Agriculture, Interior, and Health and Human Services, the government plans to test 75,000 to 100,000 samples from live and dead birds for avian flu this year. This compares to just 12,000 samples tested since 1998. In addition, the new plan, which was released on Monday, expands the number of species of birds being tested to about 55.

 

While the USDA said that the goal is "very doable" for its network of labs, Ip, for one, said it's a "huge number that boggles the mind."

 

Currently, the 39 laboratories certified to conduct H5N1 tests for USDA are working under a standard protocol mandated by the agency's Animal and Plant Health Inspection Service. That protocol recommends testing with Qiagen PCR reagent kits and Cepheid's Smart Cycler.

 

Combimatrix, Nanogen, Simbiotics, and Rockby Biomed have all developed tests for H5N1. ABI's RT-PCR can be used with the APHIS test but not as a proxy for the approved protocol, according to David Suarez of the USDA's Southeast Poultry Research Lab.  

 

"A lab can't use those tests as the official tests, but there's no regulation that says they can't use them at all," he wrote in an email to GenomeWeb News.

 

Suarez said the assay is being optimized for other PCR machines and reagents. But any changes in platform must be validated for proof of principal before it can be incorporated in the approved methodology.

 

"Whether or not they will have validation by next year - I don't know," said Gene Erickson, a virologist with the North Carolina Veterinary Diagnostic Laboratory System.

 

Erickson said that his lab was prepared for the increase in tests and noted that all labs become more efficient with practice. Still, he said, testing would benefit from "more robust" throughput, like 96-well platforms instead of the Smart Cycler currently recommended.

 

"We think the world of Cepheid and the Smart Cycler," said California's Ardans. "But it doesn't give us the throughput we need."

 

Ip agreed that while the current protocol was the best assurance of uniformity, he is exploring other technologies to address the magnitude of the new readiness plan, which could increase his facility's caseload by a factor of 1,000. In particular, he said, he is reviewing the high-throughput technologies of Roche, Cepheid, and Stratagene, as well as Beckman Coulter's automation platforms and extraction solutions from Qiagen and Ambion.

 

"There's plenty of opportunity to create the gold standard for the next go-around," he said, "or even this one."

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