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Test Enables Quick Diagnosis of Flu Strains
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.
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| CU-Boulder Professors Robert Kuchta and
Kathy Rowlen display a scanner and the Flu Chip. Credit: University
of Colorado at Boulder, Office of News Services |
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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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