To Speed Testing, Tracking of Emerging Influenza Virus
A Medical College of
Wisconsin and Children’s Research Institute team in Milwaukee has created a free website that will significantly improve diagnostic testing and genetic tracking of human and animal influenza viruses
worldwide. The website, which is automatically updated weekly, will also
facilitate rapid response as new virus strains emerge to cause either annual
epidemics or the next pandemic.
In a striking example
of translational, or bench-to-bedside, research the multidisciplinary team has
created a searchable database containing all accessible genetic sequences of
influenza A, B, and C, and integrated them into the website www.IPDR.mcw.edu .
The site was presented at two recent meetings: Seasonal & Pandemic
Influenza, 2007 in Arlington, VA, and IX International Symposium on Respiratory viral infections in Hong
With the widespread
availability of rapid genetic testing for influenza in clinics and
laboratories, considerable resources are spent on bioinformatics annually by
many researchers and funding agencies worldwide trying to improve influenza
diagnostics, according to presenting author Kelly Henrickson, M.D., professor
of pediatrics and microbiology at the Medical College.
Since the 1997 Hong
bird flu outbreak, the focus of the world and its scientific
community has intensified on all aspects of influenza,” he says. “As a result, there has been a significant
increase in the amount of genomic data for influenza, which is now greater than
46,000 genetic sequences and growing by hundreds monthly.”
Constantly updated to
keep pace with emergence of new virus strains, this tool will also reduce the
enormous resources being expended worldwide on duplicate efforts. The site’s
simple, pop-up query screen, allows all 46,000+ sequences in its database to be
searched, or probed, with a set of criteria including: gene segment, year,
species, geographic location, and subtype. The unique feature of this website
is that after quickly aligning the genetic sequences, it displays the consensus
sequence with the percentage of match, mismatch and gap at each position for rapid
identification of the strain being tested.
In addition, the
website offers two other important tools: 1) a program that can automatically
design primers and probes for the resulting consensus sequence and 2) a program
that links the user and consensus sequence to a database containing the
majority of published and already developed influenza primers and probes;
displaying this data aligned to the consensus sequence using colored
primer/probe sequences that when “clicked on” produces the complete reference
for the user.
According to Dr.
Henrickson, even though the NIH has funded improved bioinformatics for a number
of infectious diseases, including influenza, the tools currently available have
been limited and not as much help to clinicians and researchers working on molecular
diagnostics for influenza.
website only focuses on the influenza virus information. However, other
pathogens which cause respiratory tract infections, such as RSV and
parainfluenza virus, will be added to this website in the near future.
Other team members
include: pediatric research technologist Michael E. Bose, M.S., assistant
professor of pediatrics Jiang Fan, M.D.; bioinformatics center applications
manager Andrew Patzer, physiology genetics data specialist Jack Littrell, and
pediatric infections disease lab supervisor Andrea J. Kraft M.S. This work is partially funded by the National
Institute of Allergy and Infectious Diseases.