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CDC and APHL Make Influenza Virus Sequence Data Publicly Accessible


Collaboration with public health labs will foster greater research and openness

Scientists at the Centers for Disease Control and Prevention (CDC) have released genetic blueprints for over 650 genes of influenza viruses into a database accessible to researchers worldwide. The action marks the beginning of a collaboration between the CDC and the Association of Public Health Laboratories (APHL) that will allow for greater access to data on a variety of influenza virus samples obtained from patients in the United States, including avian influenza H5N1 if it should arrive here.

Through the new collaboration, CDC expects to provide genetic information for several hundred influenza viruses per year as a way to encourage more research on influenza. The sequence data will be available in nearly real time through Genbank, a public-access library for virus sequences managed by the National Institutes of Health, and through an influenza database housed at Los Alamos National Laboratories (LANL). The information added will include viruses from the annual flu season in the United States, any animal influenza viruses that infect humans and any novel strains that may emerge such as avian influenza H5N1. The new agreement will only apply to viruses isolated in the United States.

“CDC has long supported the timely and open sharing of influenza virus information to foster new research on influenza. We’re excited that this historic collaboration with APHL provides a way to make international exchange of this information possible,” said Dr. Nancy Cox, director of the CDC’s Influenza Division. “With more information, the world’s influenza experts can advance our understanding of the viruses circulating, potentially create new prevention strategies and treatments, and ultimately help us better protect the health of people around the world.”

The sequence information, which is like a DNA fingerprint of each virus, allows researchers to determine more about a virus’s origin and to compare it to other influenza viruses. This will help scientist determine whether the virus is susceptible to antiviral drugs and, in the case of avian influenza currently circulating in much of the world, to assess whether it’s changing in a way that might make the virus more easily transmissible among people – a key property the virus would need to acquire to spark a pandemic. In addition, the sequences can be used to better identify the strains that should be included in the yearly flu vaccine.

Previously, the influenza sequences were available to a small number of influenza researchers who work together with WHO to recommend which influenza viruses should be included in influenza vaccines around the world. The sequence data will now be available through GenBank to anyone with Internet access.

APHL, the national association representing public health laboratories, collaborated with its members to gain approval from all 50 state laboratories to make sequence data from influenza viruses tested in these labs publicly available. APHL promotes effective programs and public policy to strengthen laboratory capacity to protect the health of US residents and to prevent and control disease globally.

“State health department laboratories analyze and subtype thousands of influenza viruses each year. If a novel virus is out there, we will likely be the first to detect it. This is why public health labs are a critical part of our country’s early warning system for pandemic influenza, and why this collaboration with CDC is so important,” said APHL President Dr. Jane Getchell.

State public health laboratories participate in national influenza surveillance efforts by subtyping viruses and routinely submitting some influenza viruses to CDC for more in-depth characterization. CDC asks public health labs to submit samples of influenza viruses from the beginning, peak and end of each flu season, as well as any samples that are unusual. Under the new agreement, if a novel strain is identified at CDC, the state laboratory which submitted it would be notified prior to the posting in Genbank or LANL databases.

CDC has been actively working with the World Health Organization to encourage sharing of viruses from countries with avian flu activity. After the Indonesian government recently agreed to make available the sequences for viruses from Indonesian bird flu patients, CDC placed total genome sequences for over 40 H5N1 viruses into a public-access database.

“We hope these initiatives will set the stage for other countries to adopt similar approaches to the release of Influenza virus sequence data that they manage” Dr. Cox said.


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