CDC begins sharing flu virus genetic data

Aug 23, 2006 (CIDRAP News) – The Centers for Disease Control and Prevention (CDC) has published the genetic blueprints for more than 650 influenza virus genes to launch a new data-sharing program intended to stimulate influenza research.

In collaboration with the Association of Public Health Laboratories (APHL), the CDC will release genetic information on several hundred flu virus samples from US patients each year, the agency said yesterday in a news release.

The genetic sequence data will include seasonal flu viruses, any animal flu viruses that infect humans, and any emerging strains, such as H5N1, officials said.

The information will be deposited in two databases: GenBank, a public library of virus sequences managed by the National Institutes of Health, and the Los Alamos National Laboratory Influenza Sequence Database.

Until now, the sequence data were available only to a few flu researchers who work with the World Health Organization (WHO) to recommend which viruses should be included in flu vaccines. "The sequence data will now be available through GenBank to anyone with Internet access," the CDC said.

The genetic data shed light on a virus's origin and relationship to other flu viruses. Scientists can use the information to help determine whether a virus is susceptible to antiviral drugs and whether it is evolving in a way that would make it more contagious, possibly setting the stage for a pandemic, the CDC said.

The withholding of genetic data on H5N1 viruses has drawn criticism in recent months. In July, virologists quoted in a Nature article complained that Indonesia's and other countries' refusal to share H5N1 data was hindering scientists' understanding of the virus.

The CDC said it has been working with the WHO to encourage countries with H5N1 avian flu to share their data. "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," the agency said.

CDC hopes to set example
"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. Nancy Cox, director of the CDC's Influenza Divison, commented in the news release.

The APHL, which consists mainly of state and local laboratory officials, gained approval from all 50 state labs to release sequence data from flu viruses tested in the labs, the CDC said.  State labs subtype flu viruses and submit some of them, including any unusual ones, to the CDC for further characterization.

Under the new agreement, if the CDC identifies a new strain, the state lab that submitted it will be notified before the sequence data are posted in GenBank or the Los Alamos database, officials said.

APHL President Dr. Jane Getchell said in the CDC statement, "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."

WHO explains steps for releasing H5N1 data
In related news, the WHO today issued a brief explanation of how it works for the public release of H5N1 virus sequences—while downplaying somewhat the importance of such data.

The agency said the sequencing of H5N1 viruses is done collaboratively by labs in countries with H5N1 outbreaks and the international network of H5 reference labs coordinated by the WHO. The agency explained that it needs permission from the source country to publish the sequence data.

"WHO seeks to facilitate the timely release of sequence data to the public domain," the statement said. "Formal procedures exist by which the WHO reference laboratory initially informs the originating laboratory of sequence results and simultaneously requests permission to place these results in the public domain. In the event of a negative reply or no reply, WHO directly approaches the Ministry of Health in the originating country, requesting authorization to release sequence data."

While genetic sequencing is important for developing vaccines and monitoring drug resistance, the WHO said, epidemiology is the primary tool for spotting changes in the H5N1 virus. "Epidemiological findings remain the most important alert to changes in the virus that indicate improved transmissibility among humans," the agency said.

See also:

Aug 22 CDC statement about flu virus sequences
http://www.cdc.gov/media/pressrel/r060822.htm

Jul 12 CIDRAP News story "Report: H5N1 mutated rapidly in Indonesian cluster"
http://www.cidrap.umn.edu/cidrap/content/influenza/avianflu/news/jul1206mutate.html

Aug 23 WHO statement about procedures for releasing H5N1 sequences

GenBank homepage
http://www.ncbi.nlm.nih.gov/genbank/

Los Alamos National Laboratory Influenza Sequence Database homepage
http://www.flu.lanl.gov/

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