CDC joint pact opens access to flu virus fingerprints

A new agreement will make gene sequencing data related to domestically circulating flu bugs widely accessible.

By Stephanie Stapleton — Posted Sept. 25, 2006

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For the first time ever, researchers worldwide will have access to the genetic blueprints for the genes of more than 650 influenza viruses collected in the United States, the Centers for Disease Control and Prevention announced last month.

Health officials hope the trove of materials, which will be made available through two databases, will trigger a stepped-up level of influenza research -- ranging from efforts to pinpoint pandemic issues to those that lead to the development of new annual flu vaccines and treatments.

"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," said Nancy Cox, PhD, director of the CDC's influenza division, in a statement.

The new accessibility arrangement is the result of an agreement between the CDC and the Assn. of Public Health Laboratories. These labs, also known as state health laboratories, are in many ways the front lines of influenza surveillance, analyzing and sub-typing thousands of influenza viruses each year.

"If a novel virus is out there, we will likely be the first to detect it," said APHL President Jane Getchell, DrPH, in a statement. "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."

State labs pass on the samples to the CDC -- usually at the start, peak and end of each flu season as well as in the event an unusual strain is detected. There, more in-depth characterization, known as sequencing, is conducted. This information is akin to a DNA fingerprint for each virus, allowing researchers to determine more about its origin and to compare it with other influenza viruses, explained Rosemary Humes, APHL's director of infectious diseases and preparedness programs.

"In this manner, there has always been a collaboration," Humes said. This agreement marks the next step in that partnership as the CDC now has permission from all 50 state labs to post the virus sequences in a very public way, she added.

According to the agency, the data will be available in almost 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. The information will include viruses from the annual flu season in the United States, any animal influenza viruses that infect humans and any novel strains.

A positive step

Experts say this newfound access will have a positive impact in a variety of ways. "The primary aim is to get as much [influenza] data in the public domain as possible," said Michael Shaw, PhD, associate director for laboratory science in the CDC's influenza division. "The more eyes [that see it] the better."

The accessibility of the sequences may encourage more research in related areas. It could help investigators determine whether a specific influenza strain is susceptible to antiviral drugs. In the case of the avian flu currently circulating in much of the world, it could aid scientists in assessing whether it is mutating in a way that might make it easily transmissible among people. This characteristic is a key property the virus would need to acquire to spark a pandemic.

The sequences also could be used by more researchers to better identify the strains that should be included in the yearly flu vaccine. "You have to have an idea of what is already circulating before you can project what could happen next year," Dr. Shaw said.

On another level, the step encourages data transparency. The CDC has been working actively with the World Health Organization to encourage the sharing of data regarding influenza viruses from countries with avian flu activity. After the Indonesian government recently agreed to make available such information from Indonesian bird flu patients, the CDC placed the total genome sequences for more than 40 H5N1 viruses into a public access database.

The collaboration with the APHL involves only domestic sequences but is consistent with this notion of openness. "We're trying to be transparent with our data in hopes that others will be as well," said the APHL's Humes.

Dr. Cox echoed this position. "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."

Meanwhile, sharing scientific information about infectious agents sometimes draws intense scrutiny because of concerns regarding potential "dual uses" that would allow people with bad intentions to use it for harm. Such worries, though, are not germane to this collaboration, Dr. Shaw explained. What is being released, he said, is information regarding influenza strains that were collected during the normal flu season -- viruses already in the community.

"The benefit of sharing the information far outweighs any risk," Humes said.

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