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Scientists decoding genomic sequences of H1N1 using isolates from outbreak in Argentina

Results could shed light on genetic differences of outbreak between Argentina and other locations

Researchers at the Center for Infection and Immunity (CII) at Columbia University Mailman School of Public Health are working with Argentina's National Institute of Infectious Diseases, the National Administration of Laboratories and Health Institutes (ANLIS), and Roche 454 Life Sciences to decode the complete genomic sequences of influenza pandemic (H1N1) 2009 virus from patients with severe respiratory disease.

The scientists will be comparing sequences of viruses associated with the current outbreak in Argentina with those found in other locations to determine if there are differences that may be linked to higher mortality rates or provide insights into virus evolution.

The Mailman School of Public Health researchers, led by Gustavo Palacios, PhD, assistant professor of Epidemiology and CII Director W. Ian Lipkin, MD, John Snow Professor of Epidemiology, and professor of Neurology and Pathology at Columbia University, plan to completely sequence up to 150 virus specimens from nasopharyngeal swabs and cultures over the next 10 days, and will share their findings with the larger scientific community. The complete sequencing of these virus specimens will allow the team to both characterize severe versus mild cases, as well as determine how the virus evolved at different points in time. Swine flu has killed 165 people in Argentina, more than any nation with the exception of the U.S. Any significant changes in the virus might influence the effectiveness of vaccines or drugs used to fight the pandemic.

"No one knows how this pandemic will evolve. Continuous surveillance will be essential to focusing both research and public health response. We are analyzing these isolates in New York and Argentina; nonetheless, we expect that members of the broader scientific community will bring new insights. Thus, our plan is to release sequences in draft form so that the vetting process can begin as soon as possible," said Dr. Lipkin.

"While there is no evidence so far to indicate the emergence of resistance to the oseltamivir vaccine, the antiviral drug that blocks the influenza virus from spreading between cells in the body, we are cautious about the findings until we have more sequences," said Gustavo Palacios, PhD. "The changes already noted in comparing the outbreak in Argentina to the U.S. haven't previously been associated with greater virulence."

Both the Center for Infection and Immunity and INEI are members of the laboratory network of the World Health Organization and the Pan American Health Organization. Roche Holding AG's 454 Life Sciences unit, which makes genetic-sequencing technology, is helping to decode the viruses. Sequences can be accessed via the home page for the Center for Infection and Immunity at

The Center for Infection and Immunity at the Mailman School is dedicated to global research and training programs focused on pathogen surveillance and discovery, and to understanding how gene-environment-timing interactions contribute to health and disease.

About the Mailman School of Public Health

The only accredited school of public health in New York City and among the first in the nation, Columbia University Mailman School of Public Health pursues an agenda of research, education, and service to address the critical and complex public health issues affecting millions of people locally and globally. The Mailman School is the recipient of some of the largest government and private grants in Columbia University's history. Its more than 1000 graduate students pursue master's and doctoral degrees, and the School's 300 multi-disciplinary faculty members work in more than 100 countries around the world, addressing such issues as infectious and chronic diseases, health promotion and disease prevention, environmental health, maternal and child health, health over the life course, health policy, and public health preparedness.

Stephanie Berger | EurekAlert!
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