Computational Analysis Helps Researchers Understand Emerging Pathogenic Foe
NEW YORK (May 1, 2009) – As part of a broad-based effort to understand the precise genetic make-up of H1N1 – now being referred to as “swine flu” in North America – a group of virologists and computational biologists from Columbia University Medical Center has delved headlong into analyzing the mysterious virus that has infected hundreds if not thousands of people worldwide since surfacing on public health workers’ radars last week.
A computational biology group led by Raul Rabadan, Ph.D., is now analyzing the recent sequences from samples in New York, Texas, Ohio, California, Spain, New Zealand, and parts of Asia, of swine H1N1 entered into the U.S. government’s National Center for Biotechnology Information database. The results generated by that publicly available data have so far been intriguing: All samples or “isolates” of the virus in North America indicate that it is almost entirely of swine origin, according to the preliminary research now published by Dr. Rabadan and his colleagues in the April 30, 2009 journal Eurosurveillance.
Raul Rabadan, Ph.D., center, and his lab colleagues, from left to right: Vladimir Trifonov, Benjamin Greenbaum, Hossein Khiabanian and Miguel Brown. Credit: CUMC.
“Scientifically, this is a swine virus,” agreed Dr. Richard Webby, a virologist at St. Jude Children's Research Hospital in Memphis, in an interview with the Associated Press. Dr. Webby is director of the WHO Collaborating Center for Studies on the Ecology of Influenza Viruses in Lower Animals and Birds.
Influenza is an RNA viruses composed of eight segments, Dr. Rabadan says. His findings show that the new H1N1 strain is related to influenza viruses found in swine, both in North America and Eurasia. In particular, the segments from the North American lineage, were related to a swine virus isolated in 1998 that was a triple reassortment of avian, swine and human viruses. Whether his team’s findings suggest a higher or lower threat level from the virus now being transmitted human-to-human remains to be seen.
"Raul had been working in this area for some time," said George Hripcsak, M.D., chair of the department of biomedical informatics at Columbia University. "As soon as he and his team learned of the outbreak, they begain scrutinizing the near real-time data to understand the composition of the virus. They were able to share their results quickly over a listserv and an online journal and make a significant contribution to the unfolding scientific discussion that is helping public health officials grapple with this latest pathogenic threat."
Dr. Rabadan, a computational virologist, has sought to understand the role of different hosts in the origin of the 1918 pandemic and to evaluate the rate and likelihood of different reassortments. Upon hearing of the current epidemic, he has been pulling the latest data into his analysis, which has been substantiated by other researchers following the discussion, including a senior scientist at the Lawrence Livermore National Laboratory in California.
Dr. Rabadan joined Columbia University Medical Center in September from the Institute for Advanced Study in Princeton, New Jersey.
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The Department of Biomedical Informatics is among the oldest and largest in the nation. Its researchers study information and computation in biology and health. The Department strives for discovery and impact: to discover new information methods, to augment the biomedical knowledge base, and to improve the health of the population. Its 30 faculty members and 60 students work in a highly collaborative environment, applying informatics from the atomic level to global populations. Its initiatives include next-generation electronic health records, deployment of clinical records in 10 countries in Africa, systems for chronic care and health communication in Harlem, modeling the spread of infection, and using systems biology to uncover the mechanisms of cancer. For more information, please see www.dmbi.columbia.edu.
The Center for Computational Biology and Bioinformatics (C2B2) is an interdepartmental center at Columbia University Medical Center, whose goal is to catalyze research at the interface between biology and the computational and physical sciences. C2B2 supports active research programs in areas such as computational biophysics and structural biology, the modeling of regulatory, signaling and metabolic networks, pattern recognition, machine learning, and functional genomics. C2B2 is also the host of the National Center for the Multiscale Analysis of Genomic and Cellular Networks (MANGet), one of the seven National Centers for Biomedical Computing funded through the NIH Roadmap Initiative. For more information please visit www.c2b2.columbia.edu.
Columbia University Medical Center provides international leadership in basic, pre-clinical and clinical research, in medical and health sciences education, and in patient care. The medical center trains future leaders and includes the dedicated work of many physicians, scientists, public health professionals, dentists, and nurses at the College of Physicians & Surgeons, the Mailman School of Public Health, the College of Dental Medicine, the School of Nursing, the biomedical departments of the Graduate School of Arts and Sciences, and allied research centers and institutions. Established in 1767, Columbia's College of Physicians & Surgeons was the first institution in the country to grant the M.D. degree and is now among the most selective medical schools in the country. CUMC is home to the largest medical research enterprise in New York City and state and one of the largest in the country. For more information, please visit www.cumc.columbia.edu.