Computational Analysis Helps Researchers Understand Emerging H1N1 Flu Strain

May 3, 2009
Raul Rabadan, Ph.D., center, and his lab colleagues, from left to right: Vladimir Trifonov, Benjamin Greenbaum, Hossein Khiabanian and Miguel Brown. Credit: CUMC

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.

“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.

Provided by Columbia University

Explore further: Swine flu joins list of animal diseases that affect people

Related Stories

Swine flu joins list of animal diseases that affect people

April 29, 2009
The swine flu virus that is smoldering in this country and triggering a full-blown outbreak in Mexico is one of a growing number of animal pathogens to jump the species barrier -- and may be the microbe that jumpstarts the ...

H3N1 pig flu virus found in South Korea

November 20, 2006
Scientists say they have identified the H3N1 swine influenza virus in domestic pigs in South Korea.

Virus has bird, pig, human components: farm trade watchdog

April 27, 2009
The top agency for health in farm animals on Monday said Mexico's outbreak of deadly influenza was unleashed by a pathogen mixed from bird, human and hog viruses and branded the term "swine flu" as wrong and harmful to pig ...

CDC: New virus lacks genes of 1918 killer flu

May 1, 2009
(AP) -- The new swine flu virus lacks genes that made the 1918 pandemic strain so deadly, a U.S. health official said Friday.

1918 flu resulted in current lineage of H1N1 swine influenza viruses, study says

April 30, 2009
In 1918 a human influenza virus known as the Spanish flu spread through the central United States while a swine respiratory disease occurred concurrently. A Kansas State University researcher has found that the virus causing ...

Swine flu name change? Flu genes spell pig

May 1, 2009
(AP) -- No matter what you call it, leading experts say the virus that is scaring the world is pretty much all pig. So while the U.S. government and now the World Health Organization are taking the swine out of "swine flu," ...

Recommended for you

Synthetic DNA-delivered antibodies protect against Ebola in preclinical studies

November 13, 2018
Scientists at The Wistar Institute and collaborators have successfully engineered novel DNA-encoded monoclonal antibodies (DMAbs) targeting Zaire Ebolavirus that were effective in preclinical models. Study results, published ...

Scientists illuminate causes of hepatitis B virus-associated acute liver failure

November 13, 2018
National Institutes of Health scientists and their collaborators found that hepatitis B virus (HBV)-associated acute liver failure (ALF)—a rare condition that can turn fatal within days without liver transplantation—results ...

New strategy discovered toward possible prevention of cancers tied to mono, the 'kissing disease'

November 12, 2018
Researchers from the University of Minnesota, the Howard Hughes Medical Institute, and the University of Toronto have discovered a possible path forward in preventing the development of cancers tied to two viruses, including ...

Combination therapy promising against blindness-causing bacterial keratitis

November 12, 2018
Multidrug-resistant bacterial infections of the cornea are a leading cause of blindness and cannot be effectively managed with current ophthalmic antibiotics. A team of investigators has now devised a combination therapy ...

Hepatitis C treatment can be shortened in 50 percent of patients, study finds

November 12, 2018
Hepatitis C drugs cure more than 90 percent of patients, but can cost more than $50,000 per patient.

Salmonella found to be resistant to different classes of antibiotics

November 12, 2018
Brazil's Ministry of Health received reports of 11,524 outbreaks of foodborne diseases between 2000 and 2015, with 219,909 individuals falling sick and 167 dying from such diseases. Bacteria caused most outbreaks of such ...

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

THEY
not rated yet May 04, 2009
I keep hearing CT'ers say that vials of swine flu are missing from some vault. I have no idea if that is true or not, but reading this article makes me want to know if the strain that went missing is this same one....... And if vials are really missing.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.