Influenza Genome Sequencing Project


Influenza Genome Sequencing Project

The Influenza Genome Sequencing Project (IGSP) is an effort to dramatically improve the availability of genomic sequences and related information about the influenza (flu) viruses. The IGSP was started by Lone Simonsen (Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases), David Lipman and Steven Salzberg in early 2004, when they wrote a proposal to begin sequencing large numbers of influenza viruses at The Institute for Genomic Research (TIGR). The proposal was approved by the National Institutes of Health (NIH) and new technology development began that year, led by Elodie Ghedin at TIGR. Prior to this project, only a handful of flu genomes were publicly available. The project completed its first genomes in March 2005 and has rapidly accelerated since, with over 1800 genomes now in the public domain.

The project is funded by the National Institute of Allergy and Infectious Diseases (NIAID) which is a component of the NIH, which is an agency of the United States Department of Health and Human Services.

The sequencing effort, thus far conducted entirely at the NIAID Microbial Sequencing Center at TIGR, is revealing complete genetic blueprints of thousands of known human and avian influenza viruses. TIGR and NIAID are rapidly making all sequence information publicly available through GenBank, an international, searchable online database funded by NIH.

By putting critical genome knowledge in the public domain, project leaders hope to provide researchers with the information needed to develop new vaccines, therapies and diagnostics, and improve understanding of the overall molecular evolution of influenza and other genetic factors that determine their virulence. Such knowledge could not only help mitigate the impact of annual influenza epidemics, but could also improve scientific knowledge of the emergence of pandemic flu viruses.

The TIGR/NIAID IGSP has expanded to include a growing list of collaborators, who have contributed both expertise and valuable collections of influenza isolates. Key early contributors included Peter Palese of Mt. Sinai School of Medicine in New York, Jill Taylor of the Wadsworth Center at the New York State Department of Health, Lance Jennings of Canterbury Health Laboratories (New Zealand), Jeff Taubenberger of the Armed Forces Institute of Pathology (who later moved to NIH), Richard Slemons of Ohio State University and Rob Webster of St. Jude's Children's Hospital in Memphis, Tennessee. In 2006 the project was joined by Ilaria Capua of the Istituto Zooprofilattico Sperimentale delle Venezie (in Italy), who contributed a valuable collection of avian flu isolates (including multiple H5N1 strains). Nancy Cox from the Centers for Disease Control and Prevention (CDC) and Robert Couch from Baylor College of Medicine also joined the project in 2006, contributing over 150 influenza B isolates. The project will begin prospective studies of the 2007 influenza season with collaborators Florence Bourgeois and Kenneth Mandl of Children's Hospital Boston and the Harvard School of Public Health and Laurel Edelman of Surveillance Data Inc.

As of January 2007, 1813 isolates had been completely sequenced from influenza viruses that are endemic in human ("human flu") avian ("bird flu") and swine ("swine flu") populations, including many strains of H3N2 (human), H1N1 (human), and H5N1 (avian). [ [http://www.nature.com/nature/journal/v437/n7062/full/nature04239.html Nature] ]

Further reading

* [http://www.nature.com/nature/journal/v437/n7062/full/nature04239.html Nature presents the initial results of this project]
* [http://cbcb.umd.edu/~salzberg/docs/NatureFluGenomeProjectReprint.pdf Free copy of Nature paper at senior author's home page]
* [http://www.accessexcellence.org/WN/SU/flugenestorynov05.htm National Health Museum's on-line science news page summarizes the findings presented in Nature on the initial results of this project.]

ources

* [http://www.tigr.org/flu Influenza Sequencing Project home page at TIGR]
* [http://www.niaid.nih.gov/dmid/genomes/mscs/influenza.htm Influenza Genome Sequencing Project home page at NIAID]
* [http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html Influenza virus resource at NCBI (NIH)]
* [http://www.cdc.gov/ncidod/EID/vol12no01/05-0983.htm CDC]


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