Influenza Genome Sequencing Project

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The Influenza Genome Sequencing Project (IGSP), initiated in early 2004, seeks to investigate influenza evolution by providing a public data set of complete influenza genome sequences from collections of isolates representing diverse species distributions.

Contents

The project is funded by the National Institute of Allergy and Infectious Diseases (NIAID), a division of the National Institutes of Health (NIH), and has been operating out of the NIAID Microbial Sequencing Center at The Institute for Genomic Research (TIGR, which in 2006 became The Venter Institute). Sequence information generated by the project has been continually placed into the public domain through GenBank.

Origins

In late 2003, David Lipman, Lone Simonsen, Steven Salzberg, and a consortium of other scientists wrote a proposal to begin sequencing large numbers of influenza viruses at The Institute for Genomic Research (TIGR). Prior to this project, only a handful of flu genomes were publicly available.[ citation needed ] Their proposal was approved by the National Institutes of Health (NIH), and would later become the IGSP. New technology development led by Elodie Ghedin began at TIGR later that year, and the first publication describing > 100 influenza genomes appeared in 2005 in the journal Nature [1]

Research goals

The project makes all sequence data publicly available through GenBank, an international, NIH-funded, searchable online database. This research helps to provide international researchers with the information needed to develop new vaccines, therapies and diagnostics, as well as improve understanding of the overall molecular evolution of Influenza and other genetic factors that determine their virulence.[ citation needed ] Such knowledge could not only help mitigate the impact of annual influenza epidemics, but could also improve scientific knowledge of the emergence of pandemic influenza viruses.

Results

The project completed its first genomes in March 2005 and has rapidly accelerated since. By mid-2008, over 3000 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). [1]

Affiliations

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 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 the Mount 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). Some of these avian isolates were described in a publication in Emerging Infectious Diseases in 2007. [2] 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 began 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.[ citation needed ]


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<span class="mw-page-title-main">Global spread of H5N1 in 2004</span>

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<span class="mw-page-title-main">Goose Guangdong virus</span> Strain of H5N1 influenza virus

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Elodie Ghedin is a Canadian parasitologist and virologist as well as a professor at the New York University Center for Genomics and Systems Biology. Her work focuses on the molecular biology and genomics of the parasites that cause diseases such as elephantiasis, and river blindness, and on the evolution of the influenza virus. She was named a 2011 MacArthur Fellow, a 2012 Kavli Frontier of Science Fellow, and a 2017 American Academy of Microbiology Fellow. She also was Awarded the Chancellor’s Distinguished Research Award in 2010.

This is a timeline of influenza, briefly describing major events such as outbreaks, epidemics, pandemics, discoveries and developments of vaccines. In addition to specific year/period-related events, there is the seasonal flu that kills between 250,000 and 500,000 people every year and has claimed between 340 million and 1 billion human lives throughout history.

References

  1. 1 2 Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL (October 2005). "Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution". Nature. 437 (7062): 1162–6. Bibcode:2005Natur.437.1162G. doi: 10.1038/nature04239 . PMID   16208317. (as PDF Archived 2006-09-01 at the Wayback Machine
  2. Salzberg SL, Kingsford C, Cattoli G, et al. (May 2007). "Genome analysis linking recent European and African influenza (H5N1) viruses". Emerging Infect. Dis. 13 (5): 713–8. doi:10.3201/eid1305.070013. PMC   2432181 . PMID   17553249.