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.
The project is funded by the
National Institute of Allergy and Infectious Diseases
The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services (HHS). NIAID's ...
(NIAID), a division of the
National Institutes of Health
The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the lat ...
(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
The public domain (PD) consists of all the creative work to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable. Because those rights have expired ...
through
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
.
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 virus
''Orthomyxoviridae'' (from Greek ὀρθός, ''orthós'' 'straight' + μύξα, ''mýxa'' 'mucus') is a family of negative-sense RNA viruses. It includes seven genera: ''Alphainfluenzavirus'', ''Betainfluenzavirus'', '' Gammainfluenzavirus'', ' ...
es at
The Institute for Genomic Research (TIGR). Prior to this project, only a handful of flu genomes were publicly available. Their proposal was approved by the
National Institutes of Health
The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the lat ...
(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
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Research goals
The project makes all sequence data publicly available through GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
, an international, NIH-funded, searchable online database.
This research helps to provide international researchers with the information needed to develop new vaccine
A vaccine is a biological preparation that provides active acquired immunity to a particular infectious or malignant disease. The safety and effectiveness of vaccines has been widely studied and verified. s, therapies and diagnostics, as well as improve understanding of the overall molecular evolution of Influenza
Influenza, commonly known as "the flu", is an infectious disease caused by influenza viruses. Symptoms range from mild to severe and often include fever, runny nose, sore throat, muscle pain, headache, coughing, and fatigue. These symptoms ...
and other genetic factors that determine their virulence. Such knowledge could not only help mitigate the impact of annual influenza epidemic
Flu season is an annually recurring time period characterized by the prevalence of an outbreak of influenza (flu). The season occurs during the cold half of the year in each hemisphere. It takes approximately two days to show symptoms. Influe ...
s, 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
Influenza A virus subtype H3N2 (A/H3N2) is a subtype of viruses that causes influenza (flu). H3N2 viruses can infect birds and mammals. In birds, humans, and pigs, the virus has mutated into many strains. In years in which H3N2 is the predomina ...
(human), H1N1
In virology, influenza A virus subtype H1N1 (A/H1N1) is a subtype of influenza A virus. Major outbreaks of H1N1 strains in humans include the Spanish flu, the 1977 Russian flu pandemic and the 2009 swine flu pandemic. It is an orthomyxoviru ...
(human), and H5N1
Influenza A virus subtype H5N1 (A/H5N1) is a subtype of the influenza A virus which can cause illness in humans and many other animal species. A bird-adapted strain of H5N1, called HPAI A(H5N1) for highly pathogenic avian influenza virus of type ...
(avian).[
]
Affiliations
The project is funded by the National Institute of Allergy and Infectious Diseases
The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services (HHS). NIAID's ...
(NIAID) which is a component of the NIH, which is an agency of the United States Department of Health and Human Services
The United States Department of Health and Human Services (HHS) is a cabinet-level executive branch department of the U.S. federal government created to protect the health of all Americans and providing essential human services. Its motto is ...
.
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
The Icahn School of Medicine at Mount Sinai (ISMMS or Mount Sinai), formerly the Mount Sinai School of Medicine, is a private medical school in New York City. It is the academic teaching arm of the Mount Sinai Health System, which manages eight ...
in New York, Jill Taylor of the Wadsworth Center
The Wadsworth Center, located in Albany, New York, is the research-intensive public health laboratory of the New York State Department of Health.
History
The Wadsworth Center, originally the New York State's Antitoxin Laboratory, was established i ...
at the New York State Department of Health
The New York State Department of Health (NYSDOH) is the department of the New York state government responsible for public health. It is headed by Health Commissioner Mary T. Bassett, who was appointed by Governor Hochul and confirmed by the S ...
, Lance Jennings of Canterbury Health Laboratories
Canterbury (, ) is a cathedral city and UNESCO World Heritage Site, situated in the heart of the City of Canterbury local government district of Kent, England. It lies on the River Stour.
The Archbishop of Canterbury is the primate of th ...
(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
Ilaria Capua (born 21 April 1966 in Rome) is an Italian virologist and former politician, best known for her research on influenza viruses, particularly avian influenza, and her efforts promoting open access to genetic information on emerging vi ...
of the Istituto Zooprofilattico Sperimentale delle Venezie (in Italy), who contributed a valuable collection of avian flu isolates (including multiple H5N1
Influenza A virus subtype H5N1 (A/H5N1) is a subtype of the influenza A virus which can cause illness in humans and many other animal species. A bird-adapted strain of H5N1, called HPAI A(H5N1) for highly pathogenic avian influenza virus of type ...
strains). Some of these avian isolates were described in a publication in ''Emerging Infectious Diseases'' in 2007.
Nancy Cox from the Centers for Disease Control and Prevention
The Centers for Disease Control and Prevention (CDC) is the national public health agency of the United States. It is a United States federal agency, under the Department of Health and Human Services, and is headquartered in Atlanta, Georgi ...
(CDC) and Robert Couch from Baylor College of Medicine
Baylor College of Medicine (BCM) is a medical school and research center in Houston, Texas, within the Texas Medical Center, the world's largest medical center. BCM is composed of four academic components: the School of Medicine, the Graduate S ...
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.
References
External links
Influenza Sequencing Project home page at JCVI
*
Influenza Research Database
Database of influenza sequences and related information.
{{Influenza
National Institutes of Health
Genome projects
Influenza