Influenza Genome Sequencing Project
Encyclopedia
The Influenza Genome Sequencing Project (IGSP) is an American-based genome project
aimed at improving the availability of genomic sequence data from influenza viruses and related information.
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).
Sequence information generated by the project has been placed into public domain
through GenBank
.
, 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. 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
, an international, NIH-funded, searchable online database.
This research model is hoped 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. 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
.
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.
(human), H1N1
(human), and H5N1
(avian).
(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.
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.
Genome project
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features...
aimed at improving the availability of genomic sequence data from influenza viruses and related information.
The project is funded by the National Institute of Allergy and Infectious Diseases
National Institute of Allergy and Infectious Diseases
The National Institute of Allergy and Infectious Diseases is one of the 27 institutes and centers that make up the National Institutes of Health , an agency of the United States Department of Health and Human Services...
(NIAID), a division of the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
(NIH), and has been operating out of the NIAID Microbial Sequencing Center at The Institute for Genomic Research
The Institute for Genomic Research
The Institute for Genomic Research was a non-profit genomics research institute founded in 1992 by Craig Venter in Rockville, Maryland, United States. It is now a part of the J. Craig Venter Institute.-History:...
(TIGR).
Sequence information generated by the project has been placed into public domain
Public domain
Works are in the public domain if the intellectual property rights have expired, if the intellectual property rights are forfeited, or if they are not covered by intellectual property rights at all...
through GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
.
Origins
In early 2004, David Lipman, Lone Simonsen, Steven SalzbergSteven Salzberg
Steven Salzberg is an American Biologist and Computer Scientist who since 2011 has been a Professor of Medicine and Biostatistics in the Institute of Genetic Medicine at Johns Hopkins School of Medicine...
, and a consortium of other scientists wrote a proposal to begin sequencing large numbers of influenza viruses at The Institute for Genomic Research
The Institute for Genomic Research
The Institute for Genomic Research was a non-profit genomics research institute founded in 1992 by Craig Venter in Rockville, Maryland, United States. It is now a part of the J. Craig Venter Institute.-History:...
(TIGR). Prior to this project, only a handful of flu genomes were publicly available. Their proposal was approved by the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
(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
Research goals
The project is making all sequence data publicly available through GenBankGenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
, an international, NIH-funded, searchable online database.
This research model is hoped 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
Evolution of Influenza
The virus causing influenza is one of the best known pathogens found in various species. In particular, the virus is found in birds as well as mammals including horses, pigs, and humans. The phylogeny, or the evolutionary history of a particular species, is an important component when analyzing...
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 influenza viruses
Influenza pandemic
An influenza pandemic is an epidemic of an influenza virus that spreads on a worldwide scale and infects a large proportion of the human population. In contrast to the regular seasonal epidemics of influenza, these pandemics occur irregularly, with the 1918 Spanish flu the most serious pandemic in...
.
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.
Results
The project completed its first genomes in March 2005 and has rapidly accelerated since. As of 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 H3N2H3N2
Influenza A virus subtype H3N2 is a subtype of viruses that cause influenza . H3N2 Viruses can infect birds and mammals. In birds, humans, and pigs, the virus has mutated into many strains...
(human), H1N1
H1N1
'Influenza A virus is a subtype of influenza A virus and was the most common cause of human influenza in 2009. Some strains of H1N1 are endemic in humans and cause a small fraction of all influenza-like illness and a small fraction of all seasonal influenza. H1N1 strains caused a few percent of...
(human), and H5N1
H5N1
Influenza A virus subtype H5N1, also known as "bird flu", A or simply H5N1, is a subtype of the influenza A virus which can cause illness in humans and many other animal species...
(avian).
Affiliations
The project is funded by the National Institute of Allergy and Infectious DiseasesNational Institute of Allergy and Infectious Diseases
The National Institute of Allergy and Infectious Diseases is one of the 27 institutes and centers that make up the National Institutes of Health , an agency of the United States Department of Health and Human Services...
(NIAID) which is a component of the NIH, which is an agency of the United States Department of Health and Human Services
United States Department of Health and Human Services
The United States Department of Health and Human Services is a Cabinet department of the United States government with the goal of protecting the health of all Americans and providing essential human services. Its motto is "Improving the health, safety, and well-being of America"...
.
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
Peter Palese
Peter Palese, Ph.D, is an American microbiologist and Professor and Chair of the Department of Microbiology at the Mount Sinai Medical Center in New York City, and an expert in the field of RNA viruses....
of the Mount Sinai School of Medicine
Mount Sinai School of Medicine
Mount Sinai School of Medicine is an American medical school in the borough of Manhattan in New York City, currently ranked among the top 20 medical schools in the United States. It was chartered by Mount Sinai Hospital in 1963....
in New York, Jill Taylor of the Wadsworth Center
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. The Wadsworth Center is dedicated to science in the pursuit of health.-History:...
at the New York State Department of Health
New York State Department of Health
The New York State Department of Health, ', is the governmental body responsible for public health in the state of New York. The cabinet-level department is headed by the Health Commissioner, a position held since January 24, 2011 by Nirav R. Shah, M.D., M.P.H.....
, 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
H5N1
Influenza A virus subtype H5N1, also known as "bird flu", A or simply H5N1, is a subtype of the influenza A virus which can cause illness in humans and many other animal species...
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
Centers for Disease Control and Prevention
The Centers for Disease Control and Prevention are a United States federal agency under the Department of Health and Human Services headquartered in Druid Hills, unincorporated DeKalb County, Georgia, in Greater Atlanta...
(CDC) and Robert Couch from Baylor College of Medicine
Baylor College of Medicine
Baylor College of Medicine, located in the Texas Medical Center in Houston, Texas, USA, is a highly regarded medical school and leading center for biomedical research and clinical care...
also joined the project in 2006, contributing over 150 influenza B isolates.