www.fludb.org
Bioinformatics Resource CentersInfluenza Research Database (IRD)
Virus Pathogen Database and Analysis Resource (ViPR)
8 December 2010
Richard H. Scheuermann, Ph.D.Department of Pathology
U.T. Southwestern Medical Center
www.fludb.org NIAID Scientific Resources
http://www.niaid.nih.gov/labsandresources/resources/Pages/default.aspx
www.fludb.org DMID Resources List
www.fludb.orgDMID BRC Resources
www.fludb.orgCategory A Pathogens
www.fludb.orgCategory B Pathogens
www.fludb.orgCategory A Pathogens
www.fludb.orgDMID BRC Resources
www.fludb.orgBRC Portal
www.fludb.org ViPR
www.viprbrc.org
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Influenza Research Database (IRD)
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www.fludb.orgIRD Home Page
www.fludb.orgPublic Health Impact of Influenza
• Seasonal flu epidemics occur yearly during the fall/ winter months and result in 3-5 million cases of severe illness worldwide.
• More than 200,000 people are hospitalized each year with seasonal flu-related complications in the U.S.
• Approximately 36,000 deaths occur due to seasonal flu each year in the U.S.
• Populations at highest risk are children under age 2, adults age 65 and older, and groups with other comorbidities.
Source: World Health Organization - http://www.who.int/mediacentre/factsheets/fs211/en/index.html
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Known flu pandemics occurring during the 20th and 21st centuries
1) 1918 flu pandemic (Spanish flu) - Subtype H1N1
- the most severe pandemic- estimated to have claimed between 2.5% to 5.0% of the world’s population (20 > 100 million deaths)
2) Asian flu (1957 - 1958)- Subtype H2N2- 1 > 1.5 million deaths
3) Hong Kong flu (1968 - 1969)- Subtype H3N2- between 750,000 and 1 million deaths
4) 2009 H1N1- Subtype H1N1- > 16,000 deaths as of March 2010
www.fludb.orgInfluenza Virus
Orthomyxoviridae familyNegative-strand RNASegmentedEnveloped
8 RNA segments encode11 proteinsClassified based on serology of HA and NA
www.fludb.orgIRD Overview
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www.fludb.orgData - sequenceIRD Data
www.fludb.orgData - surveillanceIRD Data
www.fludb.orgSurveillance detail pageImplicit versus explicit semantics
www.fludb.orgStrain detail page
www.fludb.orgSegment detail page 1
www.fludb.orgSegment detail page 2
www.fludb.orgSegment searchtaxonomy gazeteer
www.fludb.orgData – 3D protein structureIRD Data
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3D protein structure search results
www.fludb.org3D Structures & Integration
• Visualize protein structure in 3D• Display sequence conservation heat map on
the structure• Highlight sequence features (epitopes, etc.)• Download highlighted protein structure image
www.fludb.org3D Structure
www.fludb.orgAnalysis and Visualization Tools
www.fludb.orgMy Workbench
www.fludb.orgIRD Summary
• Funded by U.S. National Institute of Allergy and Infectious Diseases (NIAID)
• Free and open access with no use restrictions• Developed by a team of research scientists, bioinformaticians
and professional software developers• Comprehensive collection of public data• Novel derived data, novel analytical tools, unique functions
• Integration – Integration – Integration• www.fludb.org
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• U.T. Southwestern– Richard Scheuermann– Burke Squires– Jyothi Noronha– Victoria Hunt– Shubhada Godbole– Brett Pickett– Mengya Liu
• MSSM– Adolfo Garcia-Sastre– Eric Bortz– Gina Conenello– Peter Palese
• Vecna– Chris Larsen– Al Ramsey
• LANL– Catherine Macken– Mira Dimitrijevic
• U.C. Davis– Nicole Baumgarth
• Northrop Grumman– Ed Klem– Mike Atassi– Kevin Biersack– Jon Dietrich– Wenjie Hua– Wei Jen– Sanjeev Kumar– Xiaomei Li– Zaigang Liu– Jason Lucas– Michelle Lu– Bruce Quesenberry– Barbara Rotchford– Hongbo Su– Bryan Walters– Jianjun Wang– Sam Zaremba– Liwei Zhou
• IRD SWG– Gillian Air, OMRF– Carol Cardona, Univ. Minnesota– Adolfo Garcia-Sastre, Mt Sinai– Elodie Ghedin, Univ. Pittsburgh– Martha Nelson, Fogarty– Daniel Perez, Univ. Maryland– Gavin Smith, Duke Singapore– David Spiro, JCVI– Dave Stallknecht, Univ. Georgia– David Topham, Rochester– Richard Webby, St Jude
• USDA– David Suarez
• Sage Analytica– Robert Taylor– Lone Simonsen
• CEIRS Centers
Acknowledgements
www.fludb.orgSFVT approachVT-1 I F D R L E T L I LVT-2 I F N R L E T L I LVT-3 I F D R L E T I V LVT-4 L F D Q L E T L V SVT-5 I F D R L E N L T LVT-6 I F N R L E A L I LVT-7 I Y D R L E T L I LVT-8 I F D R L E T L V LVT-9 I F D R L E N I V LVT-10 I F E R L E T L I LVT-11 L F D Q M E T L V S
Influenza A_NS1_nuclear-export-signal_137(10)
• Identify regions of protein/gene with known structural or functional properties – Sequence Features (SF)• an alpha-helical region, the binding site for another protein, an enzyme active site, an
immune epitope• Determine the extent of sequence variation for each SF by defining each unique sequence as a
Variant Type (VT)• High-level, comprehensive grouping of all virus strains by VT membership for each SF
independently
Influenza A_NS1_alpha-helix_171(17)
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