Richard H. Scheuermann, Ph.D.
Department of Pathology, UT Southwestern
March 30, 2011
Virus Bioinformatics Resource Centers – ViPR & IRD
Take home messages
• NIAID Bioinformatics Resource Centers– Virus Pathogen Resource (ViPR; www.viprbrc.org )– Influenza Research Database (IRD; www.fludb.org )
• Free and open access virus database and analysis resources• Comprehensive data collection
– Sequence, structure, function, phenotype, surveillance, clinical, immune response
• Integrated– Surveillance metadata with sequence– Sequence features and sequence conservation with protein structures
• Development and adoption of data standards• Data sharing infrastructure and policies• Novel approach to identification of genetic determinants of important virus
characteristics– Influenza NS1 nuclear export signal and host range
NIAID RESEARCH RESOURCES
DMID Resources
DMID Resources List
BRCs
Category A Pathogens
Category B Pathogens
Category C Pathogens
pathogenportal.net
Pathogen Portal
VIPR RESOURCE
Home pagewww.viprbrc.org
13 virus families
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Taxonomy browser expanded
Genome statistics
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Analysis
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DATA INTEGRATION
IRDwww.fludb.org
DATA STANDARDS
CEIRS Network
Other Data Standards
• Non-human mammalian surveillance• Virus isolate characteristics• Immuno-assays• Virus passage• Virus nomenclature• Clinical data
SURVEILLANCE
DATA SHARING
Policies
• Sequences – 30 days• Initial Surveillance Record – 90 days• Completed Virus Isolated Record – 1 year
Submission Infrastructure
DO VARIATIONS IN NS1 SEQUENCE FEATURES INFLUENCE INFLUENZA VIRUS HOST RANGE?
SFVT approach
VT-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)• alpha-helical region, host protein binding site, enzyme active site, 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• Genotype-phenotype association statistical analysis (virulence, pathogenesis, host range, immune
evasion, drug resistance)• While phylogenetics reflect evolutionary history of the virus, it is the focused regions in the viral
genes/proteins that effect protein expression, structure and/or protein function that are responsible for important virus characteristics
Influenza A_NS1_alpha-helix_171(17)
Protein Subtype Functional Structural Immune Epitopes Total CountPB2 - 7 10 564 585
PB1-F2 - 2 2 - 6PB1 - 6 5 733 744PA - 1 29 534 565
NS2 - 2 3 78 83NS1 - 21 15 458 494NP - 10 25 472 512NA N1 10 26 113 153NA N2 9 59 106 180M2 - 4 10 96 116M1 - 12 14 286 312HA H1 4 37 335 376HA H2 4 10 20 34HA H3 2 59 390 481HA H5 3 14 40 65HA H7 - 1 2 3
Total 97 319 4227 4709
Influenza A Sequence Features as of January 2011
ViPR SFVTs
• Starting with 3 species– DENV = 192 SF’s– HCV = 335 SF’s– Pox = 14 genes, 295 total SF’s– HSV coming soon w/ DBP
• Beginning automatic definition for other virus families–Most SF’s pulled from• UniProtKB protein annotations• IEDB immune epitopes (future)
NS1 Sequence Features
VT for SF8 (nuclear export signal)
VT-1 strains
VT for SF8 (nuclear export signal)
Causes of apparent NS1 VT-associated host range restriction
• Virus spread = capability + opportunity– Phenotypic property of the virus – limited capacity– Founder effect – limited opportunity
• Restricted spatial-temporal distribution
• Sampling bias – assumption of random sampling– Oversampling – avian H5N1 in Asia; 2009 H1N1– Undersampling – large and domestic cats
• Linkage to causative variant
VT-10 strains
VT for SF8 (nuclear export signal)
VT lineages
VT-10 lineage
VT-4 lineage
VT-4 strains
VT-4 lineage = B allele/group
VT-15 & VT-8 lineages
VT-5 strains
Summary
• Compiling list of all known influenza protein sequence features (SFs) in IRD• Observed dramatic skewing in NS1 SFVT host distributions• In some cases, attributable to sampling biases
– VT-1 and Avian H5N1 due to Asian sampling in mid-2000's– VT-2 and human due to 2009 pandemic H1N1– VT-11 and Other (Environment) in Delaware Bay
• Performing multivariate statistical analysis to control for confounding variables
• In other cases, attributable to founder effects– VT-13 and -14 and Viet Nam 2003
• However, in other cases these explanations do not appears to be consistent with the data, suggesting that these may indeed be NS1-mediated host range restrictions– Equine VT-10 lineage– Avian VT-4 lineage (B allele/group)– Human VT-8 lineage– Human VT-15 lineage
• Nuclear export vs linkage disequilibrium?
63
• U.T. Southwestern– Richard Scheuermann– Burke Squires– Jyothi Noronha– Mengya Liu– Victoria Hunt– Shubhada Godbole– Brett Pickett– Ayman Al-Rawashdeh
• 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
• SFVT experts– Gillian Air, OMRF– Toru Takimoto, Rochester– Summer Galloway, Emory– Robert Lamb, Northwestern– Benjamin Hale, Mt. Sinai
• USDA– David Suarez
• Sage Analytica– Robert Taylor– Lone Simonsen
• CEIRS Centers
Influenza SFVT Acknowledgments
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