1. Richard H. Scheuermann, Ph.D. Department of Pathology, UT Southwestern March 30, 2011 Virus Bioinformatics Resource Centers – ViPR & IRD

2. Take home messages NIAID Bioinformatics Resource Centers – Virus Pathogen Resource (ViPR; www.viprbrc.org )www.viprbrc.org – Influenza Research Database (IRD; www.fludb.org )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

3. NIAID RESEARCH RESOURCES

4. DMID Resources

5. DMID Resources List

6. BRCs

7. Category A Pathogens

8. Category B Pathogens

9. Category C Pathogens

10. pathogenportal.net Pathogen Portal

11. VIPR RESOURCE

12. Home page www.viprbrc.org

13. 13 virus families

14. Taxonomy browser

15. Taxonomy browser expanded

16. Genome statistics

17. Search, analyze and save

18. Search

19. Analysis

20. Workbench

21. DATA INTEGRATION

22. IRD www.fludb.org

24. DATA STANDARDS

25. CEIRS Network

27. Other Data Standards Non-human mammalian surveillance Virus isolate characteristics Immuno-assays Virus passage Virus nomenclature Clinical data

28. SURVEILLANCE

38. DATA SHARING

39. Policies Sequences – 30 days Initial Surveillance Record – 90 days Completed Virus Isolated Record – 1 year

40. Submission Infrastructure

43. DO VARIATIONS IN NS1 SEQUENCE FEATURES INFLUENCE INFLUENZA VIRUS HOST RANGE?

44. SFVT approach VT-1I F D R L E T L I L VT-2I F N R L E T L I L VT-3I F D R L E T I V L VT-4L F D Q L E T L V S VT-5I F D R L E N L T L VT-6I F N R L E A L I L VT-7I Y D R L E T L I L VT-8I F D R L E T L V L VT-9I F D R L E N I V L VT-10I F E R L E T L I L VT-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)

45. ProteinSubtypeFunctionalStructuralImmune EpitopesTotal Count PB2-710564585 PB1-F2-22-6 PB1-65733744 PA-129534565 NS2-237883 NS1-2115458494 NP-1025472512 NAN11026113153 NAN2959106180 M2-41096116 M1-1214286312 HAH1437335376 HAH24102034 HAH3259390481 HAH53144065 HAH7-123 Total9731942274709 Influenza A Sequence Features as of January 2011

46. 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)

47. NS1 Sequence Features

48. VT for SF8 (nuclear export signal)

49. VT-1 strains

50. VT for SF8 (nuclear export signal)

52. 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

53. VT-10 strains

54. VT for SF8 (nuclear export signal)

55. VT lineages

56. VT-10 lineage

57. VT-4 lineage

58. VT-4 strains

59. VT-4 lineage = B allele/group

60. VT-15 & VT-8 lineages

61. VT-5 strains

62. 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. 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