Comparative Genomics in the Influenza Research Database

1. Comparative Genomics in theInfluenza Research Database 17 June 2011 Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center

2. NIAID-sponsoredBioinformatics Resource Centers

3. www.fludb.org

9. Query Results

13. Workbench

14. Novel Data Features in IRD • CEIRS Surveillance Data • 3D Structures and Data Integration • Sequence Feature Variant Types

15. CEIRS

17. 3D 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

19. SFVT approach Influenza A_NS1_nuclear-export-signal_137(10) Influenza A_NS1_alpha-helix_171(17) VT-1 I F D R L E T L I L VT-2 I F N R L E T L I L VT-3 I F D R L E T IV L VT-4 L F D Q L E T L VS VT-5 I F D R L E N L T L VT-6 I F N R L E A L I L VT-7 I Y D R L E T L I L VT-8 I F D R L E T L V L VT-9 I F D R L E NIVL VT-10 I F E R L E T L I L VT-11 L F D QM E T L VS • 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

20. Influenza A Sequence Features as of10JUN2011 >4000SFs total

21. VT for SF8 (nuclear export signal)

22. VT-1 strains

23. Adaptive genetic drivers of species jump events

24. Flu pandemics of the 20th and 21st centuries initiated by species jump events • 1918 flu pandemic (Spanish flu) • subtype H1N1 (avian origin) • estimated to have claimed between 2.5% to 5.0% of the world’s population (20 > 100 million deaths) • Asian flu (1957 – 1958) • subtype H2N2 (avian origin) • 1 - 1.5 million deaths • Hong Kong flu (1968 – 1969) • subtype H3N2 (avian origin) • between 750,000 and 1 million deaths • 2009 H1N1 • subtype H1N1 (swine origin) • ~ 16,000 deaths as of March 2010

25. Pandemic stages Adaptive drivers

26. Basic reproductive number (R0) • Total number of secondary cases per case • Reasonable surrogate of fitness • Characteristics of pandemic viruses: • R0H >1, and • In genetic neighborhood of viruses with R0R>1 and R0H<1 • Adaptive drivers A1 A2 • Reservoir virus • (R0R>1 and R0H<<1) • Stuttering viruses • (R0R>1 and R0H<1) • Pandemic Viruses • (R0H >1)

27. Adaptive drivers Pepin KM et al. (2010) “Identifying genetics markers of adaptation for surveillance of viral host jump” Nature Reviews Microbiology 8: 802-814.

28. Stuttering transmission and adaptive drivers • Stuttering transmission can reveal adaptive drivers by evidence of convergent evolution • Odds of finding the same neutral mutation by chance in multiple species jumps is low • Therefore, finding same mutation in multiple independent species jump events is strong evidence for adaptive driver

29. Genetic convergence during species jump • Virus isolate groups from IRD • Avian H5N1 (PB2) from Southeast Asia* up to 2003 (260 records) – reservoirs of source viruses • Human H5N1 (PB2) from Southeast Asia 2003-present (165 records) – many examples of independent species jumps • Align amino acid sequence and calculate conservation score • Identify highly conserved positions in avian records (≤1/260 variants) (557positions/759) – functionally restricted in reservoir • Select subset in which two or more human isolates contained the same sequence variant – either due to human-human transmission or convergent evolution *China, Hong Kong, Indonesia, Thailand, Viet Nam

30. Strain Search – PB2 avian H5N1 Southeast Asia up to 2003

31. 260 PB2 records

32. Sequence variation analysis

33. Position order

34. Order by variation score

35. My Workbench

36. Convergent evolution candidates

37. E627K

38. E627K and species jump

39. K660R

40. Human influenza pandemics are initiated by species jump events followed by sustained human to human transmission (R0H>1) Multiple independent occurrences of the same mutation during stuttering transmission is evidence of convergent evolution of adaptive drivers – hypotheses for experimental testing Surveillance for adaptive drivers in reservoir species could help anticipate the next pandemic Summary N01AI40041

41. U.T. Southwestern Richard Scheuermann Burke Squires JyothiNoronha Victoria Hunt ShubhadaGodbole 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 WenjieHua Wei Jen Sanjeev Kumar Xiaomei Li Zaigang Liu Jason Lucas Michelle Lu Bruce Quesenberry Barbara Rotchford Hongbo Su Bryan Walters JianjunWang Sam Zaremba LiweiZhou Acknowledgments • IRD SWG • Gillian Air, OMRF • Carol Cardona, Univ. Minnesota • Adolfo Garcia-Sastre, Mt Sinai • ElodieGhedin, 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