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

NIAID-sponsored Bioinformatics Resource Centers

Query Results

Workbench

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

CEIRS

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

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) 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)

Influenza A Sequence Features as of 10JUN2011 >4000 SFs total

VT for SF8 (nuclear export signal)

VT-1 strains

ADAPTIVE GENETIC DRIVERS OF SPECIES JUMP EVENTS

Flu pandemics of the 20 th and 21 st 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) – 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

Pandemic stages Adaptive drivers

Basic reproductive number (R 0 ) Total number of secondary cases per case Reasonable surrogate of fitness Characteristics of pandemic viruses: – R 0 H >1, and – In genetic neighborhood of viruses with R 0 R>1 and R 0 H<1 Adaptive drivers Pandemic Viruses (R 0 H >1) Pandemic Viruses (R 0 H >1) Stuttering viruses (R 0 R>1 and R 0 H<1) Stuttering viruses (R 0 R>1 and R 0 H<1) Reservoir virus (R 0 R>1 and R 0 H<<1) Reservoir virus (R 0 R>1 and R 0 H<<1) A1A2

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

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

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

Strain Search – PB2 avian H5N1 Southeast Asia up to 2003

260 PB2 records

Sequence variation analysis

Position order

Order by variation score

My Workbench

Convergent evolution candidates

E627K

E627K and species jump

K660R

Summary Human influenza pandemics are initiated by species jump events followed by sustained human to human transmission (R 0 H>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 N01AI40041

41 Acknowledgments U.T. Southwestern – Richard Scheuermann – Burke Squires – Jyothi Noronha – 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 USDA – David Suarez Sage Analytica – Robert Taylor – Lone Simonsen CEIRS Centers