Katia Koelle Sarah Cobey Bryan Grenfell Mercedes Pascual

1. Epochal evolution shapes the phylodynamics of interpandemic influenza (H3N2) Katia Koelle Sarah Cobey Bryan Grenfell Mercedes Pascual ? SI87 VI75 ? BK79 EN72 TX77 HK68 DIMACS, 9-10 October 2006

2. Pathogen diversity and cross-immunity s

3. e.g. Gog & Grenfell, PNAS (2002) Modeling Cross-Immunity • Strains with high sequence similarity must have high cross-immunity • Strains with low sequence similarity must have low cross-immunity

4. Explaining limited diversity of hemagglutinin Strain-specific cross-immunity Actual HA1 phylogeny Simulated phylogeny Explosive diversity Ferguson, Galvani, Bush, Nature (2003)

5. Immunity Years since infection Explaining limited diversity Strain-specific cross-immunity + generalized immunity Limited diversity Ferguson, Galvani, Bush, Nature (2003)

6. Modeling cross-immunity between flu strains • Can sequence evolution be used as a proxy for antigenic evolution when modeling influenza’s hemagglutinin? • (i.e. does genotype approximate phenotype?) • Propose alternative to this genotype-phenotype map for influenza’s hemagglutinin evolution • Consider the effect of this new mapping on the phylogenetics and dynamics (i.e. phylodynamics) of influenza H3N2

7. s= >90% s= >90% s= 60-80% Unrooted ML trees of sequences in the HK68 and EN72 clusters Influenza clusters Cluster designations as in Smith et al. 2004

8. Topology of influenza clusters • Strains with high sequence similarity can have low cross-immunity • Strains with low sequence similarity can have almost complete cross-immunity Genotype cannot serve as a proxy for antigenic phenotype

9. Sequence (genotype) Sequence (genotype) …ATGATGTGCCGGAT… …ATGATCTGCCGGAT… …FLIMFYNKSR… …FLIDFYNKSR… Tertiary HA structure (phenotype) Tertiary HA structure (phenotype) Cross-immunity STRAIN 1 STRAIN 2 Genotype-phenotype mapping?

10. phenotype (shape) genotype (sequence) More genotypes than phenotypes Genotype-phenotype mapping for RNA 2o structures Fontana & Schuster, JTB (1998)

11. Neutral networks Fontana & Schuster, JTB (1998)

12. Average structure distance to target Evolutionary dynamics on neutral networks Fontana & Schuster, JTB (1998) • “A neutral mutation does not change the phenotype but it does change the potential for change… What appears to be a sudden and abrupt change at the phenotypic level has been the result of neutral genetic drift.” -Fontana

13. Neutral network mapping for proteins Lau and Dill • Single sequence changes can result in large changes in protein conformation. • Changing a sequence by a large number of mutations may have no appreciable effect on protein conformation.

14. Traditional cross-immunity models …FLIMFYNKSR… Neutral network topology Implications for modeling cross-immunity Bornberg-Bauer & Chan, PNAS (1999) Bornberg-Bauer

15. Modeling influenza’s hemagglutinin 15 a.a. (45 nucs.) 5 epitopes

16. Changing the shape of an epitope • Adaptation of Kauffman’s NK model that generates neutral networks in genotype space (Newman and Engelhardt) 3 • Framework assumes epistatic or context-dependent interaction between amino acids located in the same epitope 15 a.a. 5 epitopes

17. Neutrality and sequence evolution:subbasins, portals, and epochal evolution ? SI87 VI75 ? BK79 EN72 TX77 HK68 Adapted (for flu  ) from Crutchfield, 2002

18. Susceptible Recovered Coupling to an epidemiological model Infected Clusters Adapted for clusters, from Gog & Grenfell, PNAS (2002)

19. Dynamic Consequences of Neutral Network Model Years • Cluster transitions • Peaks in incidence during • cluster transition years • Refractory year

20. Comparison with observed influenza dynamics Greene et al. (2006)

21. Phylogenetic Consequences Simulated tree Observed HA tree (from Smith et al. sequences) • Explosion of diversity within clusters • Cluster transitions cause selective sweeps • No need for generalized immunity to limit HA diversity

22. Expected pattern in genetic diversity arising from epochal evolution

23. Supporting empirical evidence

24. Notions of neutrality Influential sites model Only changes at very few sites can precipitate a cluster jump, and their ability to do so does not depend on the genetic background in which they occur. Genetic diversification within clusters does not facilitate adaptive change, and can be safely ignored. Context-dependent model Changes at most sites can precipitate a cluster jump if those changes occur in the right genetic background. Cluster innovations are guided by the process of neutral diffusion, via changing the genetic background of sequences. See also Wagner, 2005 for a discussion on types of neutrality in non-flu systems

25. Importance of genetic background, i.e. context- dependency Influential sites

26. Pairwise nucleotide differences in HA1 Observed pattern in genetic diversity Boom-and-bust of genetic diversity empirically supported

27. Observations of tree balance Diversification within clusters cannot be rejected under the null, neutral model of random speciation.

28. Conclusions • An alternative, empirically-supported model of influenza’s hemagglutinin evolution can account for both H3N2’s dynamic and the phylogenetic patterns of its HA1. • Incorporating appropriate genotype-phenotype maps for the effect of mutations at the phenotypic level may be important for understanding pathogen evolution.

29. Acknowledgments David Alonso, Stefano Allesina, Luis Chaves, Diego Moreno, Aaron King Center for the Study of Complex Systems NSF graduate student fellowship (S.C.) McDonnell Foundation (Centennial Fellowship to M.P.) Jamie Lloyd-Smith, Igor Volkov, Mary Poss CIDD postdoctoral fellowship (K.K.) Derek Smith, Ron Fouchier, Sharon Greene, Cecile Viboud, Maciej Boni

32. Patterns of influenza phylodynamics (H3N2) 1. Annual outbreaks Greene et al. (2006) Antigenic change 3. Genetic change 2. Genetic drift Fitch et al. (1997) Smith et al. (2004)

33. Patterns of genetic diversity

34. Antigenic clusters Characteristics of Influenza Evolution Sequential replacement of clusters Cluster # Season Smith et al., Science (2004)

35. Punctuated antigenic change Gradual genetic change Characteristics of Influenza Evolution Genetic distance from 1968 strain Antigenic distance from 1968 strain Smith et al., Science (2004)