Katia Koelle Sarah Cobey Bryan Grenfell Mercedes Pascual
Epochal evolution shapes the phylodynamics of interpandemic influenza (H3N2)
DIMACS, 9-10 October 2006
HK68
EN72
VI75
TX77
BK79
SI87?
?
Pathogen diversity and cross-immunity
Modeling Cross-Immunity
• Strains with high sequence similarity must have high cross-immunity• Strains with low sequence similarity must have low cross-immunity
e.g. Gog & Grenfell, PNAS (2002)
Explaining limited diversity of hemagglutinin
Ferguson, Galvani, Bush, Nature (2003)
Explosive diversity
Strain-specific cross-immunity
Actual HA1phylogeny
Simulatedphylogeny
Explaining limited diversity
Strain-specific cross-immunity + generalized immunity
Years since infection
Imm
un
ity
Limited diversity
Ferguson, Galvani, Bush, Nature (2003)
• 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
Modeling cross-immunity between flu strains
• Consider the effect of this new mapping on the phylogenetics and dynamics (i.e. phylodynamics) of influenza H3N2
Unrooted ML trees of sequences in the HK68 and EN72 clusters
= 60-80%
= >90% = >90%
Influenza clusters
Cluster designations as in Smith et al. 2004
• Strains with high sequence similarity can have low cross-immunity• Strains with low sequence similarity can have almost complete cross-immunity
Topology of influenza clusters
Genotype cannot serve as a proxy for antigenic phenotype
STRAIN 1
Sequence (genotype)
…ATGATGTGCCGGAT…
…FLIMFYNKSR…
STRAIN 2
Sequence (genotype)
…ATGATCTGCCGGAT…
…FLIDFYNKSR…
Tertiary HA structure (phenotype)
Tertiary HA structure (phenotype)
Cross-immunity
Genotype-phenotypemapping?
Genotype-phenotype mapping for RNA 2o structures
More genotypes than phenotypes
genotype(sequence)
phenotype(shape)
Fontana & Schuster, JTB (1998)
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
Evolutionary dynamics on neutral networks
Avera
ge s
truct
ure
dis
tance
to t
arg
et
Fontana & Schuster, JTB (1998)
Neutral network mapping for proteins
• 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.
Lau and Dill
Bornberg-Bauer & Chan, PNAS (1999)
Implications for modeling cross-immunity
…FLIMFYNKSR…
Traditionalcross-immunity
models
Neutral network topology Bornberg-Bauer
Modeling influenza’s hemagglutinin
15 a.a.
(45 nucs.) 5 epitopes
Changing the shape of an epitope
15 a.a.
5 epitopes
• Adaptation of Kauffman’s NK model that generates neutral networks in genotype space (Newman and Engelhardt)
• Framework assumes epistatic or context-dependent interaction between amino acids located in the same epitope
3
Neutrality and sequence evolution:subbasins, portals, and epochal evolution
HK68
EN72
VI75
TX77
BK79
SI87?
?
Adapted (for flu ) from Crutchfield, 2002
Coupling to an epidemiological modelC
lust
ers
InfectedSusceptible Recovered
Adapted for clusters, from Gog & Grenfell, PNAS (2002)
Dynamic Consequences of Neutral Network Model
• Cluster transitions
• Peaks in incidence during
cluster transition years
• Refractory year
Years
Greene et al. (2006)
Comparison with observed influenza dynamics
0.1
Simulated tree
Observed HA tree(from Smith et al.
sequences)0.1
• Explosion of diversity within clusters• Cluster transitions cause selective sweeps• No need for generalized immunity to limit HA diversity
Phylogenetic Consequences
Expected pattern in genetic diversity arising from epochal evolution
Supporting empirical evidence
Influential sites modelOnly 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 modelChanges 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.
Notions of neutrality
See also Wagner, 2005 for a discussion on types of neutrality in non-flu systems
Epitope Residue Substitution Associated transition Clusters with neutral polymorphism at residueO 25 LI SY97-FU02
C 50 KR VI75-TX77 HK68 (K/R), BE89 (K/R), WU95 (I/K/R), SY97 (G/R)
RG SY97-FU02
C 53 ND EN72-VI75 TX77 (D/N), SI87 (D/N), BE92 (D/G), FU02 (D/N)
DN VI75-TX77
ND TX77-BK79
C 54 NS TX77-BK79 HK68 (N/S), TX77 (N/S), WU95 (G/S), SY97 (I/S)
E 62 IK TX77-BK79
KE WU95-SY97
E 75 HQ SY97-FU02 BE92 (H/N), WU95 (H/N)
E 82 EK VI75-TX77 TX77 (E/K), SI87 (E/K)
KE TX77-BK79
E 83 EK SY97-FU02 EN72 (K/T), SI87 (E/K)
A 122 TN HK68-EN72 SI87 (K/N), BE92 (K/N), WU95 (K/N)
A 124 GD BK79-SI87 BK79 (D/G/S), SI87 (D/E), BE92 (A/D/G/N), WU95 (D/G/S)
A 131 AT SY97-FU02 SI87 (A/T), SY97 (A/D)
A 133 NS TX77-BK79
SD BE89-BE92
A 137 NS EN72-VI75 HK68 (N/S), VI75 (G/S), BK79 (S/Y), SY97 (S/Y)
SY VI75-TX77
A 143 PS TX77-BK79 EN72 (P/T)
A 144 GD HK68-EN72 HK68 (D/G), BK79 (D/N/V), SI87 (I/V), SY97 (D/I/N/V)
A 145 SN EN72-VI75
NK SI87-BE89
KN BE89-BE92
NK BE92-WU95
A 146 GS TX77-BK79 HK68 (G/R), WU95 (G/S)
B 155 TY HK68-EN72
YH BK79-SI87
HT SY97-FU02
B 156 KE TX77-BK79 BK79 (E/K), SI87 (E/K)
EK BE89-BE92
KQ WU95-SY97
QH SY97-FU02
B 158 GE VI75-TX77 BE89 (D/E), BE92 (D/E)
EK WU95-SY97
B 160 TK TX77-BK79 EN72 (A/T), WU95 (K/R)
B 164 LQ EN72-VI75
QL VI75-TX77
D 172 DG TX77-BK79 TX77 (D/G), BE89 (D/G), BE92 (D/G), WU95 (D/G), SY97 (D/E)
D 174 FS EN72-VI75 BE89 (F/V)
SF VI75-TX77
B 188 ND HK68-EN72 HK68 (D/N), EN72 (D/N), BK79 (D/E), BE89 (D/E), WU95 (D/N)
B 189 QK HK68-EN72 BE92 (R/S)
KR BK79-SI87
B 190 ED BE89-BE92 EN72 (D/E), SI87 (D/E), BE89 (D/E), WU95 (D/V), SY97 (D/X)
B 193 SD EN72-VI75 EN72 (N/S), BK79 (K/N), SI87 (N/S), BE89 (K/N/S)
DN VI75-TX77
B 196 VA WU95-SY97 BK79 (I/V), BE89 (I/V), BE92 (I/V), SY97 (A/X)
B 197 QR TX77-BK79 BE92 (Q/R), WU95 (H/Q/R)
D 201 RK EN72-VI75 BE92 (G/K/R)
KR VI75-TX77
O 202 VI SY97-FU02
D 207 RK HK68-EN72 HK68 (K/R), WU95 (K/R), SY97 (K/R)
D 213 IV EN72-VI75 EN72 (I/V), BK79 (I/R/V)
VI VI75-TX77
D 217 IV EN72-VI75
VI TX77-BK79
O 222 WR SY97-FU02
O 225 GD SY97-FU02
D 230 IV EN72-VI75
VI VI75-TX77
D 244 VL TX77-BK79 HK68 (I/V), EN72 (L/V), TX77 (L/V)
E 260 MI VI75-TX77 BE92 (I/L)
E 262 TN BE89-BE92 TX77 (K/N), BK79 (K/N), SI87 (K/N), BE89 (I/T), BE92 (K/N), WU95 (N/S)C 276 NK WU95-SY97 HK68 (A/T), BE92 (I/N/T), WU95 (N/T)
C 278 IS EN72-VI75 HK68 (I/V), BE89 (N/S), BE92 (K/N/S), WU95 (N/S)
HK68 (I/K/R/S), EN72 (I/N/R/S), VI75 (K/N), BE92 (K/N), WU95 (K/N), SY97 (K/N)
HK68 (I/K/V), EN72 (I/M), VI75 (I/K), TX77 (I/K), SI87 (E/K), BE92 (E/K)
HK68 (D/N), BK79 (N/S), BE89 (N/S), BE92 (D/N), WU95 (D/N)
Importance of genetic background, i.e.
context-dependency
Influential sites
Pair
wis
e n
ucle
oti
de
diff
ere
nces in
HA
1
Boom-and-bust of genetic diversity empirically supported
Observed pattern in genetic diversity
Diversification within clusters cannot be rejectedunder the null, neutral model of random speciation.
Observations of tree balance
0.1
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.
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.)
Derek Smith, Ron Fouchier, Sharon Greene, Cecile Viboud, Maciej Boni
Jamie Lloyd-Smith, Igor Volkov, Mary PossCIDD postdoctoral fellowship (K.K.)
Patterns of influenza phylodynamics (H3N2)
1. Annual outbreaks
2. Genetic drift
3. Genetic change Antigenic change
Fitch et al. (1997)
Greene et al. (2006)
Smith et al. (2004)
Patterns of genetic diversity
Characteristics of Influenza Evolution
Sequential replacement of clusters
Season
Clu
ste
r #
Antigenic clusters
Smith et al., Science (2004)
Characteristics of Influenza Evolution
Gradual genetic change Punctuated antigenic change
Smith et al., Science (2004)
Ge
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An
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