Epochal evolution shapes the phylodynamics of
interpandemic influenza (H3N2)
Katia Koelle
Sarah Cobey
Bryan Grenfell
SI87
VI75
BK79
TX77
Mercedes Pascual
?
?
EN72
HK68
DIMACS, 9-10 October 2006
Pathogen diversity and cross-immunity
s
Modeling Cross-Immunity
e.g. Gog & Grenfell, PNAS (2002)
•
•
Strains with high sequence similarity must have high cross-immunity
Strains with low sequence similarity must have low cross-immunity
Explaining limited diversity of hemagglutinin
Strain-specific cross-immunity
Actual HA1
phylogeny
Simulated
phylogeny
Explosive diversity
Ferguson, Galvani, Bush, Nature (2003)
Explaining limited diversity
Immunity
Strain-specific cross-immunity + generalized immunity
Years since infection
Limited diversity
Ferguson, Galvani, Bush, Nature (2003)
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
Influenza clusters
s = >90%
s = >90%
s = 60-80%
Unrooted ML trees of sequences in the HK68 and EN72 clusters
Cluster designations as in Smith et al. 2004
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
STRAIN 1
STRAIN 2
Sequence (genotype)
Sequence (genotype)
…ATGATGTGCCGGAT…
…ATGATCTGCCGGAT…
…FLIMFYNKSR…
…FLIDFYNKSR…
Genotype-phenotype
mapping?
Tertiary HA structure
(phenotype)
Tertiary HA structure
(phenotype)
Cross-immunity
Genotype-phenotype mapping
for RNA 2o structures
phenotype
(shape)
genotype
(sequence)
More genotypes than phenotypes
Fontana & Schuster, JTB (1998)
Neutral networks
Fontana & Schuster, JTB (1998)
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
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.
Implications for modeling cross-immunity
Traditional
cross-immunity
models
…FLIMFYNKSR…
Neutral network
topology
Bornberg-Bauer & Chan, PNAS (1999)
Bornberg-Bauer
Modeling influenza’s hemagglutinin
15 a.a.
(45 nucs.)
5 epitopes
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
Neutrality and sequence evolution:
subbasins, portals, and epochal evolution
SI87
VI75
BK79
TX77
?
?
EN72
HK68
Adapted (for flu  ) from Crutchfield, 2002
Coupling to an epidemiological model
Infected
Recovered
Clusters
Susceptible
Adapted for clusters, from Gog & Grenfell, PNAS (2002)
Dynamic Consequences of
Neutral Network Model
Years
• Cluster transitions
• Peaks in incidence during
cluster transition years
• Refractory year
Comparison with observed
influenza dynamics
Greene et al. (2006)
Phylogenetic Consequences
Simulated tree
0.1
0.1
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
Expected pattern in genetic diversity
arising from epochal evolution
Supporting empirical evidence
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
Epitope
O
C
Residue
25
50
C
53
C
E
54
62
E
E
75
82
E
A
A
A
A
83
122
124
131
133
A
137
A
A
A
143
144
145
A
B
146
155
B
156
B
158
B
B
160
164
D
D
172
174
B
B
188
189
B
B
190
193
B
B
D
196
197
201
O
D
D
202
207
213
D
217
O
O
D
222
225
230
D
E
E
C
C
244
260
262
276
278
Substitution
LI
KR
RG
ND
DN
ND
NS
IK
KE
HQ
EK
KE
EK
TN
GD
AT
NS
SD
NS
SY
PS
GD
SN
NK
KN
NK
GS
TY
YH
HT
KE
EK
KQ
QH
GE
EK
TK
LQ
QL
DG
FS
SF
ND
QK
KR
ED
SD
DN
VA
QR
RK
KR
VI
RK
IV
VI
IV
VI
WR
GD
IV
VI
VL
MI
TN
NK
IS
Associated transition
SY97-FU02
VI75-TX77
SY97-FU02
EN72-VI75
VI75-TX77
TX77-BK79
TX77-BK79
TX77-BK79
WU95-SY97
SY97-FU02
VI75-TX77
TX77-BK79
SY97-FU02
HK68-EN72
BK79-SI87
SY97-FU02
TX77-BK79
BE89-BE92
EN72-VI75
VI75-TX77
TX77-BK79
HK68-EN72
EN72-VI75
SI87-BE89
BE89-BE92
BE92-WU95
TX77-BK79
HK68-EN72
BK79-SI87
SY97-FU02
TX77-BK79
BE89-BE92
WU95-SY97
SY97-FU02
VI75-TX77
WU95-SY97
TX77-BK79
EN72-VI75
VI75-TX77
TX77-BK79
EN72-VI75
VI75-TX77
HK68-EN72
HK68-EN72
BK79-SI87
BE89-BE92
EN72-VI75
VI75-TX77
WU95-SY97
TX77-BK79
EN72-VI75
VI75-TX77
SY97-FU02
HK68-EN72
EN72-VI75
VI75-TX77
EN72-VI75
TX77-BK79
SY97-FU02
SY97-FU02
EN72-VI75
VI75-TX77
TX77-BK79
VI75-TX77
BE89-BE92
WU95-SY97
EN72-VI75
Clusters with neutral polymorphism at residue
HK68 (K/R), BE89 (K/R), WU95 (I/K/R), SY97 (G/R)
TX77 (D/N), SI87 (D/N), BE92 (D/G), FU02 (D/N)
HK68 (N/S), TX77 (N/S), WU95 (G/S), SY97 (I/S)
HK68 (I/K/V), EN72 (I/M), VI75 (I/K), TX77 (I/K), SI87 (E/K), BE92
(E/K)
BE92 (H/N), WU95 (H/N)
TX77 (E/K), SI87 (E/K)
EN72 (K/T), SI87 (E/K)
SI87 (K/N), BE92 (K/N), WU95 (K/N)
BK79 (D/G/S), SI87 (D/E), BE92 (A/D/G/N), WU95 (D/G/S)
SI87 (A/T), SY97 (A/D)
HK68 (D/N), BK79 (N/S), BE89 (N/S), BE92 (D/N), WU95 (D/N)
HK68 (N/S), VI75 (G/S), BK79 (S/Y), SY97 (S/Y)
EN72 (P/T)
HK68 (D/G), BK79 (D/N/V), SI87 (I/V), SY97 (D/I/N/V)
HK68 (I/K/R/S), EN72 (I/N/R/S), VI75 (K/N), BE92 (K/N), WU95
(K/N), SY97 (K/N)
HK68 (G/R), WU95 (G/S)
Importance of genetic
background, i.e.
BK79 (E/K), SI87 (E/K)
BE89 (D/E), BE92 (D/E)
EN72 (A/T), WU95 (K/R)
TX77 (D/G), BE89 (D/G), BE92 (D/G), WU95 (D/G), SY97 (D/E)
BE89 (F/V)
contextdependency
HK68 (D/N), EN72 (D/N), BK79 (D/E), BE89 (D/E), WU95 (D/N)
BE92 (R/S)
EN72 (D/E), SI87 (D/E), BE89 (D/E), WU95 (D/V), SY97 (D/X)
EN72 (N/S), BK79 (K/N), SI87 (N/S), BE89 (K/N/S)
BK79 (I/V), BE89 (I/V), BE92 (I/V), SY97 (A/X)
BE92 (Q/R), WU95 (H/Q/R)
BE92 (G/K/R)
HK68 (K/R), WU95 (K/R), SY97 (K/R)
EN72 (I/V), BK79 (I/R/V)
HK68 (I/V), EN72 (L/V), TX77 (L/V)
BE92 (I/L)
TX77 (K/N), BK79 (K/N), SI87 (K/N), BE89 (I/T), BE92 (K/N), WU95
(N/S) (A/T), BE92 (I/N/T), WU95 (N/T)
HK68
HK68 (I/V), BE89 (N/S), BE92 (K/N/S), WU95 (N/S)
Influential sites
Pairwise nucleotide
differences in HA1
Observed pattern in genetic diversity
Boom-and-bust of genetic diversity empirically supported
Observations of tree balance
0.1
Diversification within clusters cannot be rejected
under the null, neutral model of random speciation.
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 genotypephenotype 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.)
Jamie Lloyd-Smith, Igor Volkov, Mary Poss
CIDD postdoctoral fellowship (K.K.)
Derek Smith, Ron Fouchier, Sharon Greene, Cecile Viboud, Maciej Boni
Patterns of influenza phylodynamics (H3N2)
1. Annual outbreaks
Greene et al. (2006)
3.
Genetic change
Antigenic change
2. Genetic drift
Fitch et al. (1997)
Smith et al. (2004)
Patterns of genetic diversity
Characteristics of Influenza Evolution
Sequential replacement of clusters
Cluster #
Antigenic clusters
Season
Smith et al., Science (2004)
Characteristics of Influenza Evolution
Punctuated antigenic change
Smith et al., Science (2004)
Antigenic distance from 1968 strain
Genetic distance from 1968 strain
Gradual genetic change