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Overview Simple models HIV case study Conclusions References Eco-evolutionary virulence of pathogens: the devil is (still) in the details Ben Bolker, McMaster University Departments of Mathematics & Statistics and Biology University of Tennessee 15 September 2016
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Page 1: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Eco-evolutionary virulence of pathogens:the devil is (still) in the details

Ben Bolker, McMaster UniversityDepartments of Mathematics & Statistics and Biology

University of Tennessee

15 September 2016

Page 2: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 3: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Acknowledgements

People Arjun Nanda and Dharmini Shah; Christophe Fraser;Daniel Park

Support NSF IRCEB grant 9977063; QSE3 IGERT; NSERCDiscovery grant

Page 4: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 5: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Host-pathogen evolutionary biology

Why?Intellectual merit

Coevolutionary loopsCryptic effectsEco-evolutionary dynamics (Luo and Koelle, 2013)Lots of data (for humans)

Broader applicationsMedicalConservation and managementOutreach

Page 6: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Host-pathogen evolutionary biology

Why?Intellectual merit

Coevolutionary loopsCryptic effectsEco-evolutionary dynamics (Luo and Koelle, 2013)Lots of data (for humans)

Broader applicationsMedicalConservation and managementOutreach

Page 7: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Virulence: definitions

General public: badnessPlant biologists: infectivityEvolutionists: loss of host fitnessTheoreticians: rate of host mortality

Page 8: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolution of virulence evolution theory

Classical avirulence theoryAnderson & May/Ewald virulence as an evolved (adaptive) trait.

Tradeoff theory, modes of transmission.post-Ewald mathematical models based on R0

Now tradeoff backlashwithin-host dynamics/multi-level modelseco-evolutionary dynamicshost effects: resistance vs tolerance vs virulence

Page 9: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolution of virulence evolution theory

Classical avirulence theoryAnderson & May/Ewald virulence as an evolved (adaptive) trait.

Tradeoff theory, modes of transmission.post-Ewald mathematical models based on R0

Now tradeoff backlashwithin-host dynamics/multi-level modelseco-evolutionary dynamicshost effects: resistance vs tolerance vs virulence

Page 10: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolution of virulence evolution theory

Classical avirulence theoryAnderson & May/Ewald virulence as an evolved (adaptive) trait.

Tradeoff theory, modes of transmission.post-Ewald mathematical models based on R0

Now tradeoff backlashwithin-host dynamics/multi-level modelseco-evolutionary dynamicshost effects: resistance vs tolerance vs virulence

Page 11: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolution of virulence evolution theory

Classical avirulence theoryAnderson & May/Ewald virulence as an evolved (adaptive) trait.

Tradeoff theory, modes of transmission.post-Ewald mathematical models based on R0

Now tradeoff backlashwithin-host dynamics/multi-level modelseco-evolutionary dynamicshost effects: resistance vs tolerance vs virulence

Page 12: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Basic tradeoff theory: assumptions

Homogeneous, non-evolving hostsNo super- or coinfectionHorizontal, direct transmissionTradeoff between rate of transmissionand length of infectious periodInfectious period ∝ 1/clearance rate

Page 13: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Tradeoffs, R0, and r

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 14: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Tradeoffs, R0, and r

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 15: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Tradeoffs, R0, and r

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 16: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 17: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Epidemiological model

SIR model

Constant population size(birth=death)

Rescale: µ = 1, N = 1(time units of host lifespan)

I

S

disease−

mortality(α)induced

mortality(µ)

birth

R

infection (β)

recovery

Page 18: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Epidemiological model

SIR model

Constant population size(birth=death)

Rescale: µ = 1, N = 1(time units of host lifespan)

I

S

disease−

mortality(α)induced

mortality(µ)

birth

R

infection (β)

recovery

Page 19: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Epidemiological model

SIR model

Constant population size(birth=death)

Rescale: µ = 1, N = 1(time units of host lifespan)

I

S

disease−

mortality(α)induced

mortality(µ)

birth

R

infection (β)

recovery

Page 20: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

The model (2): evolutionary dynamics

Incorporate trait dynamicsStandard quantitative genetics model (Abrams, 2001):

Fitness depends on mean trait value (α)and ecological context (proportion susceptible)Constant additive genetic variance Vg

Trait evolves toward increased fitness:rate proportional to ∆fitness/∆trait

Page 21: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

The model (2): evolutionary dynamics

Incorporate trait dynamicsStandard quantitative genetics model (Abrams, 2001):

Fitness depends on mean trait value (α)and ecological context (proportion susceptible)Constant additive genetic variance Vg

Trait evolves toward increased fitness:rate proportional to ∆fitness/∆trait

Page 22: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

The model (2): evolutionary dynamics

Incorporate trait dynamicsStandard quantitative genetics model (Abrams, 2001):

Fitness depends on mean trait value (α)and ecological context (proportion susceptible)Constant additive genetic variance Vg

Trait evolves toward increased fitness:rate proportional to ∆fitness/∆trait

Page 23: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

The model (2): evolutionary dynamics

Incorporate trait dynamicsStandard quantitative genetics model (Abrams, 2001):

Fitness depends on mean trait value (α)and ecological context (proportion susceptible)Constant additive genetic variance Vg

Trait evolves toward increased fitness:rate proportional to ∆fitness/∆trait

Page 24: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolutionary dynamics, cont.

Virulence

Fitn

ess

(w)

frac inf=0.1

Page 25: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Evolutionary dynamics, cont.

Virulence

Fitn

ess

(w)

frac inf=0.1

frac inf=0.3

Page 26: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Power-law tradeoff curves

Virulence

Tran

smis

sion

β(α) = cα1 γ

c = 2, γ = 2

c = 1, γ = 2

c = 1, γ = 3

Page 27: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 28: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Transient virulence

Selection differs between theoutbreak phases(Frank, 1996; Day and Proulx,2004)

endemic phase selection forper-generation offspringproduction: maximize R0,βN/(α + µ)

epidemic phase selectionfor per-unit-time offspringproduction: maximize r ,βN − (α + µ)

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 29: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Transient virulence

Selection differs between theoutbreak phases(Frank, 1996; Day and Proulx,2004)

endemic phase selection forper-generation offspringproduction: maximize R0,βN/(α + µ)

epidemic phase selectionfor per-unit-time offspringproduction: maximize r ,βN − (α + µ)

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 30: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Transient virulence

Selection differs between theoutbreak phases(Frank, 1996; Day and Proulx,2004)

endemic phase selection forper-generation offspringproduction: maximize R0,βN/(α + µ)

epidemic phase selectionfor per-unit-time offspringproduction: maximize r ,βN − (α + µ)

Disease−induced mortality

Transmissionrate

µ 0 1 2 3 4 5

Page 31: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Transient emerging virulence

When a parasite previously in eco-evolutionary equilibriumemerges in a new host population (at low density) it will showa transient peak in virulence as it spreads

How big is the peak? Does it matter?

Page 32: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 33: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Model parameters

Parameterc Transmission

scaleγ Transmission

curvatureI (0) Initial

epidemic sizeVg Genetic variance

AlternativeR∗

0 Equilibrium R0

α∗ Equilibriumvirulence

1/N0 Inversepopulation size

Page 34: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Example

Time

Fra

ctio

n in

fect

ive

0.00

0.05

0.10

0.15

0 10 20 30

Vg = 5, c = 3, I(0) = 0.001, γ = 2

(R0* = 1.5, α* = 1, N = 1000)

1.0

1.2

1.4

1.6

1.8

2.0

α

Page 35: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Response variables

Time

peaktime

peak height(α)

Page 36: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Peak height

Equilibrium transmission (R0*)

Equ

ilibr

ium

viru

lenc

e (α

* )

1

10

100

1000

1.1 2 5 10 50

1.025

CV

g=

0.1

1.025

1.05

1.1 2 5 10 50

1.05

1.075

1.5

CV

g=

0.5

1.5

2.01

10

100

1000

1.5

2.01

10

100

1000

1.5

2.02.5

3.0

I(0) = 10−2 C

Vg

=1

1.1 2 5 10 50

1.5

2.0

2.53.0

3.5

I(0) = 10−3

1.52.0

2.53.0

3.5

4.0

I(0) = 10−4

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

Page 37: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Estimates for emerging pathogens

Order of magnitude estimates for some emerging high-virulencepathogens:

Pathogen R∗0 α∗ Reference

SARS 3 640 Anderson et al. (2004)West Nile 1.61–3.24 639 Wonham et al. (2004)

HIV 1.43 6.36 Velasco-Hernandez et al. (2002)myxomatosis 3 5 Dwyer et al. (1990)

Page 38: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Emerging pathogens: where are we?

CVg = 0.5, I (0) = 10−3 (middle panel):

R0

Equ

ilibr

ium

viru

lenc

e (α

* )

1

10

100

1000

1.1 2 5 10 501.5

2.0

SARS

HIV

WNV

MYXO

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

Page 39: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Outline

1 OverviewThe evolution of host-pathogen theoryToy models

2 Transient virulence: simple modelsOverviewToy modelMyxomatosis model

3 Transient virulence: HIV case study

4 Conclusions

Page 40: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Overview

Mosquito-borne viral disease of rabbitsBenign in South American rabbits,quickly fatal in European rabbitsWell characterized (Fenner et al., 1956; Dwyer et al., 1990)

Page 41: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxomatosis tradeoff curve

Scaled virulence

Tota

ltra

nsm

ission

0 2 4 6 8 10 12

0.0

0.2

0.4

0.6

eq epi

Page 42: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Estimating evolvability (Vg)

Key parameter: genetic variance in virulence (evolvability)Despite case studies of rapid pathogen evolution:

myxomatosis (Dwyer et al., 1990)syphilis (Knell, 2004)serial passage experiments (Ebert, 1998)Plasmodium chabaudi (Mackinnon and Read, 1999)

we can rarely estimate Vg reliably

Page 43: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Estimating evolvability (Vg)

Key parameter: genetic variance in virulence (evolvability)Despite case studies of rapid pathogen evolution:

myxomatosis (Dwyer et al., 1990)syphilis (Knell, 2004)serial passage experiments (Ebert, 1998)Plasmodium chabaudi (Mackinnon and Read, 1999)

we can rarely estimate Vg reliably

Page 44: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxomatosis grades over time (Fenner et al., 1956)

1950 1954 1956 1961 1965 1968 1972 1978

Proportion

0.0

0.2

0.4

0.6

0.8

1.0Virulence grade

I II III IV V

Page 45: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxomatosis variance over time

Date

Gen

etic

varia

nce(

Vg)

0

10

20

30

40

1950 1960 1970

Vg= 10

Vg= 2.5

Vg= 40

Page 46: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxomatosis virulence dynamics: power-law tradeoff

Date

Scal

edvi

rule

nce

0

5

10

15

20

25

1950 1960 1970

h=2.5

h=10

h=40

Page 47: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxomatosis virulence dynamics: realistic tradeoff

Date

Scal

edvi

rule

nce

0

5

10

15

20

25

1950 1960 1970

h=40

h=10

h=2.5

Page 48: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxo virulence: equilibrium start, power-law tradeoff

Date

Scal

edvi

rule

nce

0

5

10

15

1950 1955

h=40h=10h=2.5

Page 49: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Myxo virulence: equilibrium start, realistic tradeoff

Date

Scal

edvi

rule

nce

0

5

10

15

1950 1955

h=40h=10h=2.5

Page 50: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Simple models: conclusions

basic intuition about transient peak is correctrough estimates justify that eco-evo dynamics can matterdetails matter: shape of tradeoff curve, variance dynamics

Page 51: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Phage dynamics (Berngruber et al., 2013)

Experimental evolution: phages started as endemic or epidemic

Page 52: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

HIV: background

Set-point viral load quantifies virus exploitation of host

Page 53: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

SPVL mediates a transmission/virulence tradeoff

transmission probability duration (years)

0.0

0.1

0.2

0.3

0

5

10

15

20

25

0.0 2.5 5.0 7.5 0.0 2.5 5.0 7.5log10 set-point viral load

Page 54: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

HIV tradeoff curve

0 10 20 30 40 50 60

0.0

0.1

0.2

0.3

0.4

0.5

Scaled virulence

Tran

smission

rate

eq epi

Page 55: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

SPVL dynamics

(Shirreff et al., 2011; Herbeck et al., 2014)

Page 56: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Pair-formation dynamics (Champredon et al., 2013)

Page 57: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Model structure

Six models:extra-pair contact [“epc”] ×instantaneous pair-formation [“instswitch”]“implicit” model: approx. (Shirreff et al., 2011)

random-mixing (no structure)Latin hypercube sampling over epidemic parameters(Champredon et al., 2013)

Page 58: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

SPVL trajectories

random pairform+epc pairform

instswitch+epc instswitch implicit

3

4

5

3

4

5

0 200 400 600 0 200 400 600 0 200 400 600

time (years)

popu

latio

n m

ean

set−

poin

t vira

l loa

d (lo

g 10)

Page 59: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Univariate summaries

peak SPVL

peak time (years)

equilibriumSPVL

relativepeakSPVL

time

viru

slo

ad

Page 60: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Results: univariate summaries

peak time peak SPVL

equilibrium SPVL relative peak

random

pairform+epc

pairform

instswitch+epc

instswitch

implicit

random

pairform+epc

pairform

instswitch+epc

instswitch

implicit

0 100 200 300 3.0 3.5 4.0 4.5 5.0

3 4 1.1 1.2 1.3 1.4 1.5value

Page 61: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Bivariate summaries

peak

tim

epe

ak S

PV

Lre

lativ

e pe

ak

equilibrium SPVL peak time peak SPVL

0

100

200

300 ●

●●

● ●

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Page 62: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Conclusions

HIV: extra-pair contact washes out structural effectsmore complexity isn’t always better —need the right complexity(the modeling question)models purport to predict HIV evolution(Payne et al., 2014; Roberts et al., 2015; Herbeck et al., 2016):can we trust them?

Page 63: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

Crome (1997) on theory

Real research is best for toy problems, and toy research isoften all one can do on real problems . . . Never do toyresearch on toy problems, and recognize the extraordinarylimitations in attempting real research on real problems.. . .Recognize that someone might take your advice based onyour research. Try to estimate what the costs will be ifyou are wrong.

Page 64: evolution of virulence: devil in the details

Overview Simple models HIV case study Conclusions References

ReferencesAbrams, P.A., 2001. Ecol Lett, 4:166–175.Anderson, R.M., Fraser, C., et al., 2004. Phil Trans R Soc London B, 359(1447):1091–1105.Berngruber, T.W., Froissart, R., et al., 2013. PLoS Pathog, 9(3):e1003209.

doi:10.1371/journal.ppat.1003209.Champredon, D., Bellan, S., and Dushoff, J., 2013. PLoS ONE, 8(12):e82906.

doi:10.1371/journal.pone.0082906.Crome, F.H.J., 1997. In W.F. Laurance and J. Richard O. Bierregard, editors, Tropical Forest

Remnants: Ecology, Management and Conservation of Fragmented Communities, chapter 31, pages485–501. University of Chicago Press, Chicago.

Day, T. and Proulx, S.R., 2004. Amer Nat, 163(4):E40–E63.Dwyer, G., Levin, S., and Buttel, L., 1990. Ecol Monog, 60:423–447.Ebert, D., 1998. Science, 282(5393):1432–1435.Fenner, F., Day, M.F., and Woodroofe, G.M., 1956. J Hyg (London), 54(2):284–302.Frank, S.A., 1996. Q Rev Biol, 71(1):37–78.Herbeck, J., Mittler, J., et al., 2016. bioRxiv, page 039560.Herbeck, J.T., Mittler, J.E., et al., 2014. PLoS Computational Biology, 10(6):e1003673.

doi:10.1371/journal.pcbi.1003673.Knell, R.J., 2004. Proc R Soc London B, 271:S174–S176.Luo, S. and Koelle, K., 2013. The American Naturalist, 181(S1):S58–S75. ISSN 0003-0147.

doi:10.1086/669952.Mackinnon, M.J. and Read, A.F., 1999. Evolution, 53(3):689–703.Payne, R., Muenchhoff, M., et al., 2014. Proceedings of the National Academy of Sciences,

111(50):E5393–E5400. ISSN 0027-8424, 1091-6490. doi:10.1073/pnas.1413339111.Roberts, H.E., Goulder, P.J., and McLean, A.R., 2015. Journal of The Royal Society Interface,

12(113):20150888.Shirreff, G., Pellis, L., et al., 2011. PLoS Computational Biology, 7(10). ISSN 1553-734X.

doi:10.1371/journal.pcbi.1002185. WOS:000297262700019.Velasco-Hernandez, J.X., Gershgorn, H.B., and Blower, S.M., 2002. Lancet, 2:487–493.Wonham, M.J., de Camino-Beck, T., and Lewis, M.A., 2004. Proc R Soc London B, 271:501–507.


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