mathematical modeling and simulation for the diffusion of ...ivorra/pres/diego-presentation.pdf ·...
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Mathematical modeling and simulation
for the diffusion of an epidemic of
classical swine fever within and
between farms
Diego de Pereda
Benjamin Ivorra
Ángel Manuel Ramos
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Introduction to epidemiology
Outlines
Numerical simulations
Mathematical modeling
• Basic concepts
• SIR models
• Application to Classical Swine Fever
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Introduction to
epidemiology
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DEFINITION:
Epidemiology consist on the study of spread
patterns and associated risk factors of the
diseases of humans or animals
The main objectives are:
Describe the distribution
Prevention and control
Indentify risk factors
Definition and objectives
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Historical evolution
Historically, epidemics had a
great impact on populations,
causing demographic changes
Nowadays, some epidemics are
persistent (HIV, malaria, tuberculosis,
flu, …)
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Historical evolution
Some important achievements:
Daniel Bernouilli (1760): First “statistical”
model for smallpox virus variolation
William Heaton (1906): Discrete time model
to explain the recurrence of measles
Ronald Ross (1911): PDE model to study the
link between malaria and mosquitoes
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Differences between diseases
Ways of transmission:
Between humans or animals (flu)
By vectors, such as insects (malaria)
By the environment (cholera)
Bacteria. No immunity
Virus. Possible immunity
Infectious agents (for instance):
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Possible states
Susceptible
Sane individuals and susceptible of being infected
Infected
Infected individuals in latent phase, can’t infect others
Infectious
Infected individuals that can infect others
Clinical signs
Infectious individuals with clear clinical signs of disease
Resistant
Individuals with immunity to the disease
S + E + I + C + R = 1
S
E
I
C
R
Population density distribution
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DEFINITION:
R0 is the expected number of secondary cases produced by a
single infection in a completely susceptible population
then infection can be endemic
If
b(a) is the average number of infected individuals that an infectious will
produce per unit time when infected for a total time a
F(a) is the probability that a newly infected individual remains infectious
for at least time a
00 )()( daaFabR
Basic reproduction number (R0)
then infection will disappear from population
If 10R
10R
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Mathematical
modeling
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New infectious individuals depends on density
of susceptible S and infectious I states
Permanent resistant state R in virus infections (S+I+R=1)
Infectious individuals remain 1/α days until becoming resistant
S I Rβ SI α I
-β SI
β SI - α I
α I
S´
I´
R´
=
=
=0R
Deterministic SIR models
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SIR models: Natural death
Individuals have a life expectancy of 1/μ days
Total population is constant (#births = #deaths)
S I Rβ SI α I
μ I μ Rμ S
μ
-β SI + μ (1-S)
β SI - α I - μ I
α I - μ R
S´
I´
R´
=
=
=0R
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SIR models: Disease deathA proportion θ of individuals that left
infectious state I, die because of the disease
Total population stills constant (#births = #deaths)
S I Rβ SI (1-θ)α I
μ I μ Rμ S
μ + θα I
-β SI + μ (1-S) + θα I
β SI - α I - μ I
(1-θ)α I - μ R
S´
I´
R´
=
=
=
θα I
0R
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R0 value
And apply formula 0R
aaaa eeaF )()1()(
)(ab
Prob. remains
infectious
Infected pigs
per unit of time
Steady
states
All states must
be positive
001All sane
(unstable if R0>1)
Stable
endemic
solution))1((
)()1(
))1((
)(
R0 value study
R0 > 10)(
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10R10R
Evolution depending on R0
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Numerical
simulations
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Classical swine fever (CSF)
Highly contagious viral disease
caused by Flaviviridae Pestivirus
High disease mortality
Symptoms: fever, hemorrhages, ...
Consequences:
What it is:
Severe economical consequences
Affects domestic and wild pigs
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CSF world distribution
Reports of Classical Swine Fever since 1990
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Our scenario
Geographical Situation
Type of production
Our data on farms (provided by province of Segovia)
Number of pigs
Ways of transmission:
Sanitary group
Integration group
Movement of pigs
Local spread
Direct contact
within a farm
Sanitary spread
Integration spread
Movement of pigs
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Farm distribution
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SEICR farm model
S I R
μS
μ + θαC
E
μE μC θαC
C
μI μR
βS(I+C) εE (1-θ)αCδI
7 d. 21 d. 30 d.
One SEICR model for each farm
New infected individuals depends on density
of susceptible and infectious (I+C) states
-βS(I+C) + μ(1-S) + θαC
βS(I+C) – εE – μE
εE – δI – μI
δI – (1-θ)αC – μC – θαC
(1-θ)αC – μR
S´
E´
I´
C´
R´
=
=
=
=
=
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CSF spread
within a farm
Value of β:
1.85
8.52
5.18
Fattening (young) Farrowing (old) Farrow-to-finish (mix)
Quick spread
within the farm
Type of farm:
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Hybrid model algorithm
t Farm 1
SEICR
model
Interaction
between
farms
Control
measures
(if any)
t+1 Farm 1
Farm 2
SEICR
model
Interaction
between
farms
Control
measures
(if any)
Farm 2
Farm 3
SEICR
model
Interaction
between
farms
Control
measures
(if any)
Farm 3
…
…
Differential equations model with discrete time
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Movement
of pigs
Movements between Segovia’s farms in 2008
When infected pigs are translated,
epidemic spreads to destination farm
Way of transmission:
Our data on pig movements (provided by the province of Segovia)
Origen and destination farms
Quantity of moved We run a one-year simulation
repeating these movementsDate of movement
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Movement
of pigs
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Sanitary and
Integration groups
Contact with infected trucks or
infected fomites (food, materials, …)
Ways of transmission:
Daily rates of infection are 0.0068 for Integration
and 0.0065 for Sanitary
Farms with same sanitary or integration group are
susceptible to spread epidemic between each other
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Sanitary and
Integration groups
Sanitary Integration
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Daily rate of infection depends
on the distance between farms
Local
spread
140
90
38
19
250m
500m
1000m
2000m
Airborne spread
or fomits
Ways of transmission:
Radius:
x 10-4
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Local
spread
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Considering all
risk factors
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Control
measures
Infected farm is depopulated:
all animals are sacrificed
Quarantine during 90 days: Incoming
and out-coming movements are limited
Detection of infection:
We consider than an infected farm is detected
when there is, at least, one pig with clinical signs1*NC
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Control
measures
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Control
measures
No control
measures
With control
measures
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Conclusions
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Conclusions
Mathematical modeling and analysis of a CSF epidemic
Simulations with real data
Infection spreads quickly within and between farms
Local spread is the most relevant risk factor
Control measures are essentials
Try other control measures
Results:
In a future:
Work done:
Compute R0 value for this hybrid model
Quantify economical consequences
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