Disease

troduction to Epidemiology, 4th Ed., Merrill & Timmreck

Computational
Epidemiology
CMPS 5323-

Definition
A condition of the body, or some part or organ of
the body, in which its functions are disturbed or
deranged; a morbid physical condition; a
departure from the state of health, especially
when caused by structural change. Oxford
English Dictionary

Disease Classification
Infectious Invading organisms (pathogens)
Communicable Infectious disease that can be

transferred
Vertical transmission parent to child
Horizontal transmission infected to susceptible

Acute Generally severe, relatively short duration

Chronic Generally less severe, relatively long duration

Note: A communicable disease is always infectious, but an

infectious disease may or may not be communicable. Tetanus and
anthrax are both infectious, but not communicable.

Focus for this class:

Acute, Communicable

Introduction to Epidemiology, 4th Ed., Merrill & Timmre

Virus

https://www.youtube.com/watch?v=Rpj0emEGShQ

Bacteria

https://www.youtube.com/watch?

Transmission
Fomite An object that can harbor a disease
agent (doorknobs, towels, )
Vector Invertebrate that can transfer an
infectious agent among vertebrates (ticks,
mosquitoes, )
Reservoir Sources (living or nonliving) which
harbor diseases (standing water, vegetables,
mammals, )
Carrier A living reservoir that is infected by a
communicable disease, often lacking symptoms

Transmission Examples
Fomite Anthrax spread through the mail
Vector Malaria spread through mosquitos
Reservoir Cholera spread through

contaminated water
Carrier Typhoid Fever spread by Mary Mallon

Typhoid Mary
Typhoid Fever Infectious disease causing fever,

headache, rash, and diarrhea.

Early 1900s, Mary Mallon served as a cook in many
homes in New York City.
Believed to be responsible for 53 cases of typhoid
fever prior to quarantine.
1907-1910, Mary was confined by health officials
in a clinic on North Brother Island
Released in 1910, began working as a cook again
under the assumed name "Mary Brown", possibly
infecting more than 200 people.
Returned to quarantine voluntarily and died in
1938 of pneumonia.

Typhoid Mary

https://www.youtube.com/watch?v=bYjsmjgtgG4

Transmission
Factors Environment
Agent

Infectivity
Pathogenicity
Virulence
Immunogenicity
Antigenic stability
Survival

Triangle of
Epidemiology

Host

Weather
Housing
Geography
Occupational
setting
Air quality
Food

Age
Sex
Genotype
Behaviour
Nutritional status
Health status
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Common Disease Stages

1. Susceptible
2. Pre-symptomatic disease

Incubation period
Latency period
3. Clinical disease
4. Recovery, disability, or death

Cases
Index the first case identified
Primary the case that brings the infection into a
population
Secondary infected by a primary case
Tertiary infected by a secondary case
T

S
Susceptible
Immune
Pre-Symptomatic

P
S

S
T

Clinical
Question: Will the index case always be the same as the primary
case?
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Disease Timeline

AR Mikler, A Bravo-Salgado and CD Corley, Global Stochastic Contact

Modeling of Infectious Diseases

Disease Model - SIR

Susceptible
Removed

Infectious

transmission
coefficient,

removal rate,

Basic Assumptions:

Constant population size

Homogeneous mixing
No latent period
Once removed, always
removed

Kermack and McKendrick, 1927, A Contribution to the Mathematical Theory of

Epidemics

SIR Equations
dS
=SI

dt
dI
= SI I
dt
dR
=I
dt

Disease Progression SIR

Variations of SIR
Susceptible

Infectious

Removed

Basic SIR Model

Susceptible

Infectious

SIS Model
Susceptible

Expose
d or
Latent

Infectious

SEIR/SLIR Model

Removed

Measures of Disease Severity

R0 - Measure of secondary infections.
Duration - How long does it take for the

outbreak to run its course?

Overall Infections - What proportion of the

population becomes infected over the course

of the outbreak?

R0
Epidemiologic indicator
Average number of secondary infections

produced from a single infective in a totally

susceptible population
R0 > 1, Epidemic likely
R0 < 1, Disease should die out

Measuring R0
Should be measured early in the outbreak
Not practical to identify the primary case in a

real outbreak
Estimation techniques vary

Total
Infected?
(not exactly)

Immunity herd immunity

Let R represent the mean number of secondary cases in a population
where a proportion, p, are immune
R = R0 (1p)
R = R0 (p R0)
What proportion needs to be immune to prevent epidemics?
If R0 = 2, then R < 1 if the proportion of immune, p, is > 0.50
If R0 = 4, then R < 1 if the proportion of immune, p, is > 0.75
If the mean number of secondary cases should be < 1, then
R0 (p R0) < 1
p > (R0 1)/ R0
P > 1 1/ R0
If R0 =15, how large will p need to be to avoid an epidemic?
p > 1-1/15 = 0.94
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Levels of Disease
Occurrence

Sporadic level: occasional cases occurring at irregular

intervals

Endemic level: persistent occurrence with a low to moderate

level
Hyperendemic level: persistently high level of occurrence
Epidemic or outbreak: occurrence clearly in excess of the
expected level for a given time period
Pandemic: epidemic spread over several countries or
continents, affecting a large number of people

http://www.dorak.info

Cases

Endemic - Epidemic Pandemic

R>1
R=1
R<1

Time

Endemic
Transmission occur, but the number of cases remains
constant

Epidemic

The number of cases increase

Pandemic

When epidemics occur at several continents global

epidemic
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Number of Cases of a Disease

Endemic vs Epidemic

Endemic

Epidemic

Time
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