Disease

Computational Epidemiology CMPS 5323-101Introduction to Epidemiology, 4th Ed., Merrill & Timmreck

DefinitionA 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 ClassificationInfectious – 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.

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

Focus for this class: Acute, Communicable

Virus

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

Bacteria

https://www.youtube.com/watch?v=TVfmUfr8VPA&spfreload=1

TransmissionFomite – 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 ExamplesFomite – Anthrax spread through the mail

Vector – Malaria spread through mosquitos

Reservoir – Cholera spread through contaminated water

Carrier – Typhoid Fever spread by Mary Mallon

Typhoid MaryTyphoid 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 IslandReleased 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

Agent

Host

Environment

• Age• Sex• Genotype• Behaviour• Nutritional status• Health status

• Infectivity• Pathogenicity• Virulence• Immunogenicity• Antigenic stability• Survival

• Weather• Housing• Geography• Occupational setting• Air quality• Food

Transmission Factors

Triangle of Epidemiology

http://www.dorak.info

Common Disease Stages

1. Susceptible2. Pre-symptomatic disease

• Incubation period• Latency period

3. Clinical disease4. Recovery, disability, or death

• 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

P

S

S

T

Susceptible

Immune

Pre-Symptomatic

Clinical

ST

Cases

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

http://www.dorak.info

Disease Timeline

AR Mikler, A Bravo-Salgado and CD Corley, Global Stochastic Contact Modeling of Infectious Diseases

Disease Model - SIRSusceptible Infectious

Removed

transmission coefficient,

removal rate,

Basic Assumptions:

• Constant population size• Homogeneous mixing• No latent period• Once removed, always

removedKermack and McKendrick, 1927, A Contribution to the Mathematical Theory of Epidemics

SIR Equations

=

=

dS= βSI

dtdI

βSI IdtdR

Idt

Disease Progression - SIR

Variations of SIR

Susceptible Infectious Removed

Basic SIR Model

Susceptible Infectious

SIS Model

Susceptible Infectious Removed

SEIR/SLIR Model

Exposed or Latent

Measures of Disease SeverityR0 - 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 immunityLet R represent the mean number of secondary cases in a population where a proportion, p, are immune

R = R0 (1–p) 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 > 0.50If 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) < 1p > (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

The higher R0, the higher proportion of immune required for herd immunity

http://www.dorak.info

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

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Endemic - Epidemic - Pandemic

EndemicTransmission occur, but the number of cases remains constant

EpidemicThe number of cases increase

PandemicWhen epidemics occur at several continents – global epidemic

Time

Case

s

R = 1

R > 1

R < 1

http://www.dorak.info

Endemic EpidemicNu

mb

er

of

Case

s of

a D

isease

Time

Endemic vs Epidemic

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