DISEASE

SIMULATIONS
Modeling Contagion in Human Populations
Anne F. Cross, PhD
Tulsa Community College
Adapted from Annenberg Learning (www.learner.og)
This lab uses a hypothetical human population with
various levels of disease, contagion and vaccination.
You will run the model several times and draw your
own conclusions about disease in human
populations.

You will also keep track of your data using the data
tables.
Overview

Human and animal diseases are often caused by viruses or bacteria. Over the past two hundred or so years, vaccines
have eradicated some of these diseases. Others have returned to haunt humans with new and ever mutating strains, or
revived when vaccination programs were interrupted. Communicable diseases may spread in different ways: through
blood, air, feces/urine, food, or water. The World Health Organization (WHO) and the Center for Disease Control (CDC)
keep constant watch over the most potentially dangerous diseases and the most likely threats to various world
populations.

New diseases (such as MRSA) and the possibility of a pandemic avian flu have also raised international concerns about
health. As populations grow, especially when packed densely as in urban areas, there is increased risk of disease
transmission. This lab will let you explore various diseases: Kold, a caricature of the common cold; Impfluenza, which
resembles influenza; Neasles, with the high transmission rate of measles; and Red Death, a fast-spreading epidemic
with a high mortality rate.

What factors come into play in the spread of these diseases? And what can we do to counter them?

THINGS to THINK ABOUT

Population mixing in a contagious area is analogous to increasing population density. Both increased density and
increased movement of people bring more contagious people into contact with susceptible people, thus increasing the
spread of disease. The rate of spread also has a lot to do with the nature of the disease: how long a sick person is
contagious, the method of transmission (air, water, food, bodily fluids), the transmission rate (i.e. the chance that any
particular encounter will transmit the disease), and the death rate due to the disease (Kold is nonlethal).

Disease spread is considered epidemic if it exceeds the norm, which differs depending on the disease in question. Less
lethal diseases will have higher transmission rates without a sense of emergency (such as the common cold or the
common flu) while a small increase above the norm in diseases such as tuberculosis, polio, HIV, Ebola, or other such
highly lethal or disabling viruses, results in a state of emergency. In addition, there are major differences between
bacterial and viral illnesses. Antibiotics work for bacterial disease, and sometimes vaccines can be developed for viral
disease. There isn't always a quick fix to an illness, however, since both bacteria and viruses mutate and alter their
genetic makeup, making previous treatments non-effective.

https://www.learner.org/series/the-habitable-planet-a-systems-approach-to-environmental-science/disease-lab/

Click on this link above to take you to the website. It will look like this:

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I have re-written the instructions for this lab on the pages below; however, if you need additional copies of the data
sheets or directions you may find them at the website.

You will need this website to access the SIMULATOR. Look for the simulator image and click on it to open it.

It will look like this. Note the location of the following buttons: LESSON, DISEASE, DETAILS (play with this later).

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LESSON 1 Step 1: SIMULATION - KOLD in medium-sized
population
Most diseases begin with what is called "the virgin field"—a scenario in which humans have no natural or man-made
immunity to the disease. To see the progress of a disease in a particular community:

1. PREDICT- how many sick days will be reported when you RUN:

i. Kold disease through a medium-sized population.

b. SET: LESSON to Virgin Field

c. SET: Population Mixing to NONE

d. SET: Simulation to 0 days

2. In this first run-through, we'll assume that the population does not move around the field; they interact with
their neighbors, but the contagion cannot travel long distances.

3. RUN the simulator three times for 100 days and RECORD the data in your table under Lesson 1.

a. Note that a Kold lasts 5 days (see the Details button next to Kold), so the number of Kold cases is
roughly the simulated number of sick days divided by 5.

KOLD: MEDIUM POPULATION DENSITY

Lesson 1 Population Starting Sick Days Contagious Contagion
Step 1 Number Number of Reported Rate
Contagious
People
Prediction 600 3 500 10 100

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 Simulation 600 3 807 0 161.4
Run 1
Simulation 600 3 737 0 147.4
Run 2
Simulation 600 3 582 0 116.4
Run 3

LESSON 1 Step 2: SIMULATION - KOLD: Low -and High-

Population Density
Unlike some of the other interactive labs, this model has some randomness built in to reflect the real spread of a
disease, which is a matter of probabilities. Despite this variability, you can get a sense for what effect each factor has
on disease spread.

1. PREDICT- The number of sick days that will be reported when you RUN:

i. The Kold disease through a low-density population.

b. SET: LESSON to Virgin Field

c. SET: Population Mixing to NONE

d. SET: Simulation days to 0

2. RUN the simulation three times for 100 day and record your data in your table under Lesson 1.

3. PREDICT- how many sick days will be reported when you RUN:

i. The Kold disease through a high-density population.

b. SET: LESSON to Virgin Field

c. SET: Population Mixing to NONE

d. SET: Simulation days to 0

4. RUN the simulation three times for 100 days and record your data in the following table.

KOLD: LOW Population Density vs. HIGH Population Density

Lesson 1: Population Population Starting Sick Days Contagious Contagion
Step 2 Number Density Number of Reported Rate
Contagious
People
Prediction 1 200 low 3 200 0 40
(low)
Simulation Run 200 low 3 42 0 8.4
1
Simulation Run 200 low 3 27 0 5.4
2
Simulation Run 200 low 3 52 0 10.4
3
Prediction 2 900 high 3 1600 0 320

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 (high)
Simulation Run 900 high 3 4392 0 878.4
1
Simulation Run 900 high 3 4382 0 876.4
2
Simulation Run 900 high 3 4377 0 875.4
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Questions:
Answer the following
1. What could be done to prevent the spread of the KOLD disease in a low population density?
Immediate quarantine of symptomatic people.

2. What kinds of challenges would high population density with the same KOLD disease?
It spreads much quicker, and one person is a vector to more people.

VACCINATIONS in POPULATIONS
Vaccinating a population has a similar effect to changing the population density. An immune person is no longer a
vehicle for transmitting the disease, thus lowering the effective density of the population. Since we can't control
population density in most cases, vaccination is one of the best means to prevent the spread of disease, not just to the
vaccinated individuals, but to the population as a whole. Stopping or slowing the mixing of people, via quarantine, or
closing businesses and schools, is also an option, with similar net effect. Although the common cold doesn't have a
vaccine available, you may choose to return to the simulator and experiment with the possibilities of immunizing a
percentage of your population to Kold.

There are four main types of vaccine: those containing a killed pathogen, those containing live strains of a pathogen,
those containing toxoids (the compounds produced by a pathogen that cause a human reaction, as opposed to injecting
with the microorganism), and those containing subunits of the pathogen (such as antigens or other proteins that create
part of the physical makeup of the microorganism). Newer genetically targeted vaccines are being developed, but
although preliminary tests look very positive, the constantly mutating genetic makeup of the more dangerous diseases
prevents us from distributing a vaccine without caution.

LESSON 2 Step 1: SIMULATION – IMPFLUENZA with/without

VACCINATION
In this lesson we look at “Impfluenza”. Start by examining the disease propagation in a virgin field.
Click the Details button on Impfluenza and Kold to compare the differences between the two diseases. Based on these
differences and what you know about Kold, predict the sick days per capita and death rate for Impfluenza at medium
population and medium mixing.

In the simulator, select Lesson Vaccination, then set Vaccinated to None to provide the virgin field effect. Population
Density and Mixing should both be Medium. Then run the simulator to 100 days three times.

1. PREDICT- The number of sick days per capita and the death rate when you RUN:

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 i. Impfluenza disease through a medium-sized; medium density, unvaccinated population.

b. SET: LESSON to Vaccination field

c. SET: Population Mixing to MEDIUM

d. SET: Population Density to MEDIUM

e. SET: Vaccinated to NONE

f. SET: Simulation to 0 days

1. RUN - the simulation THREE TIMES for 100 days

2. RECORD - your DATA

IMPFLUENZA without VACCINATION (compare to KOLD data)

Lesson 2: Population Population Starting Sick Days Contagious Dead
Step 1 Number Density Number of Reported
Contagious
People
Prediction 600 M 3 700 0 3
(medium/medium)
Simulation 600 m 3 1371 0 13
Run 1
Simulation 600 m 3 1368 0 15
Run 2
Simulation 600 m 3 1500 0 15
Run 3

Answer the following Questions:

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 3. Compare your IMPFLUEZNA data to your KOLD data: 
a. Were your predictions correct? If not, why not?
No. I assumed with the lower sick days/contagious and higher death rate there
would be fewer total sick days.
b. How are the patterns in the IMPFLUEZNA data and the KOLD data similar? How do
they differ?
Three simulations isn’t enough for me to detect obvious patterns. It appears there
may be more stability in the numbers with Impfluenza vs. Kold, but again the
sample size is too small.
c. What are the data trends that you did not expect? What did you expect?
I clearly underestimated the number of sick days and deaths. I would love to
compare the differences once we adjust the population sizes.
d. Describe other observations of your data.
I have no further observations at this time.

4. You notice that IMPFLUENZA has a death rate; whereas, KOLD has no death rate. How
many people die, on average, when you run the simulator on the virgin field?
10.3

5. How does a death toll change precautionary factors? What kinds of precautions might you
take with IMPFLUENZA that you might not have taken with KOLD?

A death toll means the potential outcomes are worse, therefore the risk is higher and the
need for prevention greater. This is especially true if you can determine certain
populations or individuals within the population are more susceptible to the virus.

6. Would you consider the IMPFLUENZA death rate to warrant a “state of emergency”? How
high would the numbers have to be for this to happen?

I’m not sure what the trigger is for a state of emergency, but I would guess that the death
of approximately 3% of the population and a majority of the population falling ill with a
potentially-deadly disease might warrant such a declaration.

LESSON 2 Step 2. IMPFLUENZA with VACCINATION

In this step we vaccinate a certain percentage of the population against Impfluenza. This represents a real-life
scenario, where the country vaccinates a certain portion of its population against the expected influenza strains for
that year.

Select Lesson Vaccination. Predict and record the sick days per capita and death toll % at medium population and
medium mixing, with 50% of the population vaccinated. Run the simulator three times and record your data. Repeat
with 90% vaccinated. Compare your results to the table in Lesson 2 Step 1.

1. PREDICTION 1- How many sick days per capita? What is the percentage dead? When you RUN:

i. Impfluenza disease through a medium-sized; medium mixing population.

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 b. SET: LESSON to Vaccination field

c. SET: Population Mixing to MEDIUM

d. SET: Population Density to MEDIUM

e. SET: Vaccinated to 50%; change to 90% see what happens!

f. SET: Simulation to 0 days

2. RUN - the simulation THREE TIMES for 100 days

3. RECORD DATA (Lesson 2; Step 2; Prediction 1(medium/medium))

4. ANSWER: For the first set of parameters (medium/medium), how does the vaccine reduce sick days? How large a
percentage of the population would have to be immunized in order to bring the sick days per capita reliably below 0.1
per capita?

IMPFLUENZA: 50% VACCINATED_MEDIUM CONTACT_MEDIUM

DENSITY
Lesson 2: Population Population Starting Percentage Sick Days Contagious
Step 2 Mixing Density Number of of Reported
Contagious Population
People Affected
Prediction 1
m m 3 2 20 0
(medium/medium)
Simulation
m m 3 5 9 0
Run 1
Simulation
m m 3 4.5 81 0
Run 2
Simulation
m m 3 1.5 27 0
Run 3

Then change the parameters to high population and high mixing. Predict what will happen at 50% and 90% vaccination,
and run the simulator three times with each, recording your data for each run.

50%

Lesson 2: Population Population Starting Percentage Sick Days Contagious

Step 2 Mixing Density Number of of Reported
Contagious Population
People Affected
Prediction 1
h h 3 20 500 0
(medium/medium)
Simulation
h h 3 34..7 936 0
Run 1
Simulation
h h 3 33.6 906 0
Run 2
Simulation
h h 3 34.2 924 0
Run 3

90%

Lesson 2: Population Population Starting Percentage Sick Days Contagious

Step 2 Mixing Density Number of of Reported
Contagious Population

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 People Affected
Prediction 1
h h 3 5 50 0
(medium/medium)
Simulation
h h 3 1 27 0
Run 1
Simulation
h h 3 .2 6 0
Run 2
Simulation
h h 3 .2 7 1
Run 3

Answer the following Questions:

7. How does using vaccination compare to changing the population mixing or the population density?

Increasing the vaccination rate from 50% to 90% brought the numbers of sick days below those in a
medium/medium population with a 50% vaccination rate.

8. For the first set of parameters (medium/medium), how does the vaccine reduce sick days? How large a
percentage of the population would have to be immunized in order to bring the sick days per
capita reliably below 0.1 per capita?
First problem is I may have misunderstood that per capita is the same as the percentage of population
affected, so that may change how I answer this question. I was dividing the number of sick days by 3 (like we
did with the Kold) and then dividing that by the total population. An additional difficulty with answering this
question is that we only ran the simulation at 50% vaccination with a medium/medium setting, so I have no
direct comparison at medium/medium upon which to base this prediction. That being said, I believe that
around 80% is when populations are considered to have herd immunity, so that would be my guess.

5. PREDICTION 2: - How many sick days per capita? What is the percentage dead? When you RUN:
Impfluenza disease through a high-sized; high- mixing population.
a. SET: LESSON to Vaccination field

b. SET: Population Mixing to HIGH

c. SET: Population Density to HIGH

d. SET: Vaccinated to 50% ;change to 90% see what happens!

e. SET: Simulation to 0 days

6. RUN - the simulation THREE TIMES for 100 days

7. RECORD DATA (Lesson 2; Step 2; Prediction 2(high/high))

IMPFLUENZA: 50% VACCINATED HIGH CONTACT and HIGH DENSITY

Lesson 2: Population Population Starting Percentage Sick Days Contagious
Step 2 Mixing Density Number of of Reported
Contagious Population
People Affected
Predication 2
h h 3 34 920 0
(high/high)
Simulation
h h 3 36 972 0
Run 1

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Simulation
h h 3 26.8 723 0
Run 2
Simulation
h h 3 32.1 868 0
Run 3

Answer the following Questions:

9. How does using vaccination compare to changing the mixing or population density?

Vaccinations have a large downward effect that appears to keep the numbers lower than a much-smaller population
without vaccination would record.

10. For the second set of parameters (high/high), how does the vaccine reduce sick days? How large a percentage of the
population would have to be immunized in order to bring the sick days per capita reliably below 0.1 per capita?
First problem is I may have misunderstood that per capita is the same as the percentage of population affected, so
that may change how I answer this question. I was dividing the number of sick days by 3 (like we did with the Kold)
and then dividing that by the total population. That being said, I’m guessing that maybe as low as 95% you could
keep the rate below .1.

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LESSON 3 Step 1. PANDEMIC SIMULATION
What if we were to face an outbreak of a disease such as bird flu? In 1918-1919, the world experienced a pandemic
unlike anything seen since the Black Plague of the mid-14th century in Europe. The Spanish Flu, or La Grippe, killed
between 20 and 40 million people worldwide. In America alone, 28% of the population was infected with the virus, the
vast majority of whom where between the ages of 20 and 40. There was no method in place at that time to deal with a
pandemic with such a high transmission rate as well as a high death rate. The disease struck a virgin field.

In this lesson, imagine a new disease for which there is no vaccine and the death rate might be very high. Examine the
details of Red Death and predict how many sick days per capita and the death toll of this new disease in low population
and low mixing. Record the prediction in your table. To see if you're correct, set Vaccinated to None, run the
simulation three times, and record your data.

1. PREDICTION 1: - How many sick days per capita? What is the percentage dead? When you RUN:
RED DEATH disease through a low-sized; low- mixing population.
a. SET: LESSON to Pandemic

b. SET: Population Mixing to LOW

c. SET: Population Density to LOW

d. SET: Vaccinated NONE

e. SET: Simulation to 0 days

2. RUN - the simulation THREE TIMES for 100 days

3. RECORD DATA (Lesson 3; Step 1; Prediction 1(low/low))

4. PREDICTION 2: - How many sick days per capita? What is the percentage dead? When you RUN:
RED DEATH disease through a high-sized; high- mixing population.
a. SET: LESSON to Pandemic

b. SET: Population Mixing to HIGH

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 c. SET: Population Density to HIGH

d. SET: Vaccinated NONE

5. SET: Simulation to 0 days

6. RUN - the simulation THREE TIMES for 100 days

7. RECORD DATA (Lesson 3; Step 1; Prediction 2(high/high))

PANDEMIC SIMULATION 1
Lesson 3: Population Population Percent Starting Sick Days Contagious Immune Dead
Step 1 Mixing Density Vaccinated Number of Reported
Contagious
People
Prediction 1
L L 0 3 100 0 50 5
(low/low)
Simulation
L L 0 3 347 0 29 6
Run 1
Simulation
L L 0 3 87 0 7 2
Run 2
Simulation
L L 0 3 47 0 4 1
Run 3
Prediction 2
H H 0 3 6000 0 700 200
(high/high)
Simulation
H H 0 3 8997 0 747 153
Run 1
Simulation
H H 0 3 8997 0 711 189
Run 2
Simulation
H H 0 3 8997 0 737 163
Run 3

Answer the following Questions:

11. Would either of these scenarios be considered epidemic? Why or why not?
This disease in a high/ high scenario would absolutely be considered an epidemic. The directions for this
assignement were to consider an epidemic above “the norm”. Since everyone in the population was affected,
I’m going to suggest this is an epidemic.
In the low/low scenario, I’m not sure that we can consider it an epidemic since in one scenario only 5 total
people were affected.

12. What practical, precautionary measure would you suggest for each situation?

For the low/low population, I would make a similar recommendation as I did for the “flu” scenario earlier:
immediate quarantine. Drawing a bit on my knowledge from our current real-world situation, encouraging
social-distancing would also be a useful step to maintain those low infection rates.

In the high/high scenario, I’m a bit at a loss. It moved so quickly through the population (with cases peaking
around day 10) that I’m not sure any recommendations would be helpful without advanced warning. We could
take a situation like what happened with COVID-19 and assume you had some advanced knowledge at which
point you could recommend social-distancing and the moment the first case was reported in your population
do a mandatory hard-quarantine with frequent checks to remove infected people from households.

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LESSON 3 Step 2. PANDEMIC SIMULATION: FAST vs SLOW CONTAGION

This is a chance to play with the virus. This time. Click on DETAILS. Change them as you
wish and see what happens in various population densities and population mixing
scenarios.
LESSON to Pandemic

PANDEMIC SIMULATION 2
Lesson 3: Population Population Percent Starting Percentage Sick Dead
Step 2 Mixing Density Vaccinated Number of of Days
Contagious Population Reported
People Affected
Prediction
“COVID” scenario H H 0 3 35 3000 6
(14, 1%, 1%)
Simulation
H H 0 3 42.7 5375 2
Run 1 (slow)
Simulation
H H 0 3 41.3 5205 3
Run 2
Simulation
H H 0 3 46.7 5880 3
Run 3
Simulation
Run 1 H M 0 3 13.6 1710 0
(mid)
Simulation
H M 0 3 13.4 1683 0
Run 2
Simulation
H M 0 3 16.6 2096 4
Run 3
Simulation
Run 1 H L 0 3 5.6 704 0
(fast)
Simulation
H L 0 3 8.7 1092 0
Run 2
Simulation
H L 0 3 .4 53 0
Run 3

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Diseases travel through populations in fairly predictable ways. Population density, or population mixing with the same
effect as changing density, is one of the key controlling factors of disease transmission.

Diseases like HIV, hepatitis, and avian influenza are currently spreading rapidly in developing countries. Ebola
outbreaks also recur. Controlled diseases such as polio have had outbreaks in Syrian refugee camps. On average, the
CDC maintains a list of 12 diseases that are epidemic or pandemic and highly lethal. Although the list rarely changes
and a majority of the diseases are found in sub-Saharan Africa, a threat continues to the world as a whole. Differences
in health care, the availability of clean water (or water in general), and socio-political agendas often define how
quickly disease spreads and to what extent those afflicted may find care and respite.

Answer the following Questions:

13. In addition to the efforts of the CDC and WHO, what might be done to either contain virulent disease or
prevent its onset?

For prevention, the most obvious efforts are those that can be taken by individuals within a population to
practice good hygiene. People should wash hands frequently, cough into their elbow, limit person-to-person
contact (or social-distance), stay home if symptoms of any kind present (very difficult to accomplish in a
capitalist society with healthcare tied to employment). Once a virus has been identified and cases have
appeared within the community, then travel outside of the home should be limited to only absolutely
necessary destinations with a gradual opening once measures have been put in place by governments.

14. In your opinion, what is the greatest viral or bacterial threat to your local population

It would be hard to argue against COVID-19 currently. However, as I wrote in my discussion post, there is a
large and growing threat of AMR “superbugs”.

15. what precautions might be taken to avoid contagion? Be creative! We need innovation.

It’s interesting because a few months ago I was predicting that things like shaking hands would probably
disappear from our society, and fully expected us to begin to embrace mask-wearing (similar to most Asian
countries). The last month has dissuaded me of that. However, I do hope that eventually the science deniers
and rabid Trump fans will go find a different hill to die on (literally?) and we can begin to have more rational
conversations over how society can and should function to avoid the next pandemic. There will definitely be
more due to the increased contact with animals and increasingly poor industrial farming practices leading to
increased zoological illnesses crossing over, though as I said in my previous answer, the next pandemic could
also be a bacterial “superbug” that we do not have the medication to treat.

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