EPIDEMEOLOGY

LAB

Lab Part 1: Explore an Outbreak of Influenza

● Purpose: To simulate an infectious disease outbreak through social interactions in the classroom
● Each student in the class will receive a vial of “bodily fluids” and be asked to interact and
“exchange fluids” with three classmates
● Each interaction will be documented with the aim to investigate an infection outbreak and
identify “patient zero”

Meet and greet

● Meet someone, write name
● Open vial and use an eyedropper pipette to transfer the content of one vial over to the other
vial
● Close the lid and mix by gently rocking the tube back and forth
● Using the eyedropper pipette, transfer approximately half of the mixed solution back to the
empty tube of your classmate - You have now “exchanged” your “bodily fluids.”
● Take 100 µL from your vial using a micropipette and pipet it into the next well (B) in your
designated column on the 96 well plate.
● Repeat steps 4-6 two additional times with different classmates. When you are finished, bring
the 96-well plate back to your TA
● The TA will then add a drop of phenol red solution to the last well of each student’s sample
column on the 96-well plates
● Wells that turn red have been exposed to the infectious agent and therefore the corresponding
individuals are “infected.”

Class discussion questions

1. What is/are the primary transmission route(s) that would allow influenza to spread in our
outbreak scenario?
○ Bodily fluids: sneezing, talking, spitting

1. Based on the number of people “infected” by the end of the outbreak scenario, what are your
observations on the spread of infection during this exercise?
○ Spreads quickly
○ Supposed to be about 50% of people affected by the end of the activity

1. If you were to repeat our in-person exercise, how could you model an intervention strategy to
see a different outcome?
○ Isolation: remain in pods
○ Vaccination: give people a solution prior
 ○ Antivirals: give sick people something after infection

Lab Part 2: A Basic Mathematical Model for Studying Infectious Disease Spread

● Purpose: To learn about disease modelling using a SEIR (Susceptible – Exposed – Infectious –
Recovered) model for seasonal influenza that is run using NetLogo (modelling software)

4 different model simulations

1. SEIR-Model-Base-Seasonal
2. SEIR-Model-vaccination-Seasonal
3. SEIR-Model-isolation
4. SEIR-Model-antivirals

In NetLogo:
● Susceptible: Individuals do not have an immune response and do not produce antibodies against
the influenza proteins.
● Exposed: Individuals who have come into close contact with an infectious individual. Usually,
influenza is spread by droplets from coughing or sneezing. The droplets can enter the mouth or
nasal passage with potential to attach to the tissue.
● Infectious: Individuals who are carrying and transmitting influenza virus. For seasonal flu, people
may become infectious within the first day of exposure and up to 5-7 days after they are
symptomatic.
● Recovered: An individual whose immune system has successfully overcome influenza virus.
Antibodies recognize and destroy the virus. This results in permanent immunity to that strain of
influenza
● Use excel to analyze data
 Lab Part 3: Testing Which Parameters Affect the Spread of Disease

Purpose: To formulate and test hypotheses about which parameters might affect the spread of
influenza on campus using NetLogo and the base seasonal model program

Formulating a Hypothesis
● A hypothesis (H) can be defined as a testable explanation to a research question or problem. It
also provides grounds to formulate specific predictions (P) about the result after manipulating
variable(s) used to test the hypothesis
● Predictions are the predicted outcome of the experiments you plan to do, while the hypothesis
is the underlying mechanism you are testing
● A hypothesis and a related prediction are usually stated as follows: If (H) … , then (P)….
● Null hypothesis (H0 = statistical term): Usually a statement of “no effect” or “no difference”
○ A hypothesis that there is no (significant) difference between two sets of results
● Alternative hypothesis (Ha): Hypothesis that is contrary to the null hypothesis
○ It is often (but not always!) the research hypothesis

Experimental Design
● Independent variable: variable being manipulated = caffeine consumption (via drinking coffee)
● Dependent variable: variable affected by changing the independent variable = academic
performance, measured based on grades
Controls can broadly be categorized as positive or negative controls.
● Negative control: group where no phenomenon is expected. They ensure that there is no effect
when there should be no effect
● Positive control: group where a phenomenon is expected. They ensure that there is an effect
when there should be an effect, by using an experimental treatment that is already known to
produce that effect
Paired vs. unpaired data
● Paired data: the same group of subjects serves as both the control and treatment group
● Unpaired data: two different groups of subjects are used for the control and treatment
● Knowing if your data is paired vs. unpaired is important when it comes to choosing the type of
statistical test you will use to analyze the data.
● Paired data can be helpful as it reduces biological variability, since the same group of subjects is
used for both the control and treatment groups
● However, it is not always possible to set up an experiment with paired data

● Change one parameter at a time