SIR models: A teaching case study to use in a course about probability models

This past summer, I created a few examples about COVID-19 to use in my course on probability models. I’ll post those materials here as I teach with them. Here is the first case study that introduces SIR models for modeling the spread of infectious disease. SIR models are widely used in epidemiology.

Infectious disease modeling: framing and modeling

Assume we have a constant population with N individuals. We can partition the population into three groups:

1. Those who are susceptible to disease (S[n], i.e., not infected).
2. Those who are infected (I[n])
3. Those who are recovered (R[n]).

We assume a discrete time model, where we are interested in how the number of susceptible, infected, and recovered individuals vary according to time. Therefore, we start at time n=0 and index these values by n. The time between time n and n+1 could represent, say, a week.

A new strain of influenza or a novel coronavirus emerges. Susceptible individuals can become infected after exposure, and infected individuals can recover. Recovered individuals have immunity from reinfection.

New infecteds, result from contact between the susceptibles, and infecteds, with contact rate beta/N, which represents the proportion of contacts an infected individual has. Infecteds are cured at a rate (gamma) proportional to the number of infecteds, which become recovered.

Question #1: Come up with an expression to relate N to S[n], I[n], and R[n].

Question #2: Develop recursive expressions for S[n+1] based on S[n] and perhaps other variables.

Question #3: Then, do the same for I[n+1] and R[n+1].

Question #4: What are the boundary conditions?

Question #5: How would you estimate the total number who become infected by time n? 

Discussion questions:

1. What other diseases fit this model?
2. What are some possible ways to reduce the infection rate?
3. What are some possible ways to increase the recovery rate?
4. How does a vaccine effect this model?
5. There is an interruption in the production of the vaccine, and your state will only receive 20% of the vaccines that you need before influenza season begins. Vaccines will slowly be released after this level. What are some criteria we could use to decide how to distribute these vaccines? What else can you do?

The second part performs computation in a spreadsheet. The assignment is here. We use the CDC 2004-5 data from a population of 157,759 samples taken from individuals with flu-like symptoms and 3 initial infections. Let n=0 represent the last week in September, the beginning of influenza season. Then, we compute these numbers in a spreadsheet to see how the disease may evolve. Next, we fit the model parameters (beta and gamma) using data that was collected by minimizing the sum squared error (SSE). Finally, we assess the impact of a vaccine. 

Files:

1. The assignment.
2. The solution.
3. The assignment for the computational part.
4. A google spreadsheet with the calculations (create a copy or download)

More examples

• pooled testing to expand testing capacity.