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Using the above app, set the initial conditions so that they fit the following assumed initial conditions. You can then verify the numbers found in the app with the calculations shown below.
While SIR models can be insightful, you should quickly realize that the model depends heavily on the assumptions made by the researchers who are developing the model. What is the transmission rate when people are wearing masks versus when they are not wearing masks? How does social distancing help to lower the transmission rate? How do the two interact? The answers to questions such as these can have massive implications for how deadly the disease can be.
Let’s take a closer look at a couple of the parameters in our simple SIR model.
Transmission RatesIf you change the transmission rate in the graphing application above, you’ll notice that lowering the transmission rate by itself does not necessarily stop the spread of the disease. The true determinant of how many people will ultimately get the disease is the ratio between the transmission rate and the recovery rate. This is often referred to as the Reproducibility Number (R). This number tells us, on average, how many additional people one infected person will infect over the entire course of their infection. As you can see in the graph, if R is greater than 1—that is, if the transmission rate is greater than the recovery rate—then an epidemic will occur since more people are being infected than are recovering. If R is less than 1, then the disease will die out as more people are recovering then being infected. If R is very close to 1, there will be a constant rate of infections
The Reproducibility Number will change over the course of the epidemic; as people move from susceptible to recovered/removed, the number of susceptible people shrinks and each infected person will be able to cause fewer new infections. Thus epidemiologists often talk about R0, or the Reproducibility Number on day 0 when everyone in the population is still susceptible. You can also calculate Rt, or the Reproducibility Number on day t, or the Reproducibility Number on day t. As we can see in the graph, when the transmission rate is greater than recovery rate, we can see that Rt is initially greater than one and the number of people wh are infected every day increases. Then, after infections reach peak on day t and start to decrease, Rt is less than 1. One of the major challenges in SIR modeling is that the transmission rate is non-constant. It is time-dependent and can vary drastically.
Initial InfectedThe initial infected parameter can also affect whether an outbreak will occur. Remember that for an epidemic to occur, each person who is infected must infect, on average, more than one additional person over the course of their infection. Let’s say the R0 for a particular disease is 1.33, and at present only one person is infected. That person can’t infect 1 and 1/3 of a person! Each whole person is either infected or not, so the calculations in the SIR model are rounded to the nearest whole number. With an R0 of 1.33, in an SIR model that person will only infect one other person (1.33 will round down to 1), who will also only infect one other person, and an epidemic will not occur. However, if 10 people are infected initially, they will infect a total of 13 people between them, who will infect a further 17 people, and the number of cases will grow into an epidemic. You can see this yourself using the graphing application or the calculations above.
Looking at the variability of SIR modelsPredicting how the COVID-19 pandemic would progress quickly proved to be an incredibly challenging task. The images below represent possible scenarios that the CDC suggested early in the pandemic based on different possible values for R0, using SIR simulations with a population of 100,000. You can see from these images that altering the transmission rate and recovery rate even slightly caused drastic changes in the predicted outcome for the pandemic. “Flattening the curve” by reducing the transmission rate does reduce the total number of infections, but it still leads to a majority of the population being infected. The number of people infected on the peak day of infections is dramatically lower, reducing the strain on the healthcare system, but the trade-off is that the epidemic lasts longer.
It is important to note that changing the recovery rate has little effect on how long the epidemic will last or how many people will ultimately be infected, unlike changing the transmission rate.
We must remember that the model we have been looking at is very basic. The differences between the possible predicted outcomes become even more apparent as researchers increase the complexity of the models by, for example, adding parameters to account for an incubation period for the disease, for quarantine or isolation measures, or for the possibility of reinfection. When there is great uncertainty around the correct numbers to use for the model inputs, or even around which parameters need to be included in the model, any predictions produced by these models will be very uncertain as well. This uncertainly prevents creating reliable projections for the course of the outbreak, which frustrates efforts to contain outbreaks and worsens the already devastating burdens on the healthcare system and the economy. Careful attention must be given to the assumptions made when using any model, whether it be an SIR or a statistical model.
Additional ResourcesTo view a more complex shiny app with more variables for modeling Covid, click here. Grinnell College students Senay Gockcebel, Britney He, Bowen Mince, and Linh Tang did a simulation study on a more complex model. See the paper here. The Github for it can be reached here.
Dataspace is supported by the Grinnell College Innovation Fund and was developed by Grinnell College faculty and students. Copyright © 2021. All rights reserved
This page was last updated on 19 July 2021.