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Improve Omicron exercise description
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sarahCobey committed Jul 12, 2022
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Expand Up @@ -41,7 +41,7 @@ python plot_two_strain_ts.py
> (6) Now change `alpha` and `a` to make the strains interact. How do the dynamics differ? Do you see differences in the dynamics when you change `alpha` v. `a`?
> (7) Let's use the model to consider the conditions under which a new variant can invade---specifically, the invasion of Omicron in late 2021. (We'll pretend there was a single resident strain, Delta, and a single invader, Omicron.) Major uncertainties at the time included the fraction of the population immune to infection with Omicron compared to prior variants such as Delta, the intrinsic reproductive numbers of Omicron and Delta, and the cross-immunity after infection with each to the other. In laboratory experiments, sera from recipients of the mRNA-1273 vaccine (containing the original Wuhan strain, estimated to be half as transmissible as Delta) experienced a 30-fold reduction in neutralization against Omicron (the reduction was ~2.5-fold for Delta). Epidemiological studies in England suggested that Omicron was 50\% more transmissible than Delta within households and potentially twice as transmissible outside households. What intrinsic reproductive numbers, differences in immunity to Delta vs. Omicron (i.e., degree of immune escape in Omicron), and values of `a` or `alpha` are consistent with rapid displacement of Delta? Try to identify a few contrasting scenarios.
> (7) Let's use the model to consider the conditions under which a new variant can invade---specifically, the invasion of Omicron in late 2021. (Pretend there was a single resident strain, Delta, and a single invader, Omicron.) Major uncertainties at the time included the fraction of the population immune to infection with Omicron compared to prior variants such as Delta, the intrinsic reproductive numbers of Omicron and Delta, and the cross-immunity after infection with each to the other. In laboratory experiments, sera from recipients of the mRNA-1273 vaccine (containing the original Wuhan strain, estimated to be half as transmissible as Delta) experienced a 30-fold reduction in neutralization against Omicron (the reduction was ~2.5-fold for Delta). Epidemiological studies in England suggested that Omicron was 50\% more transmissible than Delta within households and potentially twice as transmissible outside households. By adjusting the parameters in [`two_strain.py`](two_strain.py), what intrinsic reproductive numbers, differences in immunity to Delta vs. Omicron (i.e., degree of immune escape in Omicron), and values of `a` or `alpha` are consistent with Omicron's rapid displacement of Delta? Try to identify a few contrasting scenarios.

> (Optional) Consult [the documentation](https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.odeint.html) for SciPy's' ODE solver [`odeint`](http://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.odeint.html#scipy.integrate.odeint) in [`scipy.integrate`](http://docs.scipy.org/doc/scipy/reference/integrate.html). This solver uses an adaptive step size. See if you can implement the model using the solver--most of the content of [`two_strain.py`](two_strain.py) can be copied and pasted. Investigate the consequences of changing the tolerance limits (`rtol` and `atol`) and acceptable step sizes (`hmin` and `hmax`) of the solver. These equations are said to be [stiff](http://www.mathworks.com/company/newsletters/articles/stiff-differential-equations.html).
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