Vaccination

[ahurford]

Hi Steve,

I am wondering how vaccination is included? Is it just a matter of retaining all the vaccinated people in the S compartment and adjusting the beta accordingly? Or do you move the vaccinated people to R - but then how do you handle breakthrough infections?

Is there an example/documentation of this anywhere?

Thanks! Amy

[stevencarlislewalker]

Hi Amy,

Currently I'm putting together a forecast example. Will push soon and then push a simple vaccination example for you to work with.

The way that vaccination works is to create five copies of each compartment:

1. Unvaccinated
2. Received first dose
3. Protected by first dose
4. Receieved second dose
5. Protected by second dose

This model hasn't been updated recently obviously given that many people have more than two doese. But the assumption is that they are only really protected from their last two doses at most (this is a bad assumption but it is where the modelling team is at).

Turn on this vaccination model is reasonably straightforeward and I should be able to do that for you today.

Cheers, Steve

[stevencarlislewalker]

Hi @ahurford,

I've worked up a model with two vaccination doses and the fit is pretty bad. The bad fit is not surprising because it requires the following details on vaccination-related parameters.

Here are the vaccination-related parameters that will need values specifically for NFLD.

Here are some very detailed notes from Irena Papst, who was a main author of the vaccination model. These notes should help clarify the meaning of the vaccination parameters that you will need to specify for the NFLD case. Here are the key sections:

• The 'vaxification' of the parameter vector describes how to expand the base parameter vector so that it includes parameters relevant for vaccination models.
• The calculation of the force of infection is likely quite helpful for understanding the meaning of vaccine efficacy parameters.

Importantly, any of these parameters can be time-varying. So for example if the number of doses per day is changing in time, we can add that in the params_timevar data. I am very happy to help with any of this. What I do not know are the on-the-ground facts in NFLD. But I can very easily help with writing code to do what you want (as long as the model is capable of it). I'm happy to meet as well if that helps.

[stevencarlislewalker]

how do you handle breakthrough infections?

Vaccine efficacy parameters < 1