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ImperialCollegeLondon / epidemia

epidemia package
https://imperialcollegelondon.github.io/epidemia/index.html
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inference for multiple strains #62

Closed andreaskoher closed 3 years ago

andreaskoher commented 3 years ago

Hi and great package!

end of next week, we will give an introduction to your package at a workshop and in the run up some researchers raised their interest to infer the reproduction number for multiple strains that exist in parallel within a population. Apparently, there is weekly genome sequence data available for Denmark and I was wondering if this type of inference is already possible with Epidemia.

Many thanks and keep up this great work :)

s-mishra commented 3 years ago

Hi @andreaskoher, thanks for your comments.

So if the aim is to do only transmission advantage not worry about teasing out the advantage seen due to immune escape capabilities of a variant (look at the characterization of gamma, P1, in our science paper ), you can look at the code we did for characterizing alpha (B117) in our nature paper. The code for model is available here. Just that you need to adjust it a bit for specific use case depending on the data you have.

So yes this is very much plausible. But if interest is in characterising delta, which has immune escape capabilities, I will encourage you to look at the code here or here.