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eringill / chronic_infection_python

A simple GUI that allows users to check whether mutations from a SARS-CoV-2 genome best fit a mutational distribution of genomes derived from global, chronic, or deer infections.
https://eringill.shinyapps.io/covid-mutation-distributions/
MIT License
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Example - molnupiravir #4

Open fionabrinkman opened 2 weeks ago

fionabrinkman commented 2 weeks ago

can you include a mutator example (sequence with a signature suggestive of molnupiravir use) as a button? Ideally, it’d be great to have examples of each possible output.

eringill commented 2 weeks ago

A mutator lineage is a lineage that has a mutation (usually in the ExoN proofreading domain of Nsp14) that causes an accelerated mutation rate. I've updated the application notes tab and made a tool tip pointing to the application notes tab where there is a list of known mutator sites.

In terms of a set of lineage-defining mutations in a lineage that is associated with molnupiravir use, I can't seem to get my hands on this data. Even papers that describe the phenomenon (increase in transition: transversion ratio) only seem to plot aggregated data, then provide links to complete genome sequences. If you happen to have an example, I'll use it.

fionabrinkman commented 2 weeks ago

What about the data and sequences linked to from https://www.nature.com/articles/s41586-023-06649-6? ie. https://www.ebi.ac.uk/ena/browser/view/PRJEB57177?

fionabrinkman commented 2 weeks ago

Or use Theo Sanderson's example sequence for his earlier app? https://movbranchapp.streamlit.app/ C2595T, T3607C, C4464T, C6525T, G9092A, G11272A, G12067A, C12784T, G14430A, C14605T, G18589A, G18712A, G20839A, A22124G, C23170T, T25735C, A26169G, C28344T, C28697T, C29098T It gives a ratio of 20 (!), but doesn't get noted as being a likely molnupiravir-induced sequence?

For reference, here's more info re the app (though note the app isn't running at the moment: https://x.com/theosanderson/status/1743245032868507944

fionabrinkman commented 2 weeks ago

On a related note, could you have a word come up either at the top or end stating if the sequence has a high ratio suggestive of it being molnupiravir induced?