Search by mutation?

This might be a naive question but is it possible to search the SARS-CoV-2 sequence collection by mutation to determine (1) how many times a mutation has been observed before and (2) when a mutation was first observed and (3) in which geographic regions is that mutation prevalent.

I have a local copy of the GISAID sequences / metadata but haven’t yet learned enough to use ncov competently. I don’t know if this is something that’s done trivially through the web app or requires scripting it myself.


1 Like

Hi @iskander,

Thanks for your question. Apologies for getting back to you with such a delay. You may have answered this by now, but the way to look at this type of thing in is by selecting a mutation in the “Diversity” panel (this panel is highlighted in the following view: auspice but should be visible by default below the map). Doing so will show you information on the different residues at that site such as their occurence in the tree, location on the map, and relative prevalence over time in the “Frequencies” panel. Here is an example: auspice.

If you want to run your own ncov build and create a dataset using your local copy of sequences, check out the SARS-CoV-2 tutorial here: A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2 — Nextstrain documentation.

Please let me know if this doesn’t fully answer your question.

Nextstrain Team