search

artic-network / primer-schemes

Primer schemes for real-time genome epidemiology
https://artic.network/
Creative Commons Attribution 4.0 International
27 stars 41 forks source link

SARS-CoV-2: C44T seems to be common to all BA.2/4/5 but overlap primer 1 LEFT #16

Closed corneliusroemer closed 1 year ago

corneliusroemer commented 1 year ago

It appears that nuc:C44T is common to all BA.2/4/5 (at least) but only called in ~40% of cases because it overlaps ARTIC primer 1 LEFT (at least v4.1, but probably most other versions too).

I'm not sure whether anything can be done about this, but if there is it would be nice to address this.

C44T went up exactly when BA.2 first appeared and is also seen in BA.4/5

Since BA.2/4/5 descendants make up ~99% of current circulation it's not unreasonable to assume that 44T has fixed.

Maybe the right way is to switch the primer base instead of changing the location then? It would in any case be nice if ARTIC users called 44T consistently in the future.

image

https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?variantQuery=C44T&

BioWilko commented 1 year ago

There is nothing we can do to address this since it is the terminal primer in the scheme therefore not overlapped by any other amplicon, it is an unavoidable feature of primer scheme design unfortunately.