Angie Hinrichs

It's tempting to think of 4181T as "21J only" and 5584G as "21I only". However, with

BTW this: looks to me like Spike amplicon dropout, unfortunately very common in Omicron, combined with insufficient filtering out of stray reads from contamination (or just back-filling reference genome sequence?),...

> 21I and 21J That totally makes sense, yes, it is too bad that there is no direct Pango analog for 21I and 21J. > co-infections / contamination For distinguishing...

> Amplicon dropouts That is a really cool new feature! > Obviously, this depends on knowlege about the used primer sets. Do you have that information about those USA/UT-UPHL sequences?...

I think Midnight had to change only one primer for Omicron, pretty impressive: https://twitter.com/freed_nikki/status/1489015462570586114 This page has a lot of great info about primers and how they're affected by various...

Actually, Wuhan-Hu-1/EPI_ISL_402125/MN908947/NC_045512 (29903 bases) and WIV04/EPI_ISL_402124/MN996528 (29891 bases) are identical except that Wuhan-Hu-1's polyA at the end is 12 bases longer than WIV04's. There is no WIV04 base that differs...

Sorry, I assumed you were using WIV04|EPI_ISL_402124 because that is GISAID's preferred reference (https://www.gisaid.org/epiflu-applications/hcov-19-reference-sequence/). But I see in global_tree_gisaid.sh it's actually hCoV-19/Wuhan/WH04/2020|EPI_ISL_406801|2020-01-05. That is definitely different (relative to WIV04 or...

We've been rerooting to Wuhan-Hu-1/NC_045512 for our purposes, so this doesn't directly affect us. I was hoping to give you a reason to simply close this issue, but I was...

Hi @hforoughmand -- Rob removed the script back in October since he was no longer using it: ``` commit 55cbb8ddaddaceb2ecd0577f105a3fd37f13d304 Author: roblanf Date: Thu Oct 15 15:54:41 2020 +1100 remove...

For the curious, the issue has been moved to https://github.com/cov-lineages/pango-designation/issues/1388 .