Omicron (21K) US lineage with additional mutation N:P67S at T cell epitope and C11950T (102 seq, 6% of US omicrons)

[bitbyte2015]

A minority of US BA.1 sequences have gained an additional mutation at N:P67S but the proportion is most pronounced in the midwest where it makes up 46% (12/26) of sequences in Illinois and 27% (51/186) sequences in Wisconsin. Codon 67 in the N gene falls under a HLA class 1 epitope [1]. There was a sequence from South Africa in mid November with N:P67S on the ORF1a:V1887I clade so it's unclear why it's growing exclusively in the US. N:P67S was also present in the B.1.2 lineage which was responsible for over 40% of US sequences in November 2020.

Roemer's ncov-simplest build puts it on a branch starting with C11950T https://nextstrain.org/groups/neherlab/ncov/21K-diversity?c=gt-N_67

and since UCSC USHER is down I ran ncov-simplest with the N:P67S omicrons only

all but 2 sequences were placed on the branch with C11950T the others being the South African sequence placed on the ORF1a:V1887I clade and a UK sequence placed on the N:D343G clade in #366

Country	Sequences
USA	94
UK	3
Australia	1
Japan	1
Netherlands	1
Canada	1
Austria	1

[1] https://www.nature.com/articles/s41590-020-00808-x

[AngieHinrichs]

[a bit off-topic for pango-designation, apologies for that but this bit is concerning for me:]

and since UCSC USHER is down

Sorry to hear that it was down. Do you recall the symptoms? (Error 500? Timeout?) If you are using a link with 'hgwdev' or 'genome-test' in it, that is our development/test server, and we had to reboot it a couple times recently for filesystem troubles. The main site is https://genome.ucsc.edu/cgi-bin/hgPhyloPlace and should be more stable.

[SVN-PhD]

Visualization of this lineage in context with other Omicrons from North America, Europe, and Africa.

Zooming into this lineage show it is quite prevalent in the upper Midwest of the US.

[bitbyte2015]

165/2524 of US omicron sequences now contain N:P67S

Some simple US omicron proportion statistics beginning with the week starting November 28:

[chrisruis]

Thanks @bitbyte2015 We've added this as BA.1.20 in v1.4