Potential sub-lineage of BA.2 with S:K417T and nuc:C23248T in UK/Ireland (900 seq)

[olias120676]

Sub lineage of BA.2 with 517 sequences in UK
Contains
S:K417T
A22812C, C23248T
Earliest sequence 2022-02-19 England/ALDP-37C4703/2022

Edit by @corneliusroemer: 70% contains ORF7a:S83L, but there's significant circulation without this mutation

Fairly large potential growth advantage at this stage
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=s%3AK417T%2Corf7a%3As83l&

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_8938_dd7ed0.json?branchLabel=nuc%20mutations&c=pango_lineage_usher&label=nuc%20mutations:T670G,G4184A,C4321T,C9344T,A9424G,C9534T,C9866T,G10447A,C12880T,T15240C,C15714T,C17410T,C19955T,A20055G,C21618T,T21762C,T21846C,T22200G,C22673T,A22688G,G22775A,A22786C,A24130C,C26060T,C26858T,G27382C,A27383T,T27384C

[FedeGueli]

Nice catch, this was also found by the model built by @bitbyte2015 , initiallt thought for recombinants, but that seems good in rapid discovery of growing lineages.
So were monitoring this clade.
Looking at BA.2 baseline the potential growth advantage seems between 28% in northern ireland and 40% in England , and it is likely going further down a bit.

[FedeGueli]

626 seqs as today

[corneliusroemer]

Oh interesting, convergent evolution with #540 which is a really successful BA.3 lineage with S:417T (Gamma mutation!)

Thanks @olias120676 this is a good find - especially the combination of RBD mutation and growth.

However, could you please not use plain growth advantage but use the advanced growth advantage against a BA.2* background? Any BA.2* will have 30% growth advantage simply because it's BA.2*.

Also please filter to the country with the highest share - in this case UK. This is how you should query growth advantage:

https://cov-spectrum.org/explore/United%20Kingdom/AllSamples/Past6M/variants?pangoLineage=BA.2*&aaMutations1=s%3AK417T%2Corf7a%3As83l&pangoLineage1=BA.2*&analysisMode=CompareToBaseline&

I had a closer look: the mutation ORF7a:S83L should not be required for this lineage - it's likely not source of growth advantage and only appears in 70% of this lineage as a passenger.

However synonymous mutation nuc:C23248T is defining - to distinguish from other kinds of BA.2 with S:417T.

Lineage is present in Ireland, too where it makes up an even larger share than in UK:

First detection was end of January (if you don't use the unimportant ORF7a:S83L as requirement).

Usher tree clusters these well, although the path is a bit murky - but @AngieHinrichs may fix this.

Definitely should be designated @chrisruis

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_99b3_1ccf20.json?c=gt-nuc_22812,23248

I'll have a look at another S:417T that seems to have popped up in UK - maybe it comes from somewhere else.

[FedeGueli]

@corneliusroemer great work on S:417T i disagree on Orf7a::83L.
Remember that B.1.617.2 carry Orf7a:V82A just near that AA. I wouldnt dismiss that mutation as uninfluent (for sure i agree on the designation startimg from the nuc you found) and also AY.122 had orf7a:45L and it became the only AY. to reach top ten of more sequenced delta sub- lineages in more than 3 continents.
But maybe, you know, it is just that i am biased versus Orf3a Orf7ab and N mutations ;)

[corneliusroemer]

I just rediscovered this lineage. Was about to propose but then found it again. @chrisruis could you have a look at designating this one? It has now also been imported into the US and France and keeps growing. It is reasonable that S:417T could help with immune escape.

[chrisruis]

Thanks @olias120676 We've added this as BA.2.18 to start on the branch with A22812C (S:N417T) which is likely the first nonsynonymous mutation in this introduction(s) into the UK