New BA.5 sublineage of interest with S:R346I (520 Sequences as of 2022-07-24)

[FedeGueli]

I have spotted a BA.5 cluster with a mutation of interest S:346I:
Countries: South Africa, Switzerrland, Germany, Uk
Defining mutations: T1570C, C11674T, C18804T, G22599T (S:R346I)
tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_3ac76_30e1d0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:T1570C,C11674T,C18804T,G22599T

CovSpectrum overview:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=M%3A3N&nucMutations=G12160A%2CT1570C%2CC11674T%2CC18804T%2CG22599T&

[chrisruis]

Very small currently so will close for now but can reopen if this grows in future

[FedeGueli]

31 in Usher as today:

it further acquired
C11514T, C17676T
ORF1a:T3750I
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1735a_c9c090.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C8140T

[FedeGueli]

Hi @corneliusroemer @chrisruis @InfrPopGen @AngieHinrichs Jesse Bloom seems quite worried about S:346 mutations.
https://twitter.com/jbloom_lab/status/1537852516435521536?s=20&t=q0a8MxH_ZVv6yGgneofFEg
Please evaluate if it is worth to reopen this issue to be monitored not just by me.

[FedeGueli]

45 Seqs as today.

It seems growing very fast in Germany.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_d36b_f21e0.json?c=pango_lineage_usher&label=nuc%20mutations:T1570C,C11674T,C18804T,G22599T

[corneliusroemer]

I support designation - this now makes up ~5% or more of German sequences and it's got a mutation of high concern.

I'll reopen for consideration.

Better query here using NextcladePangoLineage BA.5*

https://cov-spectrum.org/explore/Germany/AllSamples/Past6M/variants?variantQuery=NextcladePangoLineage%3ABA.5*&variantQuery1=NextcladePangoLineage%3ABA.5*+%26+S%3A346I&analysisMode=CompareToBaseline&

[FedeGueli]

51 Sequences as today

[FedeGueli]

94 seqs on Usher as today

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_317aa_58d7b0.json?branchLabel=aa%20mutations&c=gt-S_346&label=nuc%20mutations:T1570C

[FedeGueli]

120 sequences as today.
Interestingly 6 of the new added sequences are from Uk and have an additional Rbd mutation S:471Q and a couple of Orf1ab mutations, quite a long branch that let me suspect undersampled circulation outside Europe ( and that could be supposed also by the fact this is a brand new branch of BA.5 corresponding to an early seeding from the source)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d7a0_ddffb0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C2306T,C14676T,C18788T,G22973C

[FedeGueli]

180 seqs as today.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3de46_21e970.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C14676T,G22973C

[ryhisner]

There are now five sequences with both S:E471Q and S:W886F on this tree in England—the latter being a 2-nucleotide mutation I believe. Three collected on June 23 and two on June 30.

EPI_ISL_13656619
EPI_ISL_13656538
EPI_ISL_13566766
EPI_ISL_13566890
EPI_ISL_13566845

[FedeGueli]

There are now 222 sequences on Usher.

and 13 in the small sublineage with S:471Q ( 6 with additional S:W886F).

To me the usher tree is very clear and di per se it represents an epidemiological relevant event whereas we saw a new branch of BA.5 having been seeded in Germany and subsequently it has started circulating in a sustained way and both importation and spread are clearly linked with the S:R346I (Ricky) mutation.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c83c_c573e0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:A23356T

@chrisruis @InfrPopGen @corneliusroemer I propose to designate it as soon as possible as BA.5.7

[FedeGueli]

Weirdly here we see covspectrum count being far behind the usher count.
Edited: now i have found a better CV.SP. query: 11674T, 18804T + S:346I that catches 216 sequences
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A346I&nucMutations=11674T%2C18804T&

there are 265 sequences now on Usher in 16 different countries and 4 continents. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b398_874bc0.json?label=nuc%20mutations:C11674T,G22599T

@corneliusroemer here the NCPL:BA.5*& S:346I query finds less than the less advanced mutation search.
Its growth advantage probably understimated due the missing sequences from Covspectrum is above 20% since this limeage was spotted.

[corneliusroemer]

This lineage should be designated asap start from the S:346I mutation.

The query is here: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=G22599T+%26+nextcladePangoLineage%3ABA.5+%26++C18804T+%26+T1570C&

It's >500 sequences now.

Mutations on top of BA.5: 1570C, 18804T and 22599T

Usher is very clear:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_dcbe_d64f60.json?label=nuc%20mutations:T1570C

Please designate @InfrPopGen

[silcn]

Doesn't look like the growth advantage has been sustained, it's been stuck at about 1.3% of BA.5* in Germany for the last 6 weeks.

[corneliusroemer]

Yes, it's true S:346I does not seem to do as much as to T for example.

If you compare to BA.5 (no sublineages) it's a much bigger share. I think by comparing to BA.5* you're comparing against BA.5.2.1 which has a growth advantage over BA.5 - this, plus travel may bias down the fact that BA.5 + S:346I has a growth advantage over base BA.5 albeit probably quite small.

In any case, it's 500 sequences and I see no harm in designating a lineage that branches off directly from the BA.5 polytomy.

[FedeGueli]

@corneliusroemer @silcn comparing to BA.5.2* that is the fastest of the 7 main BA.5 branches this has a growth disadvantage of 9% in Germany (past 2 months) or 8% in Europe. Still it has comparable trasmissibility or slight advantage vs BA.5.3, BA.5.5 or BA.5.6. Being the last to come had harder life than other lineages competing with BA.4s and BA.5s (which further evolved since their introduction in europe in april) instead of BA.2s , in my view it has to be designated

[InfrPopGen]

Thanks for submitting. We've added lineage BA.5.9 with 156 newly designated sequences, and 61 updated designations from BA.5. Defining mutation(s) G22599T (S:R346I), C11674T (Synonymous).