LB.1 (JN.1.9 + FLiRT) with S:S31del (105 , 13 countries) with a singlet with S:A475V (this subbranch spotted by @hynnspylor)

[FedeGueli]

Formerly known as Branch 62 of sars-cov-2-variants/lineage-proposals#1089

Edited after LB.1 designation

LB.1 [JN.1.9 > S:R346T(G22599C) > S:F456L (T22928C)] > S:S31del (21653-21655del) [Edited thx to @aviczhl2 adding the deletion at S:S31del]
Query for LB.1 FLiRT : G22111T , G22599C , T22928C,T3565C finds 7 but Usher displays 11 sequences ( plus two misplaced, on the top with 183Q REV)
Query for Flirt S:S31Del: G22599C, T22928C, T3565C, del21653, G22111T
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_3acf3_d18670.json?label=id:node_6949186
Samples : 11

Countries: 5

@HynnSpylor spotted one sublineage uploaded on 05/07 with S:A475V
Query: C22986T, C28957T,del21653, G22111T
Samples: 1 (GBW)

[aviczhl2]

This branch also has S:S31del.

[FedeGueli]

+1 France @corneliusroemer i suggest rapid designation of this one.

[FedeGueli]

This branch also has S:S31del.

Thank you @aviczhl2 , i ve completely missed that. that is a good remainder that when transferring branches, usually found very early, to re check mutations/Deletions .

[FedeGueli]

13 total 10 with S:S31del

[FedeGueli]

+1

[FedeGueli]

Designated JN.1.9.2 and LB.1 from b51c68c

[FedeGueli]

Big jump of the S:S31Del branch that went to 22 with 8 samples uploaded on April 19:
3 from NYC the remaining five from GBW airport surveillance from 3 different countries France, India and Japan,
@corneliusroemer i suggest to designate it ( or to broaden LB.1 to S:S31Del being 22 out of 26 LB.1

[FedeGueli]

There maybe a sub-branch of LB.1 that is misplaced in LB.1 but it has the S:Q183Q reversion:
Query: G17562T, G22599C , T22928C,T3565C
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_62fd1_778280.json?label=id:node_6962416
It also could be that the reversion is real maybe due a micro inter JN.1 Recombination cc @AngieHinrichs

[FedeGueli]

The LB.1 plus S:S31F is now 25 from 9 different countries including Pakistan, Qatar, India, Taiwan, Japan , France, Australia, Canada, US.

[aviczhl2]

There maybe a sub-branch of LB.1 that is misplaced in LB.1 but it has the S:Q183Q reversion: Query: G17562T, G22599C , T22928C,T3565C Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_62fd1_778280.json?label=id:node_6962416 It also could be that the reversion is real maybe due a micro inter JN.1 Recombination cc @AngieHinrichs

That's the 17562 branch with Filrt. See branch 62 of #1253

[FedeGueli]

There maybe a sub-branch of LB.1 that is misplaced in LB.1 but it has the S:Q183Q reversion: Query: G17562T, G22599C , T22928C,T3565C Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_62fd1_778280.json?label=id:node_6962416 It also could be that the reversion is real maybe due a micro inter JN.1 Recombination cc @AngieHinrichs

That's the 17562 branch with Filrt. See branch 62 of #1253

ahha yeah i ve forgot that!

[FedeGueli]

+2 Canada , US: going up very quickly

[FedeGueli]

29 +2 Australia, it seems really fast i have it as the fastest in my list of designated/undesignated lineages: @corneliusroemer is it possible to designate from a deletion only?

[AngieHinrichs]

is it possible to designate from a deletion only?

Unless the pangolin tool were upgraded to use some method other than usher, it would not be able to recognize a deletion-only lineage because deletions are invisible to usher.

[FedeGueli]

is it possible to designate from a deletion only?
Unless the pangolin tool were upgraded to use some method other than usher, it would not be able to recognize a deletion-only lineage because deletions are invisible to usher.

Thank you @AngieHinrichs , being around 3/5 of LB.1 if it is faster than parental it won't take much time to be a vast mayority of it so LB.1 will be a proxy good enough for it. @corneliusroemer should i close this issue then?

[FedeGueli]

35 now out of 42 total LB.1 samples

[AngieHinrichs]

35 now out of 42 total LB.1 samples

I don't know if the assembly pipelines have improved in this regard, but at least earlier in the pandemic, that's close to the ratio of sequences in which a deletion was correctly assembled. I.e. some of the samples that appeared not to have a deletion might actually have a deletion, but the assembly pipeline filled in NNNNs or reference bases.

[FedeGueli]

35 now out of 42 total LB.1 samples

I don't know if the assembly pipelines have improved in this regard, but at least earlier in the pandemic, that's close to the ratio of sequences in which a deletion was correctly assembled. I.e. some of the samples that appeared not to have a deletion might actually have a deletion, but the assembly pipeline filled in NNNNs or reference bases.

Yeah very likely!

[FedeGueli]

42/50 now with S:31Del

[aviczhl2]

98 now

[FedeGueli]

98 now

103