KP.3.1.1 + ORF1a:T2274I (731 seq.) >20% of cases in Iceland after June 15

[Fearuncle]

transferred from: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1653 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_37578_8f8810.json?f_userOrOld=uploaded%20sample

First Seq: 2024-05-27 Most Recent: 2024-07-05

Gisaid: C7086T, A13121T

[FedeGueli]

the H49Y L176F branch has grown getting further S:V62L: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_51035_972eb0.json?f_userOrOld=uploaded%20sample&label=id:node_7034544

[Fearuncle]

passed 500 seq.

[Mydtlwn]

@corneliusroemer

[FedeGueli]

C7086T, A13121T

@DailyCovidCases if you look at this it has noa dvantage over KP.3.1.1 that now has a significant disadvantage vs XEC, LF.7, MV.1 , MC.10.1, MC.10.2 , NP.1 XEP and especially the newly fastest one LP.8. It doesn't make much sense to designate it right now unless you see a sublineage that is growing faster than its backbone or a recombinant with this as donor.

[FedeGueli]

For example there is a very recent duplet from NY with three spike mutations (T95I,1087T,1208H) that you can find with G24794A , C21846T, G25186T . You can track one of these sublineages to see if it has any chance to compete cc @DailyCovidCases

[DailyCovidCases]

I found that most of the KP.3.1.1 on this issue is currently not designated (808/850 on Covspectrum). Can you rectify that? @corneliusroemer It also sustain a significant proportion from August to late October: https://cov-spectrum.org/explore/World/AllSamples/Y2024/variants?nucMutations=C7086T%2CA13121T&nextcladePangoLineage=KP.3.1.1*&

[FedeGueli]

I found that most of the KP.3.1.1 on this issue is currently not designated (808/850 on Covspectrum). Can you rectify that? @corneliusroemer It also sustain a significant proportion from August to late October: h

correct it is undesignated

[FedeGueli]

For example there is a very recent duplet from NY with three spike mutations (T95I,1087T,1208H) that you can find with G24794A , C21846T, G25186T . You can track one of these sublineages to see if it has any chance to compete cc @DailyCovidCases

This seems growing i didn't notice that it has also S:A264D>N before t95I 1087T and 1208H i changed the query to C5493T, G22352A, T23605G that finds 3 but already 5 in the tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_32921_bc92e0.json?c=userOrOld&label=id:node_7283281

@Fearuncle if this goes to ten i suggest to add it to the proposal

[DailyCovidCases]

828 seqs now @corneliusroemer rapid designation needed due to large number of seqs:

[FedeGueli]

For example there is a very recent duplet from NY with three spike mutations (T95I,1087T,1208H) that you can find with G24794A , C21846T, G25186T . You can track one of these sublineages to see if it has any chance to compete cc @DailyCovidCases

This seems growing i didn't notice that it has also S:A264D>N before t95I 1087T and 1208H i changed the query to C5493T, G22352A, T23605G that finds 3 but already 5 in the tree:

@Fearuncle if this goes to ten i suggest to add it to the proposal

This sublineage now it is 5