JN.1.16.1+S:T572I(52 seqs=31+9+12(additional S:S31del))

[aviczhl2]

JN.1.16.1+S:T572I(C23277T)

Given the extreme convergence I cannot find a query to describe exactly JN.1.16.1+S:T572I, and they most likely emerged separately. There are currently 3 major branches, C12073T, C24466A, and G5617T branch. They may or may not be independent branches. The sum of the seqs is 40.

GISAID query for 12073T branch : C23277T,T22928C,G22599C,C12073T GISAID query for 24466A branch: C23277T,T22928C,G22599C,C24466A GISAID query for 5617T branch (FULL QUAD + Orf9b:D16G): C23277T,T22928C,G22599C,G5617T

No. of seqs: 21(Sweden 2 Slovenia 1 Japan 2 Ireland 2 France 1 UK 13)

First: EPI_ISL_19135064, Japan, 2024-4-30 Latest: EPI_ISL_19225376, UK, 2024-6-18

usher

[aviczhl2]

23, Norway

[FedeGueli]

25, Netherlands

[aviczhl2]

There seems to be some new branches of the Trio gathered together.

[aviczhl2]

The sum of the 3 major sub-branches is 40 now.

[FedeGueli]

Now in the G5617T branch there is a subbranch sampled in Israel and in Arizona that features Orf9b:D16G (A28330G) the signature of BA.5.2 and it is a FULL QUAD BRANCH! (all the G5617T!)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_204b4_df0510.json?c=userOrOld&label=id:node_7207062

[aviczhl2]

Now in the G5617T branch there is a subbranch sampled in Israel and in Arizona that features Orf9b:D16G (A28330G) the signature of BA.5.2 and it is a FULL QUAD BRANCH! (all the G5617T!) https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_204b4_df0510.json?c=userOrOld&label=id:node_7207062

It shall be a separate branch?

[aviczhl2]

Nope it can emerge directly from JN.1.16.1+S:T572I. The 31del can be branch specific. So better designate JN.1.16.1+S:T572I as LF.x and that specific S:S31del branch as LF.x.1. @corneliusroemer

[FedeGueli]

Nope it can emerge directly from JN.1.16.1+S:T572I. The 31del can be branch specific. So better designate JN.1.16.1+S:T572I as LF.x and that specific S:S31del branch as LF.x.1. @corneliusroemer

agree no way to establish that

[FedeGueli]

The Deflirt branch went to 7 today with two samples from Israel

[FedeGueli]

8 in the new Deflirt branch (Washington)

[FedeGueli]

C23277T,T22928C,G22599C,G5617T

it looks like it now got only 7

[FedeGueli]

the Full Quad branch reached 11 and could be something to monitor closely

[aviczhl2]

It seems that all 3 branches stopped growing. Close down.