Closed aviczhl2 closed 2 weeks ago
Branch 31 seems to be an artefact, see #1466.
Branch 35 designated KU.2
Branch 36 is now 14 one sample from France , in January one Brazilian sample of this lineage had also S:A67V
There is a new (old) branch of JN.1 with S:F456L with one single FLirt sample. JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) > S:R346T(G22599C) Query: G4486T,A3058G, T22928C Samples: 3 Tree:
@FedeGueli Add branch 46 for JN.1->C4777T->S:F456L misplaced under JN.1.16 and JN.1.16.1.
@FedeGueli Add branch 46 for JN.1->C4777T->S:F456L misplaced under JN.1.16 and JN.1.16.1.
thank you i write to Angie
combo branch 29 with 572I and 456L reached 13
One of the branches of JN.1.21(1058Y) with 572I got also 456L query: C13378T, T22912C, G25775T . A singlet that i put here for remainder to check it.
Also a JN.1.11.1 branch got 572I in a singlet from Uk query: G2265A, G3483T, A5641G
There could be a JN.1.16 branch misplaced as follows: JN.1 > A18093G > S:F456L (T22928C) then > Orf3a:R122S (A25758T) > G18093A > S:A688V (C23625T)
more clear here:
cc @angiehinrichs @aviczhl2 Note that hCoV-19/Ecuador/GENSBIO-INSPI-105123/2024 Accession ID: | EPI_ISL_18967534 has not A18093G even if USher places it before the reversion driving the tree misplacement
cc @AngieHinrichs @aviczhl2 Note that hCoV-19/Ecuador/GENSBIO-INSPI-105123/2024 Accession ID: | EPI_ISL_18967534 has not A18093G even if USher places it before the reversion driving the tree misplacement
That's branch 12 detected by you. But usher is now misplacing it elsewhere.
New 456L > Flirt Branch JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) > S:R346T (G22599C )
Query for 456L : C24863T, T22928C, T3565C finds 3 samples Query for 346T :C24863T, G22599C, T3565C finds 1 sample
Apparently it doesnt belong to Jn.1.16.1 (aka JN.1.18 plus 456L) but could be instead that way being H1101Y highly homoplasic
Two new samples of JN.1.16.1 with S:F456V
@angiehinrichs could you look at this? @aviczhl2 (and i agree) thinks that it is more likely to be JN.1.18 > S:F456V than this
Two new samples of JN.1.16.1 with S:F456V
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5395a_3ef790.json?label=id:node_6971769
@AngieHinrichs could you look at this? @aviczhl2 (and i agree) thinks that it is more likely to be JN.1.18 > S:F456V than this
7 now @aviczhl2 i siggest to detach this one and propose it in Pango. with the two alternative placements
3/28: Add branch 50 (FLiRT+S:60P)
3/28: Add branch 50 (FLiRT+S:60P)
it is the sibling of Branch 66 of #1089 that branch was quite messy with some samples failing to appear in Usher , lets see if maybe they will be joined in one such as S:R346T > S:F456L S:R346T>S:Q183H or not.
Add branch 52. 53. 54. new branches of T22930A-S:F456L
There may be another JN.1.7 combo lineage with 456L in UK just two samples one only on Gisaid but worth tracking it for a bit: JN.1.7>C28849T > Orf1a:A3497V (C10755T), S:K304K(A22474G),S:F456L (T22928C), ORF9b:R58K (G28456A) Query : A22474G, G28456A,C10755T, T22928C
Tree:
Another FViRT (456V) singlet misplaced by Usher under the JN.1.9 FLirt Branch instead it belongs to the big undesignated branch with G17562T query: T22928G, C18657T
worth proposing branch 11 also to soleve the JN.1.39 thing.
Add branch 55. Branch 22 revives.
Add branch 55.
it was singlet 11 of #1089 already doubled thx
Flirt branch 50 +1 England
KQ.1 seems to have now a singlet with 456L Query : G25555T,A25582G from Hawaii
Flirt branch 50 +1 England
Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.
Flirt branch 50 +1 England
Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.
wait it is already 8! New query : C8092T, T21740C, G22599C Epi- set: EPI_ISL_18874336, EPI_ISL_18999269, EPI_ISL_18999314, EPI_ISL_19019175, EPI_ISL_19025924, EPI_ISL_19028032-19028033, EPI_ISL_19028035
Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_3acf3_d18670.json?label=id:node_6971728 Please propose it @aviczhl2
Flirt branch 50 +1 England
Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.
wait it is already 8! New query : C8092T, T21740C, G22599C Epi- set: EPI_ISL_18874336, EPI_ISL_18999269, EPI_ISL_18999314, EPI_ISL_19019175, EPI_ISL_19025924, EPI_ISL_19028032-19028033, EPI_ISL_19028035
The tree seems a little bit messy. 2 Having the Orf3a reversion and one having S:456 reversion. What's shown on usher tree may not be the correct order. Maybe some form of recomb?
Flirt branch 50 +1 England Please propose it @aviczhl2
I got it. The correct order shall be 18471->25688->3913->8092+S:S60P,R346T+25378 (Texas S:456F seq ends here)->S:F456L->recomb with JN.1+25571(and remove 25378+25688) branch (2 GBW)
So actual toll is 1(S:60P+346T)+5(S:60P+346T+456L)+2(S:60P+346T+456L+recomb)
Branch 29 designated KW.1.1
4/4: Add branch 56-63
Branch 61 is FLiRT. Branch 62 has serious misplacement issue, some placed under JN.1.16 and FLiRT sub-branch placed under JN.1.9(Flip-Flop reversion)
Flirt branch 55 now went to three the last sample is the oldest and it has no S:272H so maybe the query could be changed in: ,T22928C,C14220T,C22311A that finds all the samples of it.
tree:
4/8: Add branch 65
Branch 46 reaches 69.
4/8: Add branch 65
Branch 46 reaches 69.
propose br 46
Add FLiRT branch 66, shall be separated from KU.2.
Branch 34 revives and becomes 10. Add branch 68.
Add FLiRT branch 66, shall be separated from KU.2.
why do you think it should be separated? C7113T is quite homoplasic so i dont see evidences to be a separated lineage. Maybe a recombinant with JN.1.11.1 ? that but hard to prove
Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?
Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?
There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here.
BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.
Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?
There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here.
BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.
ah ok thx, good catch, even if we cant be completely sure that is convergence, maybe an intermediate sequence will shape the tree better.
@angiehinrichs what do you think: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2ee43_7934e0.json?c=userOrOld&label=id:node_6922569
Branch 30 revives in Canada
Add branch 70 and 71.
4/12: Add branch 72-75.
- 26894T, C7732T,G22599C, T22928C
3 continents with 5 sequences
Branch 30 FliRT is expanding
about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T
about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T
Also branch 22 shall be this.
about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T
Maybe you shall propose the Orf1a:N2147S+ S:R346T branch, clearly sth. misplaced under JN.1.18. (And has FLiRT and FViRT sub-branches)
G22599C,A6705G,C18894T gets 58.
about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e6bb_973690.json?label=id:node_6958337
Maybe you shall propose the Orf1a:N2147S+ S:R346T branch, clearly sth. misplaced under JN.1.18. (And has FLiRT and FViRT sub-branches)
G22599C,A6705G,C18894T gets 58.
yeah i will!
branch 73 has a singlet with FLiRT : BR73>C3244T, A18432T> G29383A > C17373T, S:R346T (G22599C), G29383A Query: G29383A,C17373T, G22599C
Also branch 22 shall be this.
ok i ll propose everything in one
Also branch 22 shall be this.
ok i ll propose everything in one
now both BR.22 and BR.71 proposed in https://github.com/cov-lineages/pango-designation/issues/2560
There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here. BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.
ah ok thx, good catch, even if we cant be completely sure that is convergence, maybe an intermediate sequence will shape the tree better.
@AngieHinrichs what do you think: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2ee43_7934e0.json?c=userOrOld&label=id:node_6922569
The larger branch with A3647T (ORF1a:I1128F) is KU.2 > A3647T,C7113T,C27813A (KU.2 is JN.1.30.1 > T22928C (S:F456L)) and is well-supported (13 sequences from 7 countries). Then there are only two sequences (both India/MH_BJCOG_INSACOG) placed at JN.1.30.1 > A3647T. I will prune & replace those and see what happens.
It seems that S:F456L is very convergent in JN.1 now. (last complete update June 19)
Doublets and Singlets no longer tracking. Only track >=3 branches, or branches with seqs from multiple countries now.