LF.7 + S:T572I multiple branches (updated as Feb 3)

[FedeGueli]

EDITED: It seems S:t572I is highly homoplasic on LF.7 backbone hence i transform this in a multiple lineages issue.
I will add branches with at least a sample in the past 40 days.
General query to find LF.7+572I : C5239T, C7869T, C8818T, G12892A, T16600C,C23277T

Branch 1: Now designated LF.7.7.1

now proposed in cov-lineages/pango-designation#2855
LF.7 >> Orf1a:R1225I (G3939T) > S:T572I (C23277T)
Query:C5239T, C7869T, G3939T,C23277T
Samples: 37
Places: Peru'(7+3gbw),NZL,NY,Germany, Italy, Colombia,Spain,US

Branch 2: dead
LF.7.3 >> C22855T > ORF1a:A1812T (G5699A), S:E180D (A22102T), ,S:T572I (C23277T),S:T1117A (A24911G)
Query: C22855T ,G5699A,A22102T
Samples: 1
Places : Australia

Branch 3:
LF.7.1 >> C25671T > T21408C, C29311T > ORF1a:T2283I (C7113T),Orf1b:A2132V (C19862T), S:T572I (C23277T)
Query: T21408C, C29311T ,C7113T,C19862T
Samples: 14
Places : Canada NB

Branch 4 now proposed in cov-lineages/pango-designation#2873

LF.7.1 >> S:T572I (C23277T) > T493C
Double query:
New: C6310T,C23277T,C8818T,-T493C,-A3398G, -C4068T,-C25006T,-C25671T,-G4354A,-A798G,-T20040C
plus
OLD: T493C,C23277T, C7869T
Samples:17
Places: Slovenia, US, Sweden, England,Poland,France, Finland, Netherlands

Branch 5 dead
NT.1 >> S:V475A (rev) > ORF1a:A3523V (C10833T), ORF1b:P2727L (C18647T),S:T572I (C23277T)
Query: C10833T,C18647T,G4354A
Samples: 1
Places: Qatar

Branch 6
LF.7.6 >>ORF1a:E1340D (G4285T), C18681T, S: T572I (C23277T), C23575T, G29179T
Query: C18681T, C23277T, C23575T,
Samples: 2
Singapore,US

Branch 7
LF.7 >> T21823C, A28855T > S:T572I (C23277T)
Query: C23277T,T21823C, A28855T
Samples: 2
Mozambique

[FedeGueli]

7 FROM 6 PLACES (new England, Canada, Italy)

[FedeGueli]

+3 Qatar(new) and New Brunswick

[FedeGueli]

Transformed in a multiple lineages issue because 572I is now homoplasic and the linegae proposed here is now splitted in many branches

cc. @xz-keg

[FedeGueli]

BR.1 BR.3 BR.4 grew

[FedeGueli]

BR.1: +1 GBW from Peru'

[FedeGueli]

Br.4 new query found one more sample: T493C,C23277T, C7869T

[FedeGueli]

cc @xz-keg
Br.1 jumped to 17 with 3 GBW samples from two patients from two South American countries: Peru' and Colombia. worth Proposing it?

Br.3 up to 7

[xz-keg]

cc @xz-keg Br.1 jumped to 17 with 3 GBW samples from two patients from two South American countries: Peru' and Colombia. worth Proposing it?

Br.3 up to 7

yeah please propose.

[FedeGueli]

Br.4 +3 up to 12 Michigan and Slovenia

[FedeGueli]

Br.4 >> 14 +1 Finalnd, +1 Netherlands cc @xz-keg

[xz-keg]

usher tree of branch 4 has changed and includes everything on LF.7.1+S:T572I.

There seems to be no seq with LF.7+T493C but not S:T572I so this is correct placement.

New query: C23277T, C6310T, C7869T,-C4921T, -C6525T,-T21408C =18 seqs (maybe you can find a better one)

worth proposal @FedeGueli

[FedeGueli]

thx @xz-keg i m looking into it, the query has to be adjusted because it catches some old unrelated sample. i will propose it then.

New query: C6310T,C23277T,C8818T,-A3398G, -C4068T,-C25006T,-C25671T,-G4354A,-A798G,-T20040C finds 15 very likely there are 16 of this but it is quite good to be proposed.

[FedeGueli]

usher tree of branch 4 has changed and includes everything on LF.7.1+S:T572I.

There seems to be no seq with LF.7+T493C but not S:T572I so this is correct placement.

New query: C23277T, C6310T, C7869T,-C4921T, -C6525T,-T21408C =18 seqs (maybe you can find a better one)

worth proposal @FedeGueli

now proposed in cov-lineages/pango-designation#2873

[FedeGueli]

Added a LF.7.6 singlet w 572I from Singapore

[FedeGueli]

New 572I branch from Mozambique:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_258ca_11da40.json?c=userOrOld&label=id:node_11835754

[FedeGueli]

Branch 3 went to 14

[FedeGueli]

Added a LF.7.6 singlet w 572I from Singapore

this is now at 2

[FedeGueli]

Br.1 is now LF.7.7.1 via cov-lineages/pango-designation@b1ba75a