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Multiple JN.1 sequences with S:T572I : 74 Branches as Apr 28 #1097

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FedeGueli opened this issue Nov 20, 2023 · 97 comments
Closed

Multiple JN.1 sequences with S:T572I : 74 Branches as Apr 28 #1097

FedeGueli opened this issue Nov 20, 2023 · 97 comments
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BA.2.86 JN.1 Multiple lineages partially designated S:572 To be proposed Green light for proposal
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JN.1.1.1 JN.1.8.1...

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@FedeGueli
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FedeGueli commented Nov 20, 2023 •
edited

Branch 1 > Now designated JN.1.7

France Count: 439 now proposed in cov-lineages/pango-designation#2428
JN.1 > C25566T > S:T572I (C23277T),S:E1150D (G25012T)
Query : A7842G, G25012T, C25566T,C23277T

Branch 2 > France Count:76 Slow
JN.1 > T26511C > S:T572I (C23277T) Note that 3 out of 4 have also S:N657D
Query: A7842G, T26511C,C23277T

Branch 3 > designated JN.1.8.1

Count: 458
JN.1> > Orf7a:T28I (C27476T)> A12928G > S:T572I (C23277T)
C27476T,C23277T,A12928G

Branch 4 dead

Portugal/Switzerland/Emirates Count: 12 /dead
JN.1.1> ORF1b:A520V (C15026T)> S:T572I (C23277T)
Query: C15026T,A7842G,C23277T,C1762A

Branch 5 >Count 358 designated JN.1.1.1

JN.1.1 > C11747T > C9142T > S:T572I (C23277T)
C23277T,C1762A,C9142T

Branch 6 > Count 25 Canada sublineage of JN.1.2 / DUPLICATE of Branch 13 keeping the other open

Branch 7 Dead

Count 64 Canada (Mini saltation)
JN.1.45 (G18756T) > S:D1259Y (G25337T) > ORF1a:S1510F (C4794T), A13288G, S:H49Y (C21707T), S:T572I (C23277T) , C25413T, C26873T
Query: C25413T, C26873T,A13288G

Branch 8 > designated JN.1.4.3

Count 44 Austria / now proposed in cov-lineages/pango-designation#2487
JN.1.4 > S:T572I (C23277T)
Query : C774T,C23277T,-T18453C,-G27706T ,C18894T,-C3177T,-C26111T,-C25465T,-T911A
then acquired S:R346T

Branch 9 > dead

count 6 Austria /dead
JN.1.1 > C11747T > S:S254F (C22323T) > C9142T > Orf1a:T2283I (C7113T), C8419T, S:T572I (C23277T)
Query: C7113T, C23277T,C8419T

Branch 10 > Dead

count 2 Italy /dead
JN.1.1 > C11747T >C9142T,T8677C, C24337T > S:T572I (C23277T)
Query : T8677C,C24337T,C23277T

Branch 11 Dead

count 4 Scotland / Dead
JN.1.4 > Orf7a:A105S (G27706T) > C4327T, T20217C, C21216A > S:T572I (C23277T)
Query: T20217C ,C23277T,G27706T

Branch 12 Dead

count 40 England/Denmark
JN.1.4 > T18453C >Orf1a:V274L (G1085T), G29260T > Orf1b:R340S (A14487T),S:T572I (C23277T)
Query: G1085T, ,A14487T , C23277T

Branch 13 Slow

count 54 Canada/Uk
JN.1.2 > Orf1b:T2488M (C20930T) > S:t572I (C23277T)
Query: C20930T,C23277T,G25249T

Branch 14 proposed in cov-lineages/pango-designation#2461

count 127 Uk / growing
JN.1 >> Orf3a:L85F (G25647T) > A5053G, T23629C > ORF1a:T2152I (C6720T)> S:T572I (C23277T)
Query: C23277T, A5053G ,C6720T

Branch 15 > Designated KW.1

count 122 , proposed by @Fearuncle in #1244/ cov-lineages/pango-designation#2513 Growing
Defining JN.1.28 (C24034T > A29700G) > C19545T, C24370T > Orf1a:P1640L (C5184T) > T10084A ,S:T572I (C23277T)
Query:C19545T, C24370T ,C5184T,C23277T

Branch 16 > Dead

count 2 France /Dead
Defining JN.1.1>C11747T > C280T > Orf1b:T1646I (C18404T), S:T572I (C23277T)
Query: C280T ,C18404T,C23277T

Branch 17 count 53 (always check) France, England, South Australia
Defining JN.1.1 > C11747T > S:T572I (C23277T)
Query: C1762A,C23277T,C11747T,-C9142T,-C280T,-C5314T,-C4093T,-A4912G,-C1218T,-G1820A,-A6588G,-C16650T,
Now it got a branch with S:R346T Query: C11747T ,C23277T ,G22599C ,T3565C (19)

Branch 18 > Designated KV.2

count 206 Texas /Growing
Defining JN.1.4.5 (T18453C > Orf8:S103L=C28201T) > Orf1a:P971L (C3177T), C11956T, S:T572I (C23277T)
Query: C28201T,C3177T, C11956T,

Branch 19 designated JN.1.4.6

count 107 now proposed in cov-lineages/pango-designation#2504
Defining JN.1.4 > T18453C >S:T572I (C23277T)
Query: C23277T,T18453C,C774T,-G3085T,-G3085T,-T1483C,-C4795T,-T9769C,-C401T,-C29311T,-T18471C,-C2232T,-C25465T,-C1288T,-C3177T,-G910A,-C1762A,-G7393A,-C10748A,-C6781T,-A14487T,-C28201T,-G2202T

Branch 20 now proposed in cov-lineages/pango-designation#2512

count 90 Canada, NY / Growing
Defining JN.1.4 > T18453C > G910A, Orf1a:S216N (T911A, C912A), C8668T, S:T572I (C23277T),
Query: T18453C, C8668T,G910A,C23277T

Branch 21 count 5 Denmark Dead

JN.1.4 > T18453C > S:T572I (C23277T), Orf3a:P25S (C25465T) , C27131T
Query: C23277T, C25465T, C27131T

Branch 22 > count 8 USA Nevada dead

JN.1.19 [ C1060T > Orf8:I71V (A28104G)]> C23575T > C5986T > S:T572I (C23277T),N:P67S (C28472T)
Query: A28104G,C23575T, C5986T ,C28472T

Branch 23 Dead

count 6 ( England) Mini Saltation
JN.1 > G17562T > C3784T, Orf1b:H1550Y (C18115T), S:G446I (G22899T),S:T572I (C23277T), Orf10:R24C (C29627T)
Query: G17562T , C3784T, C18115T

Branch 24 > Dead

count 3 Scotland dead
JN.1 > T2236C > Orf8:G66C (G28089T) > T14865C S:T572I (C23277T),
Query: T14865C,C23277T,G28089T

Branch 25 > Dead

count 8 England, California / dead
JN.1 > C23896G > C186T >C10165T , C12073T, Orf1b:I2568M (A21171G), S:t572I (C23277T)
Query: C10165T, A21171G,C12073T

Branch 26 > Designated JN.1.47.2

JN.1 > C8074T > C7594T > Orf1a:H374Y (C1385T) > S:T572I (C23277T) S:R683Q (G23610A)
Query: C1385T,C23277T,G23610A

Branch 27 > Designated JN.1.9.1

count : 22
JN.1.9 (S:Q183H) > Orf1a:A3143V (C9693T) > S:T572I (C23277T)
Query: C9693T, C897A, C23277T

Branch 28 Dead

count 3 Denmark mini saltation dead
JN.1> G8578A > C26499G > C24382T > Orf1a:R542H (G1890A), Orf1a:Q3346K (C10301A), S:S151I (G22014T),S:t572I (C23277T), T29515C, N:S416L (C29520T)
Query : G1890A ,C10301A

Branch 29 Dead

count 13 US (Modified: there is more than one branch with A13308G)
JN.1 > Orf1a:K4348R (A13308G) > Orf1a:W646L (G2202T) > S:T572I (C23277T)
Query: A13308G, C774T,T18453C,C23277T,G2202T

Branch 30 Dead

count 23 Spain
JN.1.31 (Orf3a:V13L )(G25429T) > C19186T > C18687T > C14403T, S:T572I (C23277T)
Query: C14403T, C23277T, G25429T

Branch 31 > dead

Count 2 Singapore dead
JN.1.5> C5986T> S:T572I (C23277T)
Query: C5986T,C23277T,G17278A

Branch 32 now it is under JN.1.4.3

Count 103 US (To be proposed ?)
JN.1.4 > Orf9b:S50L ( C28432T )> S:T572I (C23277T)
Query: C28432T,C23277T, C774T

Branch 33 Dead

Count 25 France, US
JN.1.4.7 [ Orf3a:G18D (G25445A)] > S:T572I (C23277T)
Query: G25445A,C23277T,C774T

Branch 34 > Count 5 Germany Us UK dead

JN.1.4 > G7393A > C18888T, S:T676N (C23589A) > S:T572I (C23277T)
Noted that further acquired Orf10:S23F (Recomb?)
Query: C18888T, C23589A ,C23277T

Branch 35 Dead

count 1 Arizona
JN.1.4 > S:R346T (G22599C) > C4084T, C12754T, C26885T > C29635T > C2980T, S:T572I (C23277T), Orf7a:V71L (G27604T)
Query: C2980T,G27604T,C4084T

Branch 36 dead

count 7 Italy dead
JN.1> C1060T > T9124C, T16605C, S:T572I (C23277T), A24727G
Query: T9124C, T16605C

Branch 37 > 22 US
JN.1.4.5 ( T18453C+Orf8:S103L=C28201T)> C11653T > S:T572I ( C23277T)
Query: C28201T, C11653T , C23277T

Branch 38 Dead

3 Singapore dead
JN.1.4.5 ( T18453C,Orf8:S103L =C28201T)> C28948T > C10138T > S:T572I (( C23277T) then Orf1b:K2557R
Query: C28948T ,C10138T ,C23277T

Branch 39 > count: 13 (US)
JN.1 > G17562T, C27563T > C27595T > Orf1a:S2242F (C6990T) > S:T572I (C23277T)
Query: C6990T,C27595T, C23277T

Branch 40 dead

7 UK slow
JN.1 >> G17562T > T13737C, S:T572I (C23277T), Orf3a:C200G (T25990G)
Query: T13737C, T25990G

Branch 41 Dead

4 US slow
JN.1.4 > C1288T > C2942T > S:T572I (C23277T)
Query: C1288T, C2942T ,C23277T

Branch 42

11 UK dead
JN.1.19 > Orf1a:N2065S (A6459G) > S:T572I (C23277T) , C23758T, C25521T, Orf3a:T229I (C26078T)
Query: A6459G, C23758T, C25521T

Branch 43: > 4 US Dead

JN.1 > C17676T > S:R683Q (G23610A) > S:T572I (C23277T)
Query: C17676T,G23610A,C23277T

Branch 44 DEAD

3 Uk dead
JN.1 > S:R683Q (G23610A) > C10747T, Orf1b:A1369V (C17573T), S:T572I (C23277T) ,Orf7a:P34L (C27494T)
Query: C10747T, C17573T,C23277T
Note that it is misplaced in the same tree of branch 43.

Branch 45 now proposed in cov-lineages/pango-designation#2540

37 Uk fast
JN.1.4> > T18453C > N:A35T( G28376A) > C23929T > C6781T, S:K150R (A22011G), S:T572I (C23277T)
Query: C23929T, C6781T,A22011G or C6781T,A22011G

Branch 46 Dead

10 (US:Tx,NY)
JN.1 > C26894T > C25680T > A28699T > S:T572I (C23277T)
Query: C26894T , C25680T, A28699T ,C23277T

Branch 47 > 19 (Can,Us)
JN.1 > A18093G > S:T572I (C23277T)
Query: A18093G ,C23277T,T3565C

Branch 48 dead

13 (Can Us)
JN.1 > T772C > A8122G > [Orf1b:T1555I (C18131T) then reverted]> C20178T, S:T572I (C23277T), C27804T,T28924A
Query: C20178T, C23277T, C27804T,A8122G

Branch 49 > 20 Chile ( Spotted by @aviczhl2 )
JN.1.21 (S:H1058Y) > Orf1b:K2358R (A20540G) > S:T572I (C23277T)
Query: A20540G,C23277T

Branch 50 Dead

4 US
JN.1.4 > Orf1a:Q575H (G1990T)> Orf1a:T1437I (C4575T) > S:T572I (C23277T) ,N:P383L (C29421T)
Query: G1990T,C4575T,C23277T

Branch 51 > 28 South Korea
JN.1.1> > C11747T > T16461C > A4912G > S:T572I (C23277T)
Query: C11747T , T16461C , A4912G ,C23277T

Branch 52 Dead

2 Canada
Jn.1.1 >> C11747T > C280T > Orf1b:L1551I (C18118A) > C11704T > S:H207Q (C22183A), S:T572I (C23277T), G28079T
Query: C22183A, C23277T, G28079T

Branch 53 > 9 Wales Slow
JN.1 > Orf1a:I2903M (A8974G )> Orf1a:W630C (G2155T) > Orf1b:H2010Y (C19495T), S:T572I (C23277T)
Query: G2155T,C19495T,C23277T

Branch 54 > 34 US
JN.1>C1060T > C9166T > Orf1a:T2166N (C6762A) > S:T572I (C23277T)
Query: C9166T ,C6762A,C23277T,T3565C

Branch 55 > 22 Austria,Spain
JN.1> Orf3a:D199H (G25987C) > S:T572I (C23277T)> T14179C,C25710T Orf3a:D199H reverted then
Query: T14179C,C25710T

Branch 56 > 13 Hubei
JN.1 > Orf1a:G400S (G1463A) > C3817T > A19314G > A29538G > Orf1a:P959S (C3140T), S:T572I (C23277T)
Query: A19314G ,C3140T,C3817T

Branch 57 Dead

4 France,Texas,Germany
JN.1 > Orf1a:D75Y (G488T) > S:T572I (C23277T )
Query: G488T , C23277T,T3565C (finds only 3 )

Branch 58 Australia spotted and proposed by @aviczhl2 in #1473

JN.1 >JN.1 >C9996T(Orf1a:S3244L)> C21766T, G22343C(S:G261R) >Orf1a:R2860S (A8845C),S:T572I(C23277T )
Query:C23277T, G22343C,A21766T
Samples : 13

Branch 59 Designated KP.1.2 spotted by @aviczhl2
KP.1 >C5884T, T10636G, S:T572I (C23277T), G24193C, C29218T
Query: A24819G,C23277T,T3565C new query ( old query: C5884T, T10636G)
Samples: 4 US
There is another sample clustering with this without the silent mutations but with S:S:680P and S:K1245R

Branch 60 found using @aviczhl2 's tool #1484
JN.1.4> > T18453C > Orf1a:K4348K (A13308G)> Orf1b:P1223T (C17134A) > S:T572I ( C23277T)
Query: C17134A,C23277T,A13308G
Samples : 6 (South Korea)

Branch 61 dead

found by @aviczhl2 and proposed in #1485
JN.1.1> T18173C(Orf1b:I1569T)>C16650T> S:K444R (A22893G)> S:T572I (C23277T)
Query: T18173C,C16650T,A22893G,C23277T
Samples: 4

Branch 62 combo dead

JN.1.11.1 > C6070T > C10969T, S:T572I (C23277T) ,A26579G
Query: C6070T,C10969T, A26579G
Samples: 3 Uk Israel

Branch 63 Designated KP.5
Now proposed in cov-lineages/pango-designation#2568

COMBO JN.1.11.1 >S:T572I (C23277T)
Query:C7113T,C23277T,T3565C, G24872T,-G9010A,-C6070T,-A24819G,T22928C
Samples: 15

Now TRIO Branch:
JN.1.11.1 >S:T572I (C23277T) > C3811T > C2197T, C9857T, S:R346T (G22599C) ,A23080G
Query:C3811T , C2197T, C9857T,T3565C
Samples: 4 (US)

Branch 64 Dead

JN.1 > C23086T >C4921A, C10726T, T17262C,S:T572I (C23277T), Orf3a:I37T (T25502C), C29272T
Query: C4921A, C10726T, T17262C
Samples: 5 UK

Branch 65 Dead

JN.1.19 (Orf8:I71V,C1060T) > Orf1a:N2065 (A6459G)> Orf1a:E87D(G526T)> C5806T, C19380T, S:T572I (C23277T), REV. S:N679N (C23599C)
Query:C5806T, C19380T, C23277T
Samples: 3 England

Branch 66 found by @aviczhl2 in #1513
JN.1 > Orf1a:K4483R (A13712G) > Orf1a:A2529S (G7850T) > Orf1a:D1513E (T4804G) >S:T572I (C23277T) Orf3a:S92L (C25667T), T26047C, C28115T
Query: C25667T, T26047C, C28115T
Samples : 35 Australia

Branch 67 dead

found by @aviczhl2
.1 > Orf1a:A2097V (C6555T)> T22555C > N:M210T (T28902C)>T16731C > Orf3a:Y107C (A25712G) > Orf1a:L204F (C875T), Orf1a:T2166I (C6762T), S:H146Y (C21998T), S:T572I (C23277T), Orf3a:T175I (C25916T)
Query: C875T,C6762T,T3565C
Samples: 4 ITALY

Branch 68 proposed by @aviczhl2 in #1501

JN.1> JN.1+C16323T> (Orf8:E19* (G27948T), Orf9b:A22V (C28348T) > S:T572I (C23277T)
Query: G27948T, C28348T, C23277T
Samples: 7

Branch 69: spotted and proposed by @aviczhl2 in #1518

JN.1.18+G25606A(Orf3a:A72T)+A13288G+A28834G+A3558G,C15933T, A25359G(Orf1a:K1098R,S:K1266R)+C23277T, G26367T, C28651T, C29555T(S:T572I)
Query: C23277T,A25359G, A13288G
Samples:7

branch 70: dead

Ex singlet 2 AUS QLD mini saltation
JN.1 WITH S:S31F S:Q1180K N:H300Y
Query: T11737C, C21654T, C23277T, C28603T
Samples: 2

Branch 71 : proposed in cov-lineages/pango-designation#2564

JN.1 > C6896T > A19578G > S:T572I (C23277T)
Query: C6896T , A19578G , C23277T, T3565C
Samples: 77 Australia, New Zealand Canada

Branch 72: spotted by @aviczhl2 and proposed in #1522

XDQ.1+A18184G(Orf1b:M1573V)+C3885T, A12709G, A26594T, C20320T, C20719T, C23277T, G29254A(Orf1a:P1207L, Orf1b:H2285Y, S:T572I)
query: C23277T, A18184G, C28846T
Seqs: 5(Japan)

Branch 73 spotted and proposed by @aviczhl2 in #1518

JN.1.18+G25606A(Orf3a:A72T)+A13288G+A28834G+A3558G,C15933T, A25359G(Orf1a:K1098R,S:K1266R)+C23277T, G26367T, C28651T, C29555T(S:T572I)
GISAID query for S:T572I branch: C23277T,A25359G, A13288G
(7 seqs)

Branch 74 spotted by @DoropFan
JN.1>T18471C>C7732T>C20436T>C23277T
Query: C7732T, C20436T, C23277T,T3565C
Samples: 15

Singlets:

  1. Fujan query: C6385T, A16339G, C28313T
  2. Moved to Br.70

AUS QLD mini saltation Query: T11737C, C21654T, C23277T, C28603T WITH S:S31F S:Q1180K N:H300Y

  1. moved to branch 62

JN.1.11.1 ( combo) + Orf1a:C667Y, Orf1a:G1073V +S:T572I Query: G174T, G2265A, G3483T

Query for all JN.1 + 572I = C18894T, T15756A, -C6541T,C23277T > 5209
@Memorablea Memorablea mentioned this issue Nov 23, 2023
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@aviczhl2
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aviczhl2 commented Nov 25, 2023 •
edited

Branch 5 is 5 now, plus 1 recomb with XBB* that cause it to lose C1762A

image

@FedeGueli
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Thank you @aviczhl2

@Fearuncle
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image
issue #987 got S:T572I

@FedeGueli
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Branch 5 went to 10 (ping @corneliusroemer )
branch 3 went to 4

@FedeGueli FedeGueli removed the Singlet One only sample. label Nov 29, 2023
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Oh, the recomb of branch 5 and XBB goes to 2.

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Oh, the recomb of branch 5 and XBB goes to 2.

Propose it in a separate issue

@aviczhl2 aviczhl2 mentioned this issue Nov 29, 2023
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aviczhl2 commented Dec 1, 2023 •
edited

Branch 5 +3 Sweden, 13 now

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ping @corneliusroemer i suggest direct designation of branch 5.

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thx @aviczhl2

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aviczhl2 commented Dec 2, 2023 •
edited

Branch 5 is 24 now.

1->5->24 in the last 2 weeks.

@FedeGueli
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Branch 5 is 24 now.

1->5->24 in the last 2 weeks.

@corneliusroemer please designate it(branch 5) clearly up quickly

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cov-lineages/pango-designation@10d1bb4

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thx @Memorablea
Branch 5 now designated JN.1.1.1 via cov-lineages/pango-designation@10d1bb4

@FedeGueli FedeGueli added this to the JN.1.1.1 milestone Dec 2, 2023
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FedeGueli commented Dec 4, 2023 •
edited

branch 1: +1
Branch 2 : +2

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Branch +1 >> 4
Branch +4 >> 8

ping @corneliusroemer also Branch 3 seems quite fast.

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I Multiple JN.1 sequences with S:T572I as 12/08 Dec 8, 2023
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Branch 3 at 10 (+2)

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Branch 4 : +1 Switzerland

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branch 2 went to 4 all french samles. Note that 3 out of 4 have S:N657D

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Added branch 7 mini saltation with 49Y,572I,1259Y

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 60 Branches as 2024-30-03 Multiple JN.1 sequences with S:T572I : 61 Branches as 2024-01-04 Apr 1, 2024
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image

thank you can you send the usher link please?

https://nextstrain.org/fetch/raw.githubusercontent.com/aviczhl2/usher_analyse_tool/main/usher-4.json?branchLabel=Spike%20mutations&f_userOrOld=highlighted%20sample&label=id:node_7035235

thx already proposed in the main repo

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FedeGueli commented Apr 1, 2024 •
edited

Added one more combo branch 62 and modified query for combo branch 59 spotted by @aviczhl2

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 61 Branches as 2024-01-04 Multiple JN.1 sequences with S:T572I : 62 Branches as 2024-01-04 Apr 1, 2024
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Added branch 63 combo on Jn.1.11.1 backbone

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 62 Branches as 2024-01-04 Multiple JN.1 sequences with S:T572I : 64 Branches as 2024-01-04 Apr 1, 2024
@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 64 Branches as 2024-01-04 Multiple JN.1 sequences with S:T572I : 65 Branches as 2024-01-04 Apr 1, 2024
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Branch 18 designated KV.2 via cov-lineages/pango-designation@4a1ca73

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aviczhl2 commented Apr 4, 2024 •
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image

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_d555_dff9c0.json?label=id:node_6951679

There seems to be a new branch.

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aviczhl2 commented Apr 4, 2024

image
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice14_genome_test_2d106_e057d0.json?branchLabel=Spike%20mutations&label=id:node_6966453&showBranchLabels=all

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thx @aviczhl2 missed your messages , updating it now

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https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_d555_dff9c0.json?label=id:node_6951679

There seems to be a new branch.

Orf1a:A2529V was the defining mutation of infamous AY.4 lineage, here mutated to S instead

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 65 Branches as 2024-01-04 Multiple JN.1 sequences with S:T572I : 67 Branches as 2024-07-04 Apr 7, 2024
@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 67 Branches as 2024-07-04 Multiple JN.1 sequences with S:T572I : 68 Branches as 2024-07-08 Apr 8, 2024
@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 68 Branches as 2024-07-08 Multiple JN.1 sequences with S:T572I : 69 Branches as 2024-07-13 Apr 13, 2024
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FedeGueli commented Apr 16, 2024 •
edited

Branch 59 by @aviczhl2 designated KP.1.2 via cov-lineages/pango-designation@0f3e1f8

FedeGueli referenced this issue in cov-lineages/pango-designation Apr 16, 2024
@corneliusroemer
Designate KP.1.2 (S:T572I)
0f3e1f8
FedeGueli referenced this issue in cov-lineages/pango-designation Apr 16, 2024
@corneliusroemer
Designate JN.1.47 (C8074T, C7594T), JN.1.47.1 (S:S221L, USA/Mexico), …
9fcb3e6 
…JN.1.47.2 ( S:T572I, S:R683Q, USA)
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Branch 26 designated JN.1.47.2 via cov-lineages/pango-designation@9fcb3e6

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 69 Branches as 2024-07-13 Multiple JN.1 sequences with S:T572I : 70 Branches as Apr 18 Apr 18, 2024
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Added a branch froma. former singlet.

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 70 Branches as Apr 18 Multiple JN.1 sequences with S:T572I : 71 Branches as Apr 18 Apr 21, 2024
@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 71 Branches as Apr 18 Multiple JN.1 sequences with S:T572I : 73 Branches as Apr 21 Apr 21, 2024
@FedeGueli FedeGueli mentioned this issue Apr 27, 2024
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C7732T, C20436T, C23277T
JN.1>T18471C>C7732T>C20436T>C23277T
72T572I
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e004_e43e70.json?c=country&label=id:node_6985905

@FedeGueli FedeGueli changed the title Multiple JN.1 sequences with S:T572I : 73 Branches as Apr 21 Multiple JN.1 sequences with S:T572I : 74 Branches as Apr 28 Apr 28, 2024
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C7732T, C20436T, C23277T JN.1>T18471C>C7732T>C20436T>C23277T 72T572I https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e004_e43e70.json?c=country&label=id:node_6985905

Thank you added as br.74

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I think it is time to close this one, the lineages still growing are very small and unable to compete vs FLiRT and oother fast lineages. If anyone spots something growing please propose it, just if present here please mention the branch.

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FedeGueli commented May 24, 2024 •
edited

Yesterday a S:t572I + S:R683Q sublineage has been uploaded from South Africa,
it is currentky misplaced both in JN.1.13.1 and JN.1.18
i think the path could be JN.1 + S:r346T (G22599C) > C16041T > S:T572I (C23277T), S:R683Q (G23610A)
Query: C16041T,C23277T,G23610A finds only two
but the USher tree is this one:
Screenshot 2024-05-24 alle 11 00 24https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_c852_388e0.json?c=userOrOld&label=id:node_7136869

or

Screenshot 2024-05-24 alle 11 01 03 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3e202_54ce0.json?c=userOrOld&label=id:node_7131733

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