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Multiple JN.1 sequences with S:T572I : 74 Branches as Apr 28 #1097
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Thank you @aviczhl2 |
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Branch 5 went to 10 (ping @corneliusroemer ) |
Oh, the recomb of branch 5 and XBB goes to 2. |
Propose it in a separate issue |
Branch 5 +3 Sweden, 13 now |
ping @corneliusroemer i suggest direct designation of branch 5. |
thx @aviczhl2 |
Branch 5 is 24 now. 1->5->24 in the last 2 weeks. |
@corneliusroemer please designate it(branch 5) clearly up quickly |
thx @Memorablea |
branch 1: +1 |
Branch +1 >> 4 ping @corneliusroemer also Branch 3 seems quite fast. |
Branch 3 at 10 (+2) |
Branch 4 : +1 Switzerland |
branch 2 went to 4 all french samles. Note that 3 out of 4 have S:N657D |
Added branch 7 mini saltation with 49Y,572I,1259Y |
thx already proposed in the main repo |
Added one more combo branch 62 and modified query for combo branch 59 spotted by @aviczhl2 |
Added branch 63 combo on Jn.1.11.1 backbone |
Branch 18 designated KV.2 via cov-lineages/pango-designation@4a1ca73 |
There seems to be a new branch. |
thx @aviczhl2 missed your messages , updating it now |
Orf1a:A2529V was the defining mutation of infamous AY.4 lineage, here mutated to S instead |
Branch 59 by @aviczhl2 designated KP.1.2 via cov-lineages/pango-designation@0f3e1f8 |
…JN.1.47.2 ( S:T572I, S:R683Q, USA)
Branch 26 designated JN.1.47.2 via cov-lineages/pango-designation@9fcb3e6 |
Added a branch froma. former singlet. |
C7732T, C20436T, C23277T |
Thank you added as br.74 |
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. |
Yesterday a S:t572I + S:R683Q sublineage has been uploaded from South Africa, or https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3e202_54ce0.json?c=userOrOld&label=id:node_7131733 |
Branch 1 > Now designated JN.1.7
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
Branch 4 dead
Branch 5 >Count 358 designated JN.1.1.1
Branch 6 > Count 25 Canada sublineage of JN.1.2 / DUPLICATE of Branch 13 keeping the other open
Branch 7 Dead
Branch 8 > designated JN.1.4.3
Branch 9 > dead
Branch 10 > Dead
Branch 11 Dead
Branch 12 Dead
Branch 13 Slow
Branch 14 proposed in cov-lineages/pango-designation#2461
Branch 15 > Designated KW.1
Branch 16 > Dead
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
Branch 19 designated JN.1.4.6
Branch 20 now proposed in cov-lineages/pango-designation#2512
Branch 21 count 5 Denmark Dead
Branch 22 > count 8 USA Nevada dead
Branch 23 Dead
Branch 24 > Dead
Branch 25 > Dead
Branch 26 > Designated JN.1.47.2
Branch 27 > Designated JN.1.9.1
Branch 28 Dead
Branch 29 Dead
Branch 30 Dead
Branch 31 > dead
Branch 32 now it is under JN.1.4.3
Branch 33 Dead
Branch 34 > Count 5 Germany Us UK dead
Branch 35 Dead
Branch 36 dead
Branch 37 > 22 US
JN.1.4.5 ( T18453C+Orf8:S103L=C28201T)> C11653T > S:T572I ( C23277T)
Query: C28201T, C11653T , C23277T
Branch 38 Dead
Branch 39 > count: 13 (US)
JN.1 > G17562T, C27563T > C27595T > Orf1a:S2242F (C6990T) > S:T572I (C23277T)
Query: C6990T,C27595T, C23277T
Branch 40 dead
Branch 41 Dead
Branch 42
Branch 43: > 4 US Dead
Branch 44 DEAD
Branch 45 now proposed in cov-lineages/pango-designation#2540
Branch 46 Dead
Branch 47 > 19 (Can,Us)
JN.1 > A18093G > S:T572I (C23277T)
Query: A18093G ,C23277T,T3565C
Branch 48 dead
Branch 49 > 20 Chile ( Spotted by @aviczhl2 )
JN.1.21 (S:H1058Y) > Orf1b:K2358R (A20540G) > S:T572I (C23277T)
Query: A20540G,C23277T
Branch 50 Dead
Branch 51 > 28 South Korea
JN.1.1> > C11747T > T16461C > A4912G > S:T572I (C23277T)
Query: C11747T , T16461C , A4912G ,C23277T
Branch 52 Dead
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
Branch 58 Australia spotted and proposed by @aviczhl2 in #1473
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
Branch 62 combo dead
Branch 63 Designated KP.5
Now proposed in cov-lineages/pango-designation#2568
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
Branch 65 Dead
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
Branch 68 proposed by @aviczhl2 in #1501
Branch 69: spotted and proposed by @aviczhl2 in #1518
branch 70: dead
Branch 71 : proposed in cov-lineages/pango-designation#2564
Branch 72: spotted by @aviczhl2 and proposed in #1522
Branch 73 spotted and proposed by @aviczhl2 in #1518
Branch 74 spotted by @DoropFan
JN.1>T18471C>C7732T>C20436T>C23277T
Query: C7732T, C20436T, C23277T,T3565C
Samples: 15
Singlets:
Query for all JN.1 + 572I = C18894T, T15756A, -C6541T,C23277T > 5209
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