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JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) #2560

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FedeGueli opened this issue Apr 12, 2024 · 23 comments
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JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) #2560

FedeGueli opened this issue Apr 12, 2024 · 23 comments

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@FedeGueli
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FedeGueli commented Apr 12, 2024 •
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There is an undesignated branch of JN.1 with Orf1a:N2147S
that has further got S:R346T and then both S:F456L and S:F456V but the S:R346T sublineage is currently misplaced under JN.1.18

Query for the big Orf1a:N2147S branch: A6705G,T3565C,C897A NOW JN.1.64
Samples: 941
Tree: (correctly placed as JN.1 > A6705G )
Screenshot 2024-04-13 alle 00 37 04
Screenshot 2024-04-13 alle 00 37 24

Query for S:R346T :G22599C,A6705G,C18894T. [ correct placement JN.1 > A6705G > S:R346T (G22599C)]
NOW JN.1.64.1
Samples: 280

IDs EPI_ISL_18787955, EPI_ISL_18787958, EPI_ISL_18797558, EPI_ISL_18798347, EPI_ISL_18839354, EPI_ISL_18849828, EPI_ISL_18849831, EPI_ISL_18851601, EPI_ISL_18886322, EPI_ISL_18886383, EPI_ISL_18893879, EPI_ISL_18899783, EPI_ISL_18913959, EPI_ISL_18916646, EPI_ISL_18917992, EPI_ISL_18926841, EPI_ISL_18932356, EPI_ISL_18936055, EPI_ISL_18938683, EPI_ISL_18943666, EPI_ISL_18944205, EPI_ISL_18946621, EPI_ISL_18946625, EPI_ISL_18968557, EPI_ISL_18972723-18972724, EPI_ISL_18972729-18972730, EPI_ISL_18972732, EPI_ISL_18972746, EPI_ISL_18972748, EPI_ISL_18972750, EPI_ISL_18972754-18972755, EPI_ISL_18972758-18972759, EPI_ISL_18976003, EPI_ISL_18983805, EPI_ISL_18987184, EPI_ISL_18995123, EPI_ISL_18999173, EPI_ISL_19006630, EPI_ISL_19009690, EPI_ISL_19014582, EPI_ISL_19015257, EPI_ISL_19021968, EPI_ISL_19023194, EPI_ISL_19024784, EPI_ISL_19025707, EPI_ISL_19026937, EPI_ISL_19028230, EPI_ISL_19030832, EPI_ISL_19032599, EPI_ISL_19033444, EPI_ISL_19041313, EPI_ISL_19041364, EPI_ISL_19044406, EPI_ISL_19044734,

Query for FLiRT 1 : T22930A,G22599C, A6705G,C18894T
Now MD.1
[correct placement JN.1 > A6705G > S:R346T (G22599C) >S:F456L (T22930A) ] formerly tracked as Branch 71 of sars-cov-2-variants/lineage-proposals#1253
Samples: 69 ( 16 with S:N679R - edited on May 07 )

IDs EPI_ISL_19041364, EPI_ISL_19044406, EPI_ISL_19041313

Query for FLiRT 2: C10138T, T22928C, C25708T [ correct placement JN.1 > A6705G > S:R346T (G22599C) >
C1060T > C9319T, C28657T > C10138T, S:F456L (T22928C), Orf3a:L106F (C25708T)
NOW MD.3.1
Samples: 46 ( 1 or 2 with Orf9b:T83I (C28531T) query: C10138T, C28531T,C12049T)

IDs EPI_ISL_19026937, EPI_ISL_19051601

Query for FLiRT 3 : DEAD

C2706T, T22928C,A6705G [ correct placement JN.1 > A6705G > S:R346T (G22599C) >
Orf1a:T814I (C2706T), S:F456L (T22928C)
Samples: 4

IDs EPI_ISL_19143847, EPI_ISL_19143857, EPI_ISL_19143882, EPI_ISL_19143891

Query for FViRT : G22599C, T22928G,A6705G (correct placement: JN.1 > A6705G > S:R346T (G22599C) > Orf1a:T2800I (C8664T), S:F456V (T22928G)]
NOW MD.2
formerly tracked as Branch 22 of sars-cov-2-variants/lineage-proposals#1253
Samples : 50

IDs EPI_ISL_18917992, EPI_ISL_18932356, EPI_ISL_18938683, EPI_ISL_19023194, EPI_ISL_19024784

Tree misplaced as JN.1.18
Screenshot 2024-04-13 alle 00 40 43
@FedeGueli FedeGueli mentioned this issue Apr 12, 2024
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@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T ( and this is misplaced under JN.1.18 currently) [Analyzed all along with @aviczhl2] JN.1 + Orf1a:N2147S branch got S:R346T ( and this is misplaced under JN.1.18 currently) [Spotted and Analyzed all along with @aviczhl2] and then further FLiRT or FViRT Apr 12, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T ( and this is misplaced under JN.1.18 currently) [Spotted and Analyzed all along with @aviczhl2] and then further FLiRT or FViRT JN.1 + Orf1a:N2147S branch got S:R346T 58 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (5) sublineages both spotted by @Aviczhl2 Apr 12, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 58 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (5) sublineages both spotted by @Aviczhl2 JN.1 + Orf1a:N2147S branch got S:R346T 58 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (6) sublineages both spotted by @Aviczhl2 Apr 15, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 58 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (6) sublineages both spotted by @Aviczhl2 JN.1 + Orf1a:N2147S branch got S:R346T 59 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (6) sublineages both spotted by @Aviczhl2 Apr 15, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 59 sequences ( misplaced under JN.1.18 currently) and then further FLiRT (3) or FViRT (6) sublineages both spotted by @Aviczhl2 JN.1 + Orf1a:N2147S branch got S:R346T 59 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages both spotted by @Aviczhl2 Apr 16, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 59 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages both spotted by @Aviczhl2 JN.1 + Orf1a:N2147S branch got S:R346T 61 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages both spotted by @Aviczhl2 Apr 16, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 61 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages both spotted by @Aviczhl2 JN.1 + Orf1a:N2147S branch got S:R346T 61 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages spotted by @Aviczhl2 Apr 16, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S branch got S:R346T 61 sequences ( misplaced under JN.1.18 currently) and then two further FLiRT (3 & 2 ) and one FViRT (6) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (566) branch got S:R346T (65 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (5 & 2 ) and one FViRT (8) sublineages spotted by @Aviczhl2 Apr 20, 2024
@FedeGueli
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N2147S now 566
346T now 65
FliRT-1 now 5
FViRT now 8

@corneliusroemer if you have time worth to look into it

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (566) branch got S:R346T (65 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (5 & 2 ) and one FViRT (8) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (5 & 2 ) and one FViRT (10) sublineages spotted by @Aviczhl2 Apr 23, 2024
@FedeGueli
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FViRT went to 10 today with one sample from Uk and one from Canada

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (5 & 2 ) and one FViRT (10) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (7 & 2 ) and one FViRT (10) sublineages spotted by @Aviczhl2 Apr 23, 2024
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FedeGueli commented Apr 23, 2024 •
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FLiRT 1 reached 7 with two more from Ireland (with 679R)
FviRT went to 11 one from UK

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (7 & 2 ) and one FViRT (10) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (7 & 2 ) and one FViRT (11) sublineages spotted by @Aviczhl2 Apr 23, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (588) branch got S:R346T (74 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (7 & 2 ) and one FViRT (11) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10 & 2 ) and one FViRT (12) sublineages spotted by @Aviczhl2 Apr 26, 2024
@FedeGueli
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81 for the s:R346T 10 for FLiRT 1 and 12 for FViRT ping @corneliusroemer

@FedeGueli
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81 for the s:R346T 10 for FLiRT 1 and 12 for FViRT ping @corneliusroemer

Note that FLiRT 1 has S:N>K679R in 9/10 of the samples

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10 & 2 ) and one FViRT (12) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R ) and one FViRT (12) sublineages spotted by @Aviczhl2 Apr 26, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R ) and one FViRT (12) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R & 2 ) and one FViRT (12) sublineages spotted by @Aviczhl2 Apr 26, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R & 2 ) and one FViRT (12) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R & 2 ) and one FViRT (13) sublineages spotted by @Aviczhl2 Apr 29, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (606) branch got S:R346T (81 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (10, 9 with S:K679R & 2 ) and one FViRT (13) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (11, 10 with S:K679R & 2 ) and one FViRT (14) sublineages spotted by @Aviczhl2 Apr 30, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (11, 10 with S:K679R & 2 ) and one FViRT (14) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=11, 10 with S:K679R & FliRT2 = 4 ) and one FViRT (14) sublineages spotted by @Aviczhl2 Apr 30, 2024
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FedeGueli commented Apr 30, 2024 •
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89 for 346T
11 for FLiRT1
4 for FLiRT2
14 for FViRT

cc @corneliusroemer i think designations needed here.

FliRT2 got also Orf9b:T83I (C28531T) Query: C10138T, C28531T,C12049T

Screenshot 2024-04-30 alle 11 00 31

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=11, 10 with S:K679R & FliRT2 = 4 ) and one FViRT (14) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=13, 10 with S:K679R & FliRT2 = 4 ) and one FViRT (14) sublineages spotted by @Aviczhl2 Apr 30, 2024
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13 for FLiRT1 with samples from Us, Canada, England

@FedeGueli FedeGueli mentioned this issue May 4, 2024
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@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (637) branch got S:R346T (89 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=13, 10 with S:K679R & FliRT2 = 4 ) and one FViRT (14) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (657) branch got S:R346T (97 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=14, 10 with S:K679R & FliRT2 = 5 ) and one FViRT (16) sublineages spotted by @Aviczhl2 May 6, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (657) branch got S:R346T (97 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=14, 10 with S:K679R & FliRT2 = 5 ) and one FViRT (16) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S (657) branch got S:R346T (97 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=14, 10 with S:K679R & FliRT2 = 7 ) and one FViRT (16) sublineages spotted by @Aviczhl2 May 6, 2024
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657 / 97 346T / 14 Flirt1 / 7 Flirt2 (2 not on gisaid, 1 with further S:D253G+S:T500N from NDL/ 16 for FViRT

cc @corneliusroemer big ping for this one.

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S (699 branch got S:R346T (117 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=21, 18 with S:K679R & FliRT2 = 8 ) and one FViRT (20) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (126 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=24, 21 with S:K679R & FliRT2 = 11 ) and one FViRT (22) sublineages spotted by @Aviczhl2 May 17, 2024
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@corneliusroemer even if you want not to place this outside JN.1.18 for sure the Orf1a:N2147S branch with all the 456X lineages are worth to be designated

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (126 sequences, misplaced under JN.1.18 currently) and then two further FLiRT (FliRT1=24, 21 with S:K679R & FliRT2 = 11 ) and one FViRT (22) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (135sequences, misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=25, 21 with S:K679R / FliRT2 = 13 / FLiRT3= 4 ) and one FViRT (22) sublineages spotted by @Aviczhl2 May 19, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (135sequences, misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=25, 21 with S:K679R / FliRT2 = 13 / FLiRT3= 4 ) and one FViRT (22) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (141 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=28, 21 with S:K679R / FliRT2 = 14 / FLiRT3= 4 ) and one FViRT (23) sublineages spotted by @Aviczhl2 May 22, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (141 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=28, 21 with S:K679R / FliRT2 = 14 / FLiRT3= 4 ) and one FViRT (23) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (168 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=37, 21 with S:K679R / FliRT2 = 21 / FLiRT3= 6) and one FViRT (27) sublineages spotted by @Aviczhl2 May 31, 2024
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FedeGueli commented May 31, 2024 •
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@corneliusroemer even if not designating this as separate branch as it is i suggest to designate at least the two biggest FLiRT and the FviRT one.

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (168 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1=37, 21 with S:K679R / FliRT2 = 21 / FLiRT3= 6) and one FViRT (27) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (168 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1+S:K679R= 44 / FliRT2 = 26/ FLiRT3= 6) and one FViRT (37) sublineages spotted by @Aviczhl2 Jun 10, 2024
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@corneliusroemer this haas slowed down, please consider to designate the FViRT sub lineage of this that seems still around. closing for now.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jun 10, 2024
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NkRMnZr commented Jun 17, 2024

branch 2 seems to be boosted by recent SA batch
image

@FedeGueli FedeGueli reopened this Jun 17, 2024
@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (168 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1+S:K679R= 44 / FliRT2 = 26/ FLiRT3= 6) and one FViRT (37) sublineages spotted by @Aviczhl2 JN.1 + Orf1a:N2147S got S:R346T (233 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1+S:K679R= 53 / FliRT2 = 37/ FLiRT3= 6) and one FViRT (45) sublineages spotted by @Aviczhl2 Jun 17, 2024
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branch 2 seems to be boosted by recent SA batch image

thx @NkRMnZr reopening it, ping @corneliusroemer this is worth to be designated since many weeks.

@FedeGueli FedeGueli changed the title JN.1 + Orf1a:N2147S got S:R346T (233 , misplaced under JN.1.18 currently) and then three further FLiRT (FliRT1+S:K679R= 53 / FliRT2 = 37/ FLiRT3= 6) and one FViRT (45) sublineages spotted by @Aviczhl2 JN.1.18 + Orf1a:N2147S (241 ) with three FLiRT sublienages (FliRT1+S:K679R= 54 / FliRT2 = 40/ FLiRT3= 6) and one FViRT sublinegae(47) Jun 20, 2024
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re closing this down, if @corneliusroemer then will designate i will tag it.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jun 20, 2024
@DailyCovidCases
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Branch 22 and 71 might be dying off, please update this

@FedeGueli FedeGueli changed the title JN.1.18 + Orf1a:N2147S (241 ) with three FLiRT sublienages (FliRT1+S:K679R= 54 / FliRT2 = 40/ FLiRT3= 6) and one FViRT sublinegae(47) JN.1.18 + Orf1a:N2147S (272) with three FLiRT sublienages (FLiRT1+S:K679R= 66 / FliRT2 = 45) and one FViRT sublineage(49) Jun 27, 2024
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FliRT 1 likely worth to be designated.

@FedeGueli FedeGueli reopened this Jun 27, 2024
This was referenced Jun 27, 2024
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@FedeGueli FedeGueli changed the title JN.1.18 + Orf1a:N2147S (272) with three FLiRT sublienages (FLiRT1+S:K679R= 66 / FliRT2 = 45) and one FViRT sublineage(49) JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublienages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) Jul 1, 2024
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Slowing down.

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xz-keg commented Jul 1, 2024

Designated JN.1.64, JN.1.64.1, MD.1, MD.1.1, MD.2, MD.3 and MD.3.1

FedeGueli referenced this issue Jul 1, 2024
@corneliusroemer
Designate JN.1.64 (ORF1a:N2147S (A6705G)), JN.1.64.1 (S:R346T), MD.1 …
c0c9b1b 
…(JN.1.64.1.1, S:F456L (T22930A)) ...

MD.1.1 Alias of B.1.1.529.2.86.1.1.64.1.1.1, S:K679R
MD.2   Alias of B.1.1.529.2.86.1.1.64.1.2, S:F456V, ORF1a:T2800I
MD.3   Alias of B.1.1.529.2.86.1.1.64.1.3, C1060T, C9319T, C28657T
MD.3.1 Alias of B.1.1.529.2.86.1.1.64.1.3.1, S:F456L (T22928C), ORF3a:L106F, C10138T, South Africa
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Designated JN.1.64, JN.1.64.1, MD.1, MD.1.1, MD.2, MD.3 and MD.3.1

via c0c9b1b

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Just designated and one singlet with S:31del popped up in Singapore (MD.1.1) query: A6705G,C18894T ,del21653,T22930A

@FedeGueli FedeGueli changed the title JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublienages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) Sep 5, 2024
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@xz-keg @FedeGueli @DailyCovidCases @NkRMnZr