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

[FedeGueli]

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
Samples: 551
Tree: (correctly placed as JN.1 > A6705G )

Query for S:R346T :G22599C,A6705G,C18894T. [ correct placement JN.1 > A6705G > S:R346T (G22599C)]
Samples:58

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 [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: 19 ( 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)
Samples: 4 ( 1 or 2 with Orf9b:T83I (C28531T) query: C10138T, C28531T,C12049T)

IDs

EPI_ISL_19026937, EPI_ISL_19051601

Query for FViRT : G22599C, T22928G,A6705G (correct placement: JN.1 > A6705G > S:R346T (G22599C) > Orf1a:T2800I (C8664T), S:F456V (T22928G)] formerly tracked as Branch 22 of sars-cov-2-variants/lineage-proposals#1253
Samples : 5

IDs

EPI_ISL_18917992, EPI_ISL_18932356, EPI_ISL_18938683, EPI_ISL_19023194, EPI_ISL_19024784

Tree misplaced as JN.1.18

[FedeGueli]

N2147S now 566
346T now 65
FliRT-1 now 5
FViRT now 8

@corneliusroemer if you have time worth to look into it

[FedeGueli]

FViRT went to 10 today with one sample from Uk and one from Canada

[FedeGueli]

FLiRT 1 reached 7 with two more from Ireland (with 679R)
FviRT went to 11 one from UK

[FedeGueli]

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

[FedeGueli]

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]

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

[FedeGueli]

13 for FLiRT1 with samples from Us, Canada, England

[FedeGueli]

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]

growing 106/19/7/18

[FedeGueli]

FliRt1 > 21 and FViRT > 20 now

[FedeGueli]

+1 (2 on Usher) FLiRT2 both from Sweden