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Repository for suggesting new lineages that should be added to the current scheme
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XCV: EG.5.1.3/XBB.1.16.19 recombinant in USA and Canada (162 seqs, 3 countries) #2210

Closed xz-keg closed 1 year ago

xz-keg commented 1 year ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/600

Mutations on top of EG.5.1: T2334C(rev), A5720G(rev), T5422C, C7044A, T9693C(rev), C22570T, C27507A(rev), G27065A, A28182G, A28447G, T29625C(rev) C29386T

XBB.1.16.19---EG.5.1.3---XBB.1.16.19 Breakpoint 1: between 9694 and 11749 Breakpoint 2: between 22996 and 27064

Private mutations: T5422C, C7044A(Orf1a:P2260H), G27065A,A28182G(Orf8:S97G) T5422C, C7044A, G27065A are from an American XBB.1.16.19 branch. A28182G is unique.

Usher places it under EG.5.1.1 but it has all 3 EG.5.1.1 defining mutations reverted.

It has one of the EG.5.1.3 defining mutations (C22570T) and the other defining mutation for EG.5.1.3(C1889T) is on XBB.1.16 part. So the EG.5.1-side donor is likely EG.5.1.3.

This one is basically EG.5.1-spike with XBB.1.16-Orf9b.

GISAID query: C22570T, G27065A,A28182G No. of seqs: 16(USA 12(7 states), Canada 4)

FIrst: EPI_ISL_18095385, Utah, 2023-7-12 Latest: EPI_ISL_18129876, Canada, 2023-8-14

usher

image

FedeGueli commented 1 year ago

One more from Oregon

FedeGueli commented 1 year ago

43

xz-keg commented 1 year ago

image

Usher now treats this as a sibling branch of EG.5.1.3

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3634_7b3760.json?label=id:node_6989053

xz-keg commented 1 year ago

102 now @corneliusroemer @InfrPopGen

FedeGueli commented 1 year ago

This is quite clear and over 100 seqs @corneliusroemer

xz-keg commented 1 year ago

134 now, a lot of new seqs from Japan.

JosetteSchoenma commented 1 year ago

XCV

JosetteSchoenma commented 1 year ago

This turned up in the Netherlands. 1 sample. 177 in totaal now.