Another EG.5.1.1 with S:L455F via G22927C (90 seqs, China, South Korea)

[NkRMnZr]

Taken from Branch 3 of multitask tracker sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C11779T > C6781T, C17802T, G22927C(S:L455F)
Query: C6781T, C17802T, G22927C
Earliest seq: 2023-07-04 (EPI_ISL_17994488, Shanghai, China)
Latest seq: 2023-07-24 (EPI_ISL_18105818, Shanghai, China)
Sampled Countries: China (17, Shanghai)

Genomes:

EPI_ISL_17994488, EPI_ISL_18074751, EPI_ISL_18074754, EPI_ISL_18105750, EPI_ISL_18105752, EPI_ISL_18105756-18105765, EPI_ISL_18105768, EPI_ISL_18105818

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_172f6_cd0e70.json?f_userOrOld=uploaded%20sample&label=id:node_6790894

[xz-keg]

33 seqs now.

[NkRMnZr]

Tracking updates:

08-17, 16 seqs from Shanghai

EPI_ISL_18108500, EPI_ISL_18108503-18108506, EPI_ISL_18108514, EPI_ISL_18108516-18108517, EPI_ISL_18108519-18108520, EPI_ISL_18108522-18108523, EPI_ISL_18108525, EPI_ISL_18108570, EPI_ISL_18108580-18108581

08-26, 10 seqs from Shanghai

EPI_ISL_18114761, EPI_ISL_18138167, EPI_ISL_18138190-18138191, EPI_ISL_18138195, EPI_ISL_18138200-18138201, EPI_ISL_18138203-18138205

09-02, 1 more from Anhui EPI_ISL_18213209

09-06, 2 more from Shanghai EPI_ISL_18232624, EPI_ISL_18232629

09-12, 1 more from Sichuan EPI_ISL_18246261

09-15, 10 seqs from Shanghai

EPI_ISL_18268373, EPI_ISL_18268378, EPI_ISL_18268387, EPI_ISL_18268391-18268392, EPI_ISL_18268395, EPI_ISL_18268397-18268398, EPI_ISL_18268402, EPI_ISL_18268483

09-20, 9 seqs from Shanghai

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_19d0d_b33e70.json?label=id:node_6988141

EPI_ISL_18284818, EPI_ISL_18284909, EPI_ISL_18284911, EPI_ISL_18284913, EPI_ISL_18284917, EPI_ISL_18284919-18284920, EPI_ISL_18284974, EPI_ISL_18284979

09-29, 2 seqs from Shanghai EPI_ISL_18320777, EPI_ISL_18320779

10-08, 3 seqs from China and South Korea

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_57b8_2af4f0.json?f_userOrOld=uploaded%20sample&label=id:node_3455110

EPI_ISL_18320777, EPI_ISL_18320779, EPI_ISL_18354319, EPI_ISL_18360285, EPI_ISL_18360293

[xz-keg]

It becomes 43 after the new Shanghai upload.

[FedeGueli]

@corneliusroemer super ping here.

[xz-keg]

62 seqs now

[corneliusroemer]

I've been watching this for a while and would have designated if it was not phylogenetically unstable and mostly restricted to Shanghai. It's notably got G22927C instead of G22927T (put this into the issue title next time as that's probably the most interesting thing about this lineage right now).

Somehow I'm not sure this isn't an artefact, especially as Shanghai seems to have another lineage of G22927C but on top of EG.5.1 rather than EG.5.1.1.

[corneliusroemer]

I've designated a few more EG.5.1 + 455F, but there's so much homoplasy, it's hard to tell what's real and what's actually an artefact branch of an another already designated lineage.

[NkRMnZr]

Thanks @corneliusroemer

there are two lineages that seemingly misplacement with weird reversions, one pointed out by @FedeGueli on f655671, for mostly Danish seqs.

there's another follows EG.5.1.1 > C22264T > G22927T(S:L455F) > T22264C_reversion for mostly Finnish seqs.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_404dd_2012c0.json?c=gt-nuc_22264&gmax=23264&gmin=21264&label=id:node_6941300

could you check those lineages @AngieHinrichs ?

aside of those, the rest can be monitored for some time to see if they are potential artifact either by phylogenetic assessment or sequencing.

[FedeGueli]

Thanks @corneliusroemer

there are two lineages that seemingly misplacement with weird reversions, one pointed out by @FedeGueli on f655671, for mostly Danish seqs.

there's another follows EG.5.1.1 > C22264T > G22927T(S:L455F) > T22264C_reversion for mostly Finnish seqs.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_404dd_2012c0.json?c=gt-nuc_22264&gmax=23264&gmin=21264&label=id:node_6941300

could you check those lineages @AngieHinrichs ?

aside of those, the rest can be monitored for some time to see if they are potential artifact either by phylogenetic assessment or sequencing.

thx , @AngieHinrichs could you check please?

cc @corneliusroemer it could also recombination between similar lineages? they all or quite all have been bred in the same country and in the same timeframe and exceptionally fit well over other lineages so not unlikely coinfecting people ?

[corneliusroemer]

Let's wait and see. The fact it's mostly one city/lab is very suspicious.

[xz-keg]

Let's wait and see. The fact it's mostly one city/lab is very suspicious.

Worth noticing the 63th seq comes from Anhui, the first outside Shanghai.

Let's wait for it to appear in another country?

[xz-keg]

+1 Sichuan

[NkRMnZr]

Designated as HK.14 via c7550b1