XBB.1.5.39 with 3 steps: FT.3, S:Q52H; FT.3.1, S:T478R and S:D1168H; FT.3.1 with S:A348S (20+1 seqs, mainly in the USA, 5+1 countries)

[NkRMnZr]

Original proposal for what designated as FT.3 and FT.3.1 now:

_now this seems to be a 3-step, 1st S:Q52H, 2nd S:T478R and S:D1168H, 3rd S:A348S_ **Defining Mutations:** [_on top of XBB.1.5.39's T11316C/ORF1a:M3684T_] > G21718T(S:Q52H) > C6628T, A18366G, C22995G(S:T478R), G25064C(S:D1168H) > **Query:** A18366G, C22995G, G25064C **Earliest seq:** 2023-05-02 (EPI_ISL_17778244, New Mexico, USA) **Latest seq:** 2023-06-21 (EPI_ISL_17960823, Arizona, USA) **Sampled Countries:** USA (13, New Mexico/4, California/2, Texas/2, Maryland/1, Iowa/1, Arizona/1, New Jersey/1, Ohio/1), UK (8, all Scotland), Canada (2, all Ontario), Germany (1), Netherlands (1)

Genomes WITHOUT further S:A348S, query:A18366G, C22995G, G25064C, -G22604T:

EPI_ISL_17722784, EPI_ISL_17838316-17838320, EPI_ISL_17838474, EPI_ISL_17842741, EPI_ISL_17950377, EPI_ISL_17952151, EPI_ISL_17952164, EPI_ISL_17952446, EPI_ISL_17953468, EPI_ISL_17955753

Genomes WITH further S:A348S, query:G22604T, C22995G, G25064C:

EPI_ISL_17722787, EPI_ISL_17778244, EPI_ISL_17778247, EPI_ISL_17854262, EPI_ISL_17950631, EPI_ISL_17950921, EPI_ISL_17960823, EPI_ISL_17964557, EPI_ISL_17965738, EPI_ISL_17965766, EPI_ISL_17971244

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_14ee2_8235a0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all Overview from XBB.1.5.39 polytomy:  Detailed view from S:Q52H branch:  **Trivia:** - S:Q52H(G21718T) is on the rise, probably driven by EG.5.1, but also found on EE.4(BQ.1.1.4.4), GP.1(CH.1.1.11.1), XBB.2.10, probably it should be designated first? (XBB.1.5.39 with S:Q52H, query:T11316C, G21718T, T10204C returns 175 ) - S:D1168H is rare, only sampled 530-ish times during the whole pandemic, last wave was driven by some BA.2* and AY.122* - Futher step S:A348S (G22604T), which is predicted to have extra immune escape. - All three steps seems growing at the moment. Tracking updates:

Update 1: 23-06-30, 4 seqs from the USA

previously GenBank sequence from Maryland: EPI_ISL_17854262 1 from Ohio EPI_ISL_17950921 1 from Cali EPI_ISL_17950631 1 from Jersey with metadata showing travel history to Switzerland: EPI_ISL_17950377

Update 2: 23-07-02, 3 seqs from UK and USA

2 previously non-GISAID seqs from Scotland: EPI_ISL_17952151, EPI_ISL_17952164 1 from Texas: EPI_ISL_17952446

Update 3: 23-07-06, 3 seqs from UK and USA

1 from Scotland: EPI_ISL_17953468 1 from Texas: EPI_ISL_17955753 1 from Arizona: EPI_ISL_17960823

UShER after 3 updates:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_179_6768b0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all 

Update 4: 23-07-07, 4 seqs from 3 countries

2 from New Mexico, USA:EPI_ISL_17965738, EPI_ISL_17965766 new entry: 1 from Germany: EPI_ISL_17964557 2 from Netherlands: EPI_ISL_17971244

Update 5: 23-07-13, 3 seqs from USA

1 from California: EPI_ISL_17979172 2 from Florida: EPI_ISL_17976613, EPI_ISL_17979199

Update 6: 23-07-15, 4 seqs from USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2ba43_254bc0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all  EPI_ISL_17985445, EPI_ISL_17985484, EPI_ISL_17985498, EPI_ISL_17985556

Update 7: 23-07-19, 3 seqs from USA

 Florida: EPI_ISL_17996258 New Mexico: EPI_ISL_18006013 New Jersey: EPI_ISL_18006058

Update 8: 23-07-23, 4 seqs from USA and Mexico

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a65_d52be0.json?f_userOrOld=uploaded%20sample  1 from California: EPI_ISL_18011163 1 from Puerto Rico:EPI_ISL_18012148 New entry: 2 from Mexico: EPI_ISL_18011910, EPI_ISL_18011954

Further proposal for S:A348S sub-branch:

Defining Mutations: FT.3.1 > G22604T(S:A348S) Query: G22604T, C22995G, G25064C Earliest seq: 2023-05-02 (EPI_ISL_17778244, New Mexico, USA) Latest seq: 2023-07-14 (EPI_ISL_18012787, Delaware, USA) Sampled Countries: USA (15, New Mexico/5, Florida/3, New Jersey/2, Arizona/1, California/1, Delaware/1, Maryland/1, Ohio/1, Puerto Rico/1), Canada (1, Ontario), Germany (1), Mexico (1), Netherlands (1)

Genomes:

EPI_ISL_17722787, EPI_ISL_17778244, EPI_ISL_17778247, EPI_ISL_17854262, EPI_ISL_17950631, EPI_ISL_17950921, EPI_ISL_17960823, EPI_ISL_17964557, EPI_ISL_17965738, EPI_ISL_17965766, EPI_ISL_17971244, EPI_ISL_17976613, EPI_ISL_17979199, EPI_ISL_17985445, EPI_ISL_17985484, EPI_ISL_17996258, EPI_ISL_18006013, EPI_ISL_18011910, EPI_ISL_18012148, EPI_ISL_18012787

non-GISAID Genomes:

Wales/CLIMB-CM7Y8ID7/2023|2023-07-05

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_abe8_fbcff0.json?f_userOrOld=uploaded%20sample

[NkRMnZr]

Tracking updates:

(updated sequences moved to archived main proposal)

[NkRMnZr]

@FedeGueli need milestone for this, and maybe need "partially designated" label as well

[FedeGueli]

@NkRMnZr please when a lineage seems growing write a comment so i can see that growth.

[NkRMnZr]

@NkRMnZr please when a lineage seems growing write a comment so i can see that growth.

The original proposal is for S:T478R and S:D1168H, not S:A348S, you can check the historical updates by clicking the drop-down button after "edited" https://github.com/sars-cov-2-variants/lineage-proposals/issues/266#issuecomment-1615137165 . I'll update follow up S:A348S sequences there.

[FedeGueli]

Please propose the lineage with S:A348S

[FedeGueli]

@NkRMnZr please when a lineage seems growing write a comment so i can see that growth.

The original proposal is for S:T478R and S:D1168H, not S:A348S, you can check the historical updates by clicking the drop-down button after "edited" #266 (comment) . I'll update follow up S:A348S sequences there.

If you edit just the main text i m not notified of anything . So whem something happems please writen a comment.

[NkRMnZr]

@NkRMnZr please when a lineage seems growing write a comment so i can see that growth.

The original proposal is for S:T478R and S:D1168H, not S:A348S, you can check the historical updates by clicking the drop-down button after "edited" #266 (comment) . I'll update follow up S:A348S sequences there.

If you edit just the main text i m not notified of anything . So whem something happems please writen a comment.

Ah, that makes sense. I was trying to keep the proposal tidy, but guess I'll just link the comments below, that should do it.

Anyway, transferred to cov-lineages/pango-designation#2140