Multiple XBB.1.5.49* branches with S:T478R

NkRMnZr commented 1 year ago

### Multiple XBB.1.5.49* branches with S:T478R
- [ ] [Branch 1](#branch_1): `XBB.1.5.49` > `G14973A` > `C22995G(S:T478R)` [Query: `T6886C, G14973A, C22995G, -T15399C`, 27 seqs, 09/15]
- [ ] [Branch 2](#branch_2): Transferred to, refused from cov-lineages/pango-designation#2266 `XBB.1.5.49` > `T8593C` > `C3096T(ORF1a:S944L)` > `C22995G(S:T478R)` [Query: `C3096T, T8593C, C22995G`, 56 seqs, 09/16]
- [ ] [Branch 3](#branch_3): `XBB.1.5.49` > `T8593C` > `C6843T(ORF1a:S2193F)` > `C19961T(ORF1b:T2165M)` > `C16830T` > `T1582A, T11437C, C22995G(S:T478R), C27425A(ORF7a:T11K)` [Query: `T1582A, T11437C`, 13 seqs, 09/16]
- [ ] [Branch 4](#branch_4): ~~`XBB.1.5.49` > `G14973A` > `T15399C` > `C1392T(ORF1a:S376L)` > `C22995G(S:T478R)` [Query: `C1392T, T15399C, C22995G`, 6 seqs, 08/05]~~ _Inactive_
- [ ] [Branch 5](#branch_5): `XBB.1.5.49` > `C26013T` > `G9844A` > `T1906C, C2106T(ORF1a:T614I), A2375C(ORF1a:N704H), G5572T(ORF1a:M1769I), A10518G(ORF1a:D3418G), C22995G(S:T478R), G23429A(S:A623T), C28717A` [Query:`A10518G, C22995G, G23429A`, 26 seqs, 09/16]
- [ ] [Branch 6](#branch_6): `HT.2` _(XBB.1.5.49.2)_ > `C22995G(S:T478R)` [Query: `T6886C, C21714T, C22995G, -G11521T`, 7 seqs, 09/15]
- [ ] [Branch 7](#branch_7): Transferred to, refused from cov-lineages/pango-designation#2275 `HT.2` > `G11521T(ORF1a:M3752I), C15960T` > `C22995G(S:T478R)` [Query: `G11521T, C21714T, C22995G`, 19 seqs, 09/13]
- [ ] [Branch 8](#branch_8): `XBB.1.5.49` > `C26013T` > `A7234G, C8172T(ORF1a:A2636V), C14403T, G16207A(ORF1b:A914T), G19666T(ORF1b:D2067Y), C22995G(S:T478R), C25585T(ORF3a:L65F), C26645T, C27972T(ORF8:Q27*)` [Query: `G19666T, C22995G, C25585T`, 2 seqs, 08/11]
- [ ] [Tracking updates](https://github.com/sars-cov-2-variants/lineage-proposals/issues/451#issuecomment-1655278406): Query for all XBB.1.5.49 + S:T478R: `T6886C, T10204C, T17124C, C22995G`, 216 seqs, 09/18]

Branch 1:

Defining Mutations: XBB.1.5.49 > G14973A > C22995G(S:T478R) Query: C22995G, G14973A, T6886C, -T15399C Earliest seq: 2023-04-09 (EPI_ISL_17615719, California, USA) Latest seq: 2023-06-19 (EPI_ISL_18011974, Colima, Mexico) Sampled Countries: USA (6, California/4, Texas/1, Puerto Rico/1), Mexico (4)

Genomes:

`EPI_ISL_17615719, EPI_ISL_17788797, EPI_ISL_17856335, EPI_ISL_17950648, EPI_ISL_17951062, EPI_ISL_18011955-18011956, EPI_ISL_18011973-18011974, EPI_ISL_18012144`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25b8d_bf8070.json?f_userOrOld=uploaded%20sample branch1

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Branch 2:

Transferred to Main repo

_Transferred to cov-lineages/pango-designation#2266_ **Defining Mutations:** `XBB.1.5.49` > `T8593C` > `C3096T(ORF1a:S944L/nsp3_S126L)` > `C22995G(S:T478R)` **Query:** `C22995G, C3096T, T8593C` **Earliest seq:** 2023-05-12 (`EPI_ISL_17700383`, California , USA, Travel history to Mexico) **Latest seq:** 2023-06-22 (`EPI_ISL_17987285`, Arizona, USA) **Sampled Countries:** USA (6, California/5, Arizona/1), Canada (1, Alberta)

Genomes:

`EPI_ISL_17700383, EPI_ISL_17700397, EPI_ISL_17761319, EPI_ISL_17818510, EPI_ISL_17838456, EPI_ISL_17987285, EPI_ISL_18008823`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_227d3_bf7110.json?f_userOrOld=uploaded%20sample ![branch2](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/54e2d707-41ac-4022-816f-42626cd4e941)

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Branch 3

Defining Mutations: XBB.1.5.49 > T8593C > C6843T(ORF1a:S2193F/nsp3_S1375F) > C19961T(ORF1b:T2165M/nsp15_T114M) > C16830T > T1582A, T11437C, C22995G(S:T478R), C27425A(ORF7a:T11K) Query: T1582A, T11437C Earliest seq: 2023-06-07 (EPI_ISL_18011951, Veracruz, Mexico) Latest seq: 2023-07-20 (EPI_ISL_18055249, Ontario, Canada) Sampled Countries: USA (3, Arizona, California, Texas), Canada (1, Ontario), Mexico (1, Veracruz)

Genomes:

`EPI_ISL_17960826, EPI_ISL_18011951, EPI_ISL_18055249, EPI_ISL_18055483, EPI_ISL_18045992`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2862b_a1f6d0.json?f_userOrOld=uploaded%20sample Branch3

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Branch 4

Inactive

**Defining Mutations:** `XBB.1.5.49` > `G14973A` > `T15399C` > `C1392T(ORF1a:S376L/nsp2_S196L)` > `C22995G(S:T478R)` **Query:** `C1392T, T15399C, C22995G` **Earliest seq:** 2023-06-25 (`EPI_ISL_18071314`, New York, USA) **Latest seq:** 2023-07-12 (`EPI_ISL_18071356`, New York, USA) **Sampled Countries:** USA (6, NY)

Genomes:

`EPI_ISL_18022891, EPI_ISL_18071300, EPI_ISL_18071314, EPI_ISL_18071329, EPI_ISL_18071345, EPI_ISL_18071356`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16aba_f93160.json?f_userOrOld=uploaded%20sample ![Branch4](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/db30e6c9-6be2-49ca-85ea-77931fedd687)

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Branch 5

Defining Mutations: XBB.1.5.49 > C26013T > G9844A > T1906C, C2106T(ORF1a:T614I/nsp2_T434I), A2375C(ORF1a:N704H/nsp2_N524H), G5572T(ORF1a:M1769I/nsp3_M951I), A10518G(ORF1a:D3418G/nsp5_D155G), C22995G(S:T478R), G23429A(S:A623T), C28717A Query: A10518G, C22995G, G23429A Earliest seq: 2023-07-12 (EPI_ISL_18055497, New Mexico, USA) Latest seq: 2023-07-23 (EPI_ISL_18058191, Utah, USA) Sampled Countries: USA (5; UT/4, NM/1)

Genomes:

`EPI_ISL_18055497, EPI_ISL_18058148, EPI_ISL_18058172, EPI_ISL_18058190-18058191`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1e120_f987f0.json?f_userOrOld=uploaded%20sample Branch5

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Branch 6

Defining Mutations: HT.2 > C22995G(S:T478R) Query: T6886C, C21714T, C22995G, -G11521T Earliest seq: 2023-04-27 (EPI_ISL_17653192, Maryland, USA) Latest seq: 2023-06-21 (EPI_ISL_18046339, California, USA) Sampled Countries: USA (4; California/3, Maryland/1)

Genomes:

`EPI_ISL_17653078, EPI_ISL_17653083, EPI_ISL_17653192, EPI_ISL_18046339`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2333b_f9b7b0.json?c=gt-S_478&f_userOrOld=uploaded%20sample Branch6

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Branch 7

Transferred to main repo

_Transferred to cov-lineages/pango-designation#2275_ **Defining Mutations:** `HT.2` > `G11521T(ORF1a:M3752I/nsp6_M183I), C15960T` > `C22995G(S:T478R)` **Query:** `G11521T, C21714T, C22995G` **Earliest seq:** 2023-07-05 (`EPI_ISL_17985212`, Basque, Spain) **Latest seq:** 2023-07-20 (`EPI_ISL_18044159`, Basque, Spain) **Sampled Countries:** Spain (2), France (1), USA (1, California)

Genomes:

`EPI_ISL_17985212, EPI_ISL_18044159, EPI_ISL_18049081, EPI_ISL_18060664`

**UShER:** ![Branch7](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/533d4ff1-9d4e-479e-97b0-9d9a99fd27e7)

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Branch 8

Defining Mutations: XBB.1.5.49 > C26013T > A7234G, C8172T(ORF1a:A2636V), C14403T, G16207A(ORF1b:A914T), G19666T(ORF1b:D2067Y), C22995G(S:T478R), C25585T(ORF3a:L65F), C26645T, C27972T(ORF8:Q27*) Query: G19666T, C22995G, C25585T Earliest seq: 2023-07-31 (EPI_ISL_18094894, California, USA) Latest seq: 2023-07-31 (EPI_ISL_18094957, California, USA, Travel history to: Mexico) Sampled Countries: USA (2, ex. Mexico)

Genomes:

`EPI_ISL_18094894, EPI_ISL_18094957`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_42d31_7775f0.json?f_userOrOld=uploaded%20sample Branch8

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Trivia:

There are many more XBB.1.5.49 branches with S:T478X, but only small clusters. Branch 1, 2 and 6 are uploaded (not collected) recently, many with travel history to Mexico. Branch 3, 4, 5 and 7 just emerged after proposal.

NkRMnZr commented 1 year ago

Tracking updates:

07-28:

Branch 1: 2 seqs from California, Texas and New York: EPI_ISL_18044999, EPI_ISL_18045494 Branch 2: 3 seqs from California: EPI_ISL_18045567, EPI_ISL_18045616, EPI_ISL_18046223

08-01, 5 seqs on branch 1 from USA; 1 seq on Branch 2 from USA

08-02, Adding emerged branch 3

08-05, Branch 2 +2, USA (ex. Mexico); Branch 3 +1, USA

08-06, Adding Branch 4~7

08-08, Branch 2, +3; Branch 3, +1; Branch 7, +2

08-11 Branch 1, +1; Branch 2, +3; Branch 5, +4; Branch 7, +2 (USA and Spain); Adding Branch 8

08-18, Branch, 2 +8 (USA, UK); Branch 3, +1 (USA); Branch 5, +7 (USA, Mexico); Branch 7, +1 (USA)

08-26, Branch 1, +1 (Mexico); Branch 2, +3 (Mexico, USA); Branch 3, +1 (Mexico); Branch 5, +2 (USA); Branch 7, +2 (Mexico, USA)

09-02: Branch 1, +1; Branch 2, +5; Branch 3, +1; Branch 5, +3; Branch 6, +1

NkRMnZr commented 1 year ago

08-01:

Branch 1: 5 sequences from USA (10 to 17 in a week after proposal): EPI_ISL_18053540, EPI_ISL_18053622, EPI_ISL_18053934, EPI_ISL_18054830, EPI_ISL_18057221 Branch 2: 1 sequence from Arizona, USA (7 to 12 in a week): EPI_ISL_18053808

EPI_ISL_18022891 from last update now falls under G14973A > T15399C > C1392T(ORF1a:S376L) > C22995G(S:T478R) , so it needs to be deducted using query: -T15399C

UShER for one week update on Branch 1, plus EPI_ISL_18022891 from side branch: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_133c4_8f3320.json?f_userOrOld=uploaded%20sample&label=id:node_6928187

UShER for one week update on Branch 2 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_177e3_8f5ca0.json?f_userOrOld=uploaded%20sample

NkRMnZr commented 1 year ago

08-02, Adding emerged branch 3.

NkRMnZr commented 1 year ago

08-05, 2 seqs from California, USA with travel history to Mexico on Branch 2: EPI_ISL_18067155, EPI_ISL_18067165; 1 sequence from California, USA on Branch 3: EPI_ISL_18065097

NkRMnZr commented 1 year ago

08-06, Adding Branch 4 mentioned above, the singlet now clusters into a 6 seqs branch. Adding Branch 5, 6 and 7

FedeGueli commented 1 year ago

Branch 1 up to 23 Branch 2 up to 17 Branch 3 up to 7

NkRMnZr commented 1 year ago

08-08, Branch 2, +3; Branch 3, +1; Branch 7, +2

Branch 2, 3 seqs from USA: EPI_ISL_18072730, EPI_ISL_18073890, EPI_ISL_18076259 Branch 3, 1 sequence from USA: EPI_ISL_18073887 Branch 7, 2 seqs from USA: EPI_ISL_18072611, EPI_ISL_18073902

NkRMnZr commented 1 year ago

Also, there's another cluster suspected to be XBB.1.5.49 with S:T478R, follows:

XBB.1.5 [T17124C > T23018C] > C13517T(ORF1b:T17I) > T6886C, C29272T, A29687G > A4987G > T10204C > C22995G(S:T478R), C25658T(ORF3a:T89I), G26056T(ORF3a:D222Y) [Query: C22995G, C25658T, G26056T, 13 seqs, 08/04]

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_1c149_372120.json?f_userOrOld=uploaded%20sample details

not sure if this is something new, or just misplacement

NkRMnZr commented 1 year ago

08-11 Branch 1, +1; Branch 2, +3; Branch 5, +4; Branch 7, +2 (USA and Spain); Adding Branch 8

+1 on Branch 1: EPI_ISL_18081541 +3 on Branch 2: EPI_ISL_18079744, EPI_ISL_18080672, EPI_ISL_18080912 +4 on Branch 5: EPI_ISL_18090234, EPI_ISL_18095025, EPI_ISL_18095384, EPI_ISL_18095474 +2 (USA and Spain) on Branch 7: EPI_ISL_18094328, EPI_ISL_18095035

Adding Branch 8

FedeGueli commented 1 year ago

Apparent growth dis/ advantages vs EG.5.1.1 (26/08) Branch 1 : -28% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C22995G%2CG14973A%2CT6886C%2C15399T&analysisMode=CompareToBaseline&

Branch 2: -1% C22995G, C3096T, T8593C

Branch 3: -9% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T1582A%2CT11437C&analysisMode=CompareToBaseline&

Branch 4: -8% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C1392T%2CT15399C%2CC22995G&analysisMode=CompareToBaseline&

Branch 5: ? + https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A10518G%2CC22995G%2CG23429A&analysisMode=CompareToBaseline&

Branch 6: ?- https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T6886C%2CC21714T%2CC22995G%2C11521G&analysisMode=CompareToBaseline&

Branch 7: 31% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G11521T%2CC21714T%2CC22995G&analysisMode=CompareToBaseline&

Branch 8: // https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G19666T%2CC22995G%2CC25585T&analysisMode=CompareToBaseline&

NkRMnZr commented 1 year ago

08-18, Branch, 2 +8 (USA, UK); Branch 3, +1 (USA); Branch 5, +7 (USA, Mexico); Branch 7, +1 (USA)

Branch 2, +6 USA (AZ, CA, OH, TX); +2 UK (NI, SC) : EPI_ISL_18097894, EPI_ISL_18098201, EPI_ISL_18098577, EPI_ISL_18098867, EPI_ISL_18099983, EPI_ISL_18104385, EPI_ISL_18114275, EPI_ISL_18114479
Branch 3, +1 USA (AZ): EPI_ISL_18099979
Branch 5, +5 USA (CA, MI, UT); +2 Mexico : EPI_ISL_18103771, EPI_ISL_18103777, EPI_ISL_18104208, EPI_ISL_18104820, EPI_ISL_18108165, EPI_ISL_18108171, EPI_ISL_18114042
Branch 7, +1 USA (HI) EPI_ISL_18108081

NkRMnZr commented 1 year ago

08-26, Branch 1, +1 (Mexico); Branch 2, +3 (Mexico, USA); Branch 3, +1 (Mexico); Branch 5, +2 (USA); Branch 7, +2 (Mexico, USA)

Branch 1, +1 (Mexico): EPI_ISL_18137461
Branch 2, +3 (Mexico, USA): EPI_ISL_18120617, EPI_ISL_18137358, EPI_ISL_18137431
Branch 3, +1 (Mexico): EPI_ISL_18137396
Branch 5, +2 (USA): EPI_ISL_18120718, EPI_ISL_18120810
Branch 7, +2 (Mexico, USA): EPI_ISL_18121993, EPI_ISL_18137298

FedeGueli commented 1 year ago

pparent growth dis/ advantages vs EG.5.1.1 Branch 1 : -28% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C22995G%2CG14973A%2CT6886C%2C15399T&analysisMode=CompareToBaseline&

Branch 2: -1% C22995G, C3096T, T8593C

Branch 3: -9% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T1582A%2CT11437C&analysisMode=CompareToBaseline&

Branch 4: -8% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C1392T%2CT15399C%2CC22995G&analysisMode=CompareToBaseline&

Branch 5: +12% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A10518G%2CC22995G%2CG23429A&analysisMode=CompareToBaseline&

Branch 6: -8% https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T6886C%2CC21714T%2CC22995G%2C11521G&analysisMode=CompareToBaseline&

Branch 7: 8% (--)https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G11521T%2CC21714T%2CC22995G&analysisMode=CompareToBaseline&

Branch 8: // https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G19666T%2CC22995G%2CC25585T&analysisMode=CompareToBaseline&

updated

NkRMnZr commented 1 year ago

09-02: Branch 1, +1; Branch 2, +5; Branch 3, +1; Branch 5, +3; Branch 6, +1

Branch 1, +1 (Denmark) EPI_ISL_18210493 Branch 2, +5 (AZ, CA, TX) EPI_ISL_18145401, EPI_ISL_18145481, EPI_ISL_18210436, EPI_ISL_18211531, EPI_ISL_18211539 Branch 3, +1 (CA) EPI_ISL_18212748 Branch 5, +3 (VA) EPI_ISL_18144228-18144229, EPI_ISL_18144234 Branch 6, +1 (South Korea) EPI_ISL_18140313

FedeGueli commented 1 year ago

Please propose branch 2

FedeGueli commented 1 year ago

All together these lineages reach less than 5% in Mexico. I think you should propose Branch 7. for the rest i am closing it for now. please ping me if something changes.

FedeGueli commented 1 year ago

Branch 7 was refused from the other repo. i would think it is good track it there while closed. I have to say all of thema re not the fastest but for sure there were high homoplasy of 478R especially in Mexico

FedeGueli commented 1 year ago

Branch 2 was refused too. A pity cause MExico uploaded less than 600 seqsuences and less than 50 in August .. 23 out of 39 had S:T478R with 15 out of 23 being XBB.1.16

FedeGueli commented 1 year ago

Branch 2 now 60 Branch 7 now 19

sars-cov-2-variants / lineage-proposals