Multiple JD.1.1* Lineages with S:T478X

NkRMnZr commented 11 months ago

### Multiple `JD.1*` Lineages with `S:T478R` or `S:T478I`
- [ ] [Branch 1](#branch_1) **JD.1.1.7** > C22687T(S:F375F) > C13326T(ORF1a:T4354I/nsp10_T101I), C22995G(**S:T478R**), G27993T(ORF8:D34Y) [Query: `C13326T, G20238T, C22995G, -G425T, -T3313C`, 40 seq, 01/08]dead
- [ ] [Branch 2](#branch_2) **JD.1.1** > C19185T > A29683T > T19848C > C22995G(**S:T478R**), G23149T(**S:K529N**) [Query: `C19185T, T19848C, C22995G or G8572T, C16222T`, 13 seqs, 02/04], many with further `S:E554K/G23222A`

Checking Singlets, Doublets, Triplets, Quadruplets and Quintuplets. Query for all **JD.1*** with S:T478X minus already designated ones: spike_T478, -spike_T478K, C6896T, A14634G, 75 seqs, 01/11

Branch 1

Defining Mutations: JD.1.1.7 > C22687T(S:F375F) > C13326T(ORF1a:T4354I/nsp10_T101I), C22995G(S:T478R), G27993T(ORF8:D34Y) Query: C13326T, G20238T, C22995G, -G425T, -T3313C Earliest seq: 2023-11-07 (EPI_ISL_18524314, Ontario, Canada) Latest seq: 2023-11-20 (EPI_ISL_18549145, Ontario, Canada) Sampled Countries: Canada (10: ON)

Genomes:

`EPI_ISL_18523263, EPI_ISL_18524015, EPI_ISL_18524313-18524314, EPI_ISL_18549118, EPI_ISL_18549121, EPI_ISL_18549125, EPI_ISL_18549145, EPI_ISL_18549203, EPI_ISL_18549480`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_646c_2be640.json?label=id:node_3700410

Trivia:

Looks like a carehome cluster according to metadata

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Branch 2: many with further `S:E554K/G23222A`

Defining Mutations: JD.1.1 > C19185T > A29683T > T19848C > C22995G(S:T478R), G23149T(S:K529N) Query: C19185T, T19848C, C22995G Earliest seq: 2023-10-07 (EPI_ISL_18429180, Wales, UK) Latest seq: 2023-12-31 (EPI_ISL_18722021, Dublin, Ireland) Sampled Countries: Denmark (3), Luxembourg (2), UK (2: EN; WS), Ireland (1)

Genomes:

`EPI_ISL_18429180, EPI_ISL_18596293, EPI_ISL_18596305, EPI_ISL_18680529, EPI_ISL_18688102, EPI_ISL_18722021, EPI_ISL_18727994, EPI_ISL_18728006`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31845_39eb60.json?label=id:node_3713459

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Singlets

Brazil/PE-FIOCRUZ-IAM15826/2023|EPI_ISL_18694881|2023-12-07 JD.1 > C14189T > C28087T > G13379A(ORF1a:V4372I) > T28705C > C22530T(S:T323I) > G4444T > T772C, C24034T(S:N824N) > C13665T, C15368T(ORF1b:T634I), C22995G(S:T478R), G25234T(S:L1224F) [Query: T772C, G4444T, C22995G, 12/27] Dead
Spain/CT-HUB08625/2023|EPI_ISL_18255998|2023-08-29 JD.1.1 (XBB.1.5.102.1.1) > T9403C > T26171A(ORF3a:M260K) > C11339T, C22995G(S:T478R) [Query: T9403C, C22986T, C22995G,09/13] Dead
Spain/EX-BA_18611957/2023|EPI_ISL_18672909|2023-12-01 JD.1.1 > C19185T > C11681T > G22899T(S:G446I) > C15960T > C22995G(S:T478R) [Query: C11681T, C15960T, C22995G, 12/12] Dead
Germany/TH-RKI-I-1138753/2023|EPI_ISL_18455093|2023-10-12 JD.1.1 > C19185T > C28603T > C657T(ORF1a:A131V), C2433T(ORF1a:S723F), C22995T(S:T478I), G25314A(S:G1251E) [Query: C19185T, C22995T, C28603T, 11/01] Dead
Peru/LIM-INS-47145/2023|EPI_ISL_18572595|2023-10-31 JD.1.1 > C19185T > G29227A > C2401T, A5128G, C19164T, C19170T, C19862T(ORF1b:A2132V), C22995T(S:T478I), C28435T(ORF9b:P51L), C29762T [Query: C19185T, C22995T, G29227A, 12/01]Dead
USA/WV-WVU-WV145629/2023|EPI_ISL_18665146|2023-11-09 JD.1.1 > C19185T > C25714T(ORF3a:L108F) > T2425C, C5144T(ORF1a:D1742N), G5489A, A22994C(S:T478Q), T23443C(S:D627D) [Query: C19185T, A22994C, C25714T, 12/20] dead
England/CLIMB-CM7YEHHG/2023|EPI_ISL_18454911|2023-10-24 JD.1.1.2 > G6839A(ORF1a:A2192T), A16668G > C2939T(ORF1a:P892S), C22995G(S:T478R), A24813T(S:D1084V), C26110T(ORF3a:P240S) [Query: G6839A, A16668G, C22995G, 11/01] dead
France/GES-IPP31472/2023|EPI_ISL_18717397|2023-12-11 JD.1.1.7 > G1505A(ORF1a:V414I), C3787T, T11398C > A12358G, A22994G(S:T478E), C26681T [Query: G1505A, C3787T, A22994G, 01/04] dead
Slovakia/uvzsr-BA_23_00022-A07-BA_23_00009546/2023|EPI_ISL_18642007|2023-10-24 JD.1.1.7 > T3313C > A28220C(ORF8:L109F) > T1330C, C2445T(ORF1a:T727I), C22995G(S:T478R) [Query: T3313C, G20238T, C22995G, -G425T, 12/04]dead
Puerto_Rico/PR-CVL-020493/2023|EPI_ISL_18594161 JD.1.1.7 > T22726C(S:N388N) > C22995T(S:T478I), G28713A(N:G147D) [Query: G20238T, C22995T, 12/06] dead

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Doublets

Thailand/NIC_KBI_8369/2023|EPI_ISL_18556584|2023-11-02 and Thailand/NIC_KBI_8460/2023|EPI_ISL_18556638|2023-11-13 JD.1.1 > C12747T(ORF1a:T4161I) > G29648T(ORF10:D31Y) > C6145T, C26681T > T11368C > G2012A(ORF1a:A583T), C20178T, C22995T(S:T478I) [Query: C6145T, T11368C, C22995T, 2, Nov29]dead
Spain/CT-LabRefCat-5844242/2023|EPI_ISL_18485649|2023-10-14 and Belgium/AZDelta-2343-00764/2023|EPI_ISL_18486561|2023-11-02 JD.1.1 > C19185T > C28603T > C3241T, C3587T(ORF1a:H1108Y), A12368G(ORF1a:T4035A), T14441G(ORF1b:F325C), C22995G(S:T478R) [Query: C19185T, C22995G, C28603T, -T148A, 2, 11/09]dead
USA/RI-RISHL2400029/2023|EPI_ISL_18746912|2023-12-12 and USA/RI-RISHL2400027/2023|EPI_ISL_18746914|2023-12-12 JD.1.1.1 > T11601C > C22995G(S:T478R) [Query: T11601C, C19185T, C22995G, 5 seqs, 02/10]

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Triplets

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Quadruplets

USA/CA-CDC-QDX87530303/2023|EPI_ISL_18548132|2023-11-10; USA/CA-CDC-QDX87530304/2023|EPI_ISL_18548100|2023-11-10; USA/CA-CDPH-500129493/2023|EPI_ISL_18679282|2023-11-14 and CA-CDPH-500129551/2023|EPI_ISL_18679334|2023-11-16 JD.1.1.3 > C14599T > A929G(ORF1a:I222V), A22994C(S:T478Q), C26645T, G27214A(ORF6:V5I) [Query: G5015A, C14599T, A22994C, 4 seqs, 12/22] dead

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NkRMnZr commented 11 months ago

Tracking updates:

12-04, 14 seqs from Canada EPI_ISL_18581954-18581955, EPI_ISL_18582157, EPI_ISL_18582453, EPI_ISL_18583078-18583080, EPI_ISL_18583084, EPI_ISL_18583087, EPI_ISL_18583097, EPI_ISL_18583175-18583178 12-08, converted to multitask 12-11, Branch 1, +4 (Canada) EPI_ISL_18610452, EPI_ISL_18610455, EPI_ISL_18610592, EPI_ISL_18610671 12-18, Branch 1 +8 (Canada)

FedeGueli commented 11 months ago

12-11 Branch 1, +4 (Ontario) EPI_ISL_18610452, EPI_ISL_18610455, EPI_ISL_18610592, EPI_ISL_18610671

still canadain clusters as today

FedeGueli commented 11 months ago

Branch 1 parental lineage with ORF1b:R2257S designated JD.1.1.7

NkRMnZr commented 11 months ago

12-18, Branch 1 +8 (Canada) EPI_ISL_18645161, EPI_ISL_18645266, EPI_ISL_18645425, EPI_ISL_18645628, EPI_ISL_18645634, EPI_ISL_18645639, EPI_ISL_18645644, EPI_ISL_18645920

FedeGueli commented 11 months ago

C19185T, G20238T, C22995G, -G425T

it looks like aclustr in some long term care home

FedeGueli commented 10 months ago

JD.1.1 > A29683T > T19848C > G6127T(ORF1a:E1954D), G13427A(ORF1a:E4388K), C22995G(S:T478R), G23149T(S:K529N) [Query: C19185T, T19848C, C22995G, 3 seqs, 12/07]

this one expanded further gaining also S:E554K : Schermata 2023-12-26 alle 19 46 03 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_30c3a_b1f0c0.json?label=id:node_3680822 Query : G8572T, C16222T, samples 7 Denmark England: EPI_ISL_18596293, EPI_ISL_18596305, EPI_ISL_18673315, EPI_ISL_18680529, EPI_ISL_18688102, EPI_ISL_18688198, EPI_ISL_18688232

I suggest to propose it separately having 3 spike/rbd mutations cc @NkRMnZr

FedeGueli commented 10 months ago

Please branch 2 should be proposed it is now 10 with the query G8572T, C16222T (doubling fast)

FedeGueli commented 9 months ago

branch 2 up to 13 with 3 samples in Janauary

FedeGueli commented 9 months ago

Almost everything dead. Please keep branch 2 updated to be sure of it.

FedeGueli commented 9 months ago

Thx for tracking @NkRMnZr

sars-cov-2-variants / lineage-proposals