xz-keg
commented
1 year ago Branch 53 seems exploding.
Closed NkRMnZr closed 11 months ago
xz-keg
commented
1 year ago Branch 53 seems exploding.
FedeGueli
commented
1 year ago Branch 23 designated HK.2.1 via https://github.com/cov-lineages/pango-designation/commit/d75dabedbd433e944eeaee05222453dbda071cf1 milestone edited
FedeGueli
commented
1 year ago Branch 26 is now HK.11.1 via https://github.com/cov-lineages/pango-designation/commit/e268dbfb10735703aeec95cf82092020689f4f4d
FedeGueli
commented
1 year ago Branch 53 seems exploding.
@NkRMnZr plese propose Branch 53 when it reaches 35
xz-keg
commented
1 year ago @FedeGueli You can add multiple milestones and not fix everything to one milestone.
FedeGueli
commented
1 year ago @FedeGueli You can add multiple milestones and not fix everything to one milestone.
Thank you didnt know it would have worked with the automated code.
xz-keg
commented
1 year ago Multiple Canadian clusters bring Branch 35 to 29 seqs.
xz-keg
commented
1 year ago Thank you didnt know it would have worked with the automated code.
It would work.
NkRMnZr
commented
1 year ago Branch 15 transferred to cov-lineages/pango-designation#2340 Branch 17 transferred to cov-lineages/pango-designation#2341 Branch 27 transferred to cov-lineages/pango-designation#2342
FedeGueli
commented
1 year ago Thx @ryhisner who spotted that Branch 48 jumped to 34 gaining further N:229R and S:G1267R in an australian branch, i suggest to propose it.
FedeGueli
commented
1 year ago Branch 15 transferred to cov-lineages/pango-designation#2340 Branch 17 transferred to cov-lineages/pango-designation#2341 Branch 27 transferred to cov-lineages/pango-designation#2342
Thank you
xz-keg
commented
1 year ago There seems to be a new EG.5.1.6+Flip branch, first under EG.5.1.6.
(Edited):
Query: A15270T ,T877C
samples 4 (Canada)
Defining mutations:
EG.5.1.6>Orf8:R115C (C28236T) > C16092T > C10969T > ORF1a:E87D (G526T) > C23380T >Orf1a:I4074V (A12485G) >T877C, Orf1b:E601D(A15270T), S:L455F (G22927T)
xz-keg
commented
1 year ago EG.5.1 > A3210G(ORF1a:D982G) > G26227T(TRS of Envelope), G26888A, C28720T(TRS of ORF9c) > T8909C, T21201C, G22927T(S:L455F), A23702T(S:I714L), A29221G, C29774T, C29803T [Query: A3210G, G22927T, G26227T, 2 seqs, 09/14]
This one is 14 now.
Editing here instead of posting(fed):
The tree now changed and T21201C, A23702T(S:I714L), A29221G, C29774T, C29803T should be excluded from the defining mutations :https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3f074_790990.json?label=id:node_3425846
So the new defining of putative "Branch 65" should be :
EG.5.1 > A3210G(ORF1a:D982G) > G26888A >G26227T, C28720T > T8909C> G22927T(S:L455F)
FedeGueli
commented
1 year ago There seems to be a new EG.5.1.6+Flip branch, first under EG.5.1.6.
@NkRMnZr this should become Branch 64
FedeGueli
commented
1 year ago EG.5.1 > A3210G(ORF1a:D982G) > G26227T(TRS of Envelope), G26888A, C28720T(TRS of ORF9c) > T8909C, T21201C, G22927T(S:L455F), A23702T(S:I714L), A29221G, C29774T, C29803T [Query: A3210G, G22927T, G26227T, 2 seqs, 09/14]
This one is 14 now.
This should become Branch 65 @NkRMnZr
FedeGueli
commented
1 year ago Tell me when added i will remove the comments
@aviczhl2 i have edited your commments not to drive further crazy @NkRMnZr
NkRMnZr
commented
1 year ago 10-26
Adding Branch 64 and 65 thanks to @aviczhl2 and @FedeGueli; Adding Branch 66 from former triplet; Adding Branch 67, a quintuplet from Singapore; Adding Branch 68 from former quintuplet. Adding Branch 69 from former triplet
Branch 24, 35, 42 almost reach 50;
FedeGueli
commented
1 year ago Thank you propose everything is 50.
xz-keg
commented
1 year ago New branch on EG.5.1.3 on Orf8:I47V branch , 6 seqs
query: C3608A,C18261,G22927T,28032
FedeGueli
commented
1 year ago New branch on EG.5.1.3 on Orf8:I47V branch , 6 seqs
query: C3608A,C18261,G22927T,28032
Branch 74 now
FedeGueli
commented
1 year ago thank you nkrmnzr and @aviczhl2 great work.
NkRMnZr
commented
1 year ago Branch 24 transferred to cov-lineages/pango-designation#2353 Branch 35 transferred to cov-lineages/pango-designation#2354 Branch 42 transferred to cov-lineages/pango-designation#2355
FedeGueli
commented
1 year ago Branch 24 transferred to cov-lineages/pango-designation#2353 Branch 35 transferred to cov-lineages/pango-designation#2354 Branch 42 transferred to cov-lineages/pango-designation#2355
Thank you outstanding work!
FedeGueli
commented
1 year ago Branch 77 seems fast. ORF1b:A1643V in Branch 78 is a known mutation: it popped up in an undesignated side branch of AY.41 (sibling to AY.103) that did very bad in south eastern Europe at the end of summer 2021
FedeGueli
commented
1 year ago Branch 24 designated HK.20 and HK.20.1 ( starting with S:G482R) https://github.com/cov-lineages/pango-designation/commit/71cf97b211299abf8f997396b40419285016b435
xz-keg
commented
1 year ago New branch EG.5.1.1+G1274T(Orf1a:V337F)+S:L455F(22927T)
6 seqs but already has an additional level of S:256L
NkRMnZr
commented
1 year ago New branch EG.5.1.1+G1274T(Orf1a:V337F)+S:L455F(22927T)
6 seqs but already has an additional level of S:256L
C19983T which already pulled back to HK.3G1274T is a sub-lineage of Branch 15 tooS:S256L everything else seems way too homoplastic, besides there are GBW seqs, so very skeptical NkRMnZr
commented
1 year ago Branch 48 transferred to cov-lineages/pango-designation#2360
FedeGueli
commented
1 year ago Both Branch 80 and 81 +1 today both of them looking fast.
FedeGueli
commented
12 months ago Branch 13 now reached 49 one of the two samples from Singapore was from a traveller from India please propose it:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice15_genome_test_2d7e5_a33d70.json?c=userOrOld&label=id:node_3501029
xz-keg
commented
12 months ago New branch
EG.5.1.1+N:T362I+Orf1a:P193S,Orf3a:T175I,S:L455F
NkRMnZr
commented
12 months ago Branch 13 transferred to cov-lineages/pango-designation#2364 Branch 51 transferred to cov-lineages/pango-designation#2365 Branch 53 transferred to cov-lineages/pango-designation#2366
FedeGueli
commented
12 months ago Thank you great job!
FedeGueli
commented
12 months ago Branch 46 + S:L452Q is now dsignated HK.22
FedeGueli
commented
11 months ago Branch 11 now has 79 please propose it.
Just set new threeshold to be proposed at 80 seqs. while exceptions are possible if something fast will emerge
FedeGueli
commented
11 months ago Branch 11 now has 79 please propose it.
scratch i missed the new query still 37 .
FedeGueli
commented
11 months ago Branch 54 over 50 now.
FedeGueli
commented
11 months ago Branches 63&64&66&67&68&69&76&78 seem fast
ryhisner
commented
11 months ago To me, branch 28 deserves to be moved to the main Pango page. There are lots of interesting branches there, and a really interesting sequence from Shanghai just showed up as well—EPI_ISL_18518361. The one branch has C26681T, the synonymous mutation in M that is also in BA.2.86 and many other sequences/lineages of interest.
M:K15Q is an A->C nuc mutation and N:T166R is C->G. These are rare nuc mutations, and I don't think they happened by accident.
FedeGueli
commented
11 months ago To me, branch 28 deserves to be moved to the main Pango page. There are lots of interesting branches there, and a really interesting sequence from Shanghai just showed up as well—EPI_ISL_18518361. The one branch has C26681T, the synonymous mutation in M that is also in BA.2.86 and many other sequences/lineages of interest.
M:K15Q is an A->C nuc mutation and N:T166R is C->G. These are rare nuc mutations, and I don't think they happened by accident.
Thank you @ryhisner lineages that reach 50 seqs will be proposed and B28 is 55 so it will be proposed as soon as @NkRMnZr will update this issue. I agree with you i found myself in the Branch 28 tree and saying wow.
FedeGueli
commented
11 months ago To me, branch 28 deserves to be moved to the main Pango page. There are lots of interesting branches there, and a really interesting sequence from Shanghai just showed up as well—EPI_ISL_18518361. The one branch has C26681T, the synonymous mutation in M that is also in BA.2.86 and many other sequences/lineages of interest. M:K15Q is an A->C nuc mutation and N:T166R is C->G. These are rare nuc mutations, and I don't think they happened by accident.
Thank you @ryhisner lineages that reach 50 seqs will be proposed and B28 is 55 so it will be proposed as soon as @NkRMnZr will update this issue. I agree with you i found myself in the Branch 28 tree and saying wow.
@NkRMnZr please propose it, it has the S:A475V branch highlighted as quadruplet in the multiple EG.5.1 +475V issue: https://github.com/sars-cov-2-variants/lineage-proposals/issues/978
FedeGueli
commented
11 months ago There maybe another EG.5.1.3 branch with S:L455F
Defining mutations:
EG.5.1.3 >> S:T874I(C24183T) > S:L455F (G22927T)
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_28083_f2c180.json?c=userOrOld&label=id:node_11125060
Query:
The last two UK samples have S:T874I reverted and gained instead S:T22N , they cluster with a couple of GBW samples from South Korea.
Unsure if it could help with this uncertain placement but at least i put here if someone else finds it.
G28871A,G1085T catches the 2 GBW samples and the 2 Uk sample. could serve as control query to get an Usher in future for it.
FedeGueli
commented
11 months ago New triolet EG.5.1.3 from Australia EG.5.1.3 > C1057T > G18462A > ORF1a:L2105F (C6578T) > S:L455F (G22927T), C26058T, T27210C
FedeGueli
commented
11 months ago Branch 55 designated HK.24.1 via https://github.com/cov-lineages/pango-designation/commit/77596389b8d6291450be40a5b8a7c1701c9e5309
FedeGueli
commented
11 months ago Branch 15 is now HK.23.1 and HK.23.1.1 via https://github.com/cov-lineages/pango-designation/commit/b47c3ca2d6369c236951efde3b954e9ac022e5b7
FedeGueli
commented
11 months ago Branch 73 is now stemming out of HK.28
FedeGueli
commented
11 months ago Branch 76 parental lineage is now HK.30
FedeGueli
commented
11 months ago Branch 12 is now EG.5.1.17 via https://github.com/cov-lineages/pango-designation/commit/5a8103c3bf593a0b0e238b354488fed0e9c07e4b
FedeGueli
commented
11 months ago EG.5.1.18 is now the parental of Branch 93
FedeGueli
commented
11 months ago Branch 33 now designated EG.5.1.19 via https://github.com/cov-lineages/pango-designation/commit/0807c239597f9ab2d4bd86f7c789508877643be6
S:L455Fin EG.5.1 backbone. Checking updates.C66T,C346T,G598A,G1820A,C4423T,C6843T,A10323G(ORF1a:K3353R),C12651T(ORF1a:T4129I),C13860T,A15159G,C19983T,C22096T(S:D178D),C22264T(S:N234N),C22792T(S:I410I),C22998T(S:P479L),C26681T,C27059T,C27507T,C27884T,A29700GBranch 1:
Transferred to main repo. Designated as HK.8
**Designated as HK.8 (EG.5.1.1.8) via cov-lineages/pango-designation@9527e15** _Transferred to cov-lineages/pango-designation#2230_ **Defining Mutations:** `EG.5.1.1` > `C11779T` > `G22927T(S:L455F)` **Query:** `C6541T, C11779T, G22927T` **Earliest seq:** 2023-06-27 (`EPI_ISL_18060870`, Yibin, Sichuan, China) **Latest seq:** 2023-07-17 (`EPI_ISL_18060877`, Zi'yang, Sichuan, China) **Sampled Countries:** China (2, Sichuan)Genomes:
`EPI_ISL_18060870, EPI_ISL_18060877`Back to Tasklist
Branch 2:
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2229_ **Defining Mutations:** `EG.5.1.1` > `C12053T(ORF1a:L3930F)` > `C503T(ORF1a:P80S)` > `C7732T, C18175T(ORF1b:P1570S), G22927T(S:L455F)` **Query:** `C503T, C6541T, G22927T` **Earliest seq:** 2023-07-15 (`EPI_ISL_18060497`, Tokyo, Japan) **Latest seq:** 2023-07-18 (`EPI_ISL_18065046`, Miyagi, Japan) **Sampled Countries:** Japan (2)Genomes:
`EPI_ISL_18060497, EPI_ISL_18065046`Back to Tasklist
Branch 3
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2194_ **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:** 2023-07-18 (`EPI_ISL_18074754`, Shanghai, China) **Sampled Countries:** China (3, Shanghai)Genomes:
`EPI_ISL_17994488, EPI_ISL_18074751, EPI_ISL_18074754`Back to Tasklist
Branch 4
Transferred to main repo
Transferred to cov-lineages/pango-designation#2224 **Defining Mutations:** `EG.5.1` > `C12100G, G22927T`(**S:L455F**) **Query:** `C12100G, G22927T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18060822`, Shanghai, China) **Latest seq:** 2023-07-31 (`EPI_ISL_18094969`, Washington, USA with Travel History to: Japan) **Sampled Countries:** China (2, Shanghai, 1 ex. Thailand), USA (2, Washington, ex. Japan)Genomes:
`EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946, EPI_ISL_18094969`Back to Tasklist
Branch 5
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2250_ **Defining Mutations:** `EG.5.1.1` > `G22927C`(**S:L455F**, different to **HK.3**'s `G22927T`) **Query:** `C6541T, G22927C, -C3653T, -C6317T, -C6327T, -A6659G, -T7111C, -C8074T, -G8768A, -C10702T, -C11779T, -C13968A, -T17811C, -A21137G, -T21748C, -C22482T, -C24023T, -C27741T, -G29734T` **Earliest seq:** 2023-07-08 (`EPI_ISL_18012368`, Sichuan, China) **Latest seq:** 2023-07-27 (`EPI_ISL_18105834`, Shanghai, China) **Sampled Countries:** China (3: Shanghai/2; Sichuan/1)Genomes:
`EPI_ISL_18012368, EPI_ISL_18074450, EPI_ISL_18105834`Back to Tasklist
Branch 6
Many sequences pulled back to HK.3, the reversion probably due to dropout rather than recombinant
**Defining Mutations:** `EG.5.1.1` > _T22480C_Reversion_ > `G22927T`(**S:L455F**) **Query:** `C6541T, G13627A, G22927T, -C7948T, -C22480T` **Earliest seq:** 2023-07-05 (`EPI_ISL_17988079`, Xiangyang, Hubei) **Latest seq:** 2023-08-07 (`EPI_ISL_18105560`, Xiangyang, Hubei) **Sampled Countries:** China (4, Hubei)Genomes:
`EPI_ISL_17988079, EPI_ISL_18105559-18105560, EPI_ISL_18105562`Back to Tasklist
Branch 7
Defining Mutations:
EG.5.1.1>C6627T(ORF1a:T2121I)>T17147C(ORF1b:I1227T)>G22927T(S:L455F) Query:C6627T, T17147C, G22927TEarliest seq: 2023-07-06 (EPI_ISL_18074610, Shanghai) Latest seq: 2023-08-05 (EPI_ISL_18108436, Shanghai, Travel history: Singapore) Sampled Countries: China (3: Shanghai)Genomes:
`EPI_ISL_18074610, EPI_ISL_18108436, EPI_ISL_18108490`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1999b_eabba0.json?f_userOrOld=uploaded%20sample&label=id:node_10741278
Back to Tasklist
Branch 8
Defining Mutations:
EG.5.1.1>C5284T>T14655C>C15951T, G22927T(S:L455F) Query:C5284T, T14655C, G22927TEarliest seq: 2023-07-23 (EPI_ISL_18105571, Shanghai) Latest seq: 2023-08-11 (EPI_ISL_18114886, Shanghai) Sampled Countries: China (3, Shanghai)Genomes:
`EPI_ISL_18105571, EPI_ISL_18108625, EPI_ISL_18114886`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28a92_b9eb0.json?f_userOrOld=uploaded%20sample&label=id:node_6895881
Back to Tasklist
Branch 9
Defining Mutations:
EG.5.1.1>C19983T>G22927T(S:L455F) Query:C6541T, G13627A, C19983T, G22927T, -C6695T **Earliest seq:** 2023-06-30 (EPI_ISL_18074254, Liaoning, China) **Latest seq:** 2023-08-27 (EPI_ISL_18239976`, Utah, USA) Sampled Countries: China (3: Liaoning/2; Shanghai/1)Genomes:
`EPI_ISL_18074249, EPI_ISL_18074254`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2cc80_bc030.json?f_userOrOld=uploaded%20sample&label=id:node_6895986
Back to Tasklist
Branch 10
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2251_ **Defining Mutations:** EG.5.1.1 > C11173T > G22927T(**S:L455F**) **Query:** `C11173T, G13627A, G22927T, -T22228C, -C27406T, -T28157C` **Earliest seq:** 2023-07-16 (`EPI_ISL_18049850`, Qinghai) **Latest seq:** 2023-08-01 (`EPI_ISL_18114762`, Shanghai) **Sampled Countries:** China (3, Qinghai, Shanghai, Xinjiang)Genomes:
`EPI_ISL_18049850, EPI_ISL_18108872, EPI_ISL_18114762`Back to Tasklist
Branch 11
Defining Mutations:
EG.5.1>C9430T>T1939C, C10039T, C20873G(ORF1b:A2469G), G22927T(S:L455F)Query:C9430T, G21718T, G22927T, -C1889T, -G13627A, -C21622AEarliest seq: 2023-07-31 (EPI_ISL_18127303, Tokyo, Japan) Latest seq: 2023-08-07 (EPI_ISL_18127606, Kanagawa, Japan) Sampled Countries: Japan (3: Tokyo/2; Kanagawa/1)Genomes:
`EPI_ISL_18127215, EPI_ISL_18127303, EPI_ISL_18127606`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_1293d_792f00.json?f_userOrOld=uploaded%20sample
Back to Tasklist
Branch 12:
Designated EG.5.1.17
_Designated as **EG.5.1.17** via cov-lineages/pango-designation@5a8103c_ **Defining Mutations:** `EG.5.1` > `G22927C(S:L455F)` **Query:** `C2334T, A18492G, G22927C, -G1069A, -A22106C, -C22570T, -C25572T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18108295`, Anhui, China) **Latest seq:** 2023-08-15 (`EPI_ISL_18138165`, Shanghai, China) **Sampled Countries:** China (4: Shanghai/3; Anhui/1)Genomes:
`EPI_ISL_18108295, EPI_ISL_18114797, EPI_ISL_18138165, EPI_ISL_18138282`Back to Tasklist
Branch 13:
Transferred to main repo
_transferred to cov-lineages/pango-designation#2364_ **Defining Mutations:** `EG.5.1.1` > `C19011T` > `C8991T(ORF1a:A2909V)` > `G22927T(S:L455F)` **Query:** `C8991T, C19011T, G22927T` **Earliest seq:** 2023-08-14 (`EPI_ISL_18146054`, Hubei, China) **Latest seq:** 2023-10-31 (`EPI_ISL_18473645`, Singapore, travel history: India) **Sampled Countries:** China (38: HB/23; SH/4; AH/3; BJ/2; YN/2; GS/1; HA/1; QH/1; XJ/1), Singapore (5: Local/2; ex. China/2; ex. India/1), Netherlands (3), Australia (2: NSW), Austria (1), Croatia (1), France (1), Laos (1)Genomes:
`EPI_ISL_18141179, EPI_ISL_18146054, EPI_ISL_18146087, EPI_ISL_18217222, EPI_ISL_18217236, EPI_ISL_18254205, EPI_ISL_18268148-18268149, EPI_ISL_18268153, EPI_ISL_18268244, EPI_ISL_18284712, EPI_ISL_18284755, EPI_ISL_18306934, EPI_ISL_18313098, EPI_ISL_18313105, EPI_ISL_18313198, EPI_ISL_18313226, EPI_ISL_18349877, EPI_ISL_18354962, EPI_ISL_18363349, EPI_ISL_18376465, EPI_ISL_18376494, EPI_ISL_18384477, EPI_ISL_18384508, EPI_ISL_18388887, EPI_ISL_18388889, EPI_ISL_18388891, EPI_ISL_18438085, EPI_ISL_18438311, EPI_ISL_18438356, EPI_ISL_18438359, EPI_ISL_18438427, EPI_ISL_18441693, EPI_ISL_18442727, EPI_ISL_18442730, EPI_ISL_18447747, EPI_ISL_18457659, EPI_ISL_18461703, EPI_ISL_18461971, EPI_ISL_18463327, EPI_ISL_18463426, EPI_ISL_18464919, EPI_ISL_18464984, EPI_ISL_18465193, EPI_ISL_18465381, EPI_ISL_18465391, EPI_ISL_18466345, EPI_ISL_18473414, EPI_ISL_18473645, EPI_ISL_18475163, EPI_ISL_18475178`Back to Tasklist
Branch 14
Defining Mutations:
EG.5.1.1>A8443G>G22927T(S:L455F)Query:C6541T, A8443G, G22927TEarliest seq: 2023-07-22 (EPI_ISL_18060879Ziyang, Sichuan) Latest seq: 2023-08-09 (EPI_ISL_18146071, Xiaogan, Hubei) Sampled Countries: China (3: Sichuan/2; Hubei/1)Genomes:
`EPI_ISL_18060879, EPI_ISL_18146071, EPI_ISL_18166195`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_140e3_db750.json?f_userOrOld=uploaded%20sample
Back to Tasklist
Branch 15
Designated with levels: HK.23, HK.23.1 and HK.23.1.1
Designated as three levels: [HK.23](https://github.com/cov-lineages/pango-designation/commit/12691b30210c9ab9b68ebfe04bda957d9a09b806), [HK.23.1](https://github.com/cov-lineages/pango-designation/commit/b83d9aa28a32b8a70a6e049b29986577cf07f23a) and [HK.23.1.1](https://github.com/cov-lineages/pango-designation/commit/b47c3ca2d6369c236951efde3b954e9ac022e5b7) _Transferred to cov-lineages/pango-designation#2340_ **Defining Mutations:** `EG.5.1.1` > `C28087T(ORF8:A65V)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C28087T, -A4306G, -G4444A, -A6889G, -G8171A, -T8305C, -C10039T, -C19185T, -C25207T` **Earliest seq:** 2023-08-10 (`EPI_ISL_18138246`, Shanghai) **Latest seq:** 2023-08-14 (`EPI_ISL_18208534`, Shanghai) **Sampled Countries:** China (3: Shanghai)Genomes:
`EPI_ISL_18138040, EPI_ISL_18138246, EPI_ISL_18208534`Back to Tasklist
Branch 16
Defining Mutations:
EG.5.1.1>C8074T > T17811C>C7604T, C10789T, C10834T, C12815T, G20348T(ORF1b:S2294I), G22927C(S:L455F), A25998GQuery:C6541T, C8074T, G22927CEarliest seq: 2023-08-22 (EPI_ISL_18217203, Hubei, China) Latest seq: 2023-08-22 (EPI_ISL_18217204, Hubei, China) Sampled Countries: China (3)Genomes:
`EPI_ISL_18217202-18217204`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2cf_6feba0.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_6949824
Back to Tasklist
Branch 17
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2341_ **Defining Mutations:** `EG.5.1.1` > `C9118T` > `G22927T(S:L455F)` **Query:** `C6541T, C9118T, G22927T, -C25546A` **Earliest seq:** 2023-08-14 (`EPI_ISL_18214798`, Osaka, Japan) **Latest seq:** 2023-10-02 (`EPI_ISL_18373543`, England, UK) **Sampled Countries:** Japan (37), USA (4: TX/2; NJ; SC), South Korea (2), UK (2: EN), Australia (1: WA), Canada (1: ON), France (1)Genomes:
`EPI_ISL_18162837, EPI_ISL_18166739, EPI_ISL_18214798, EPI_ISL_18214838, EPI_ISL_18226559, EPI_ISL_18235760, EPI_ISL_18236014, EPI_ISL_18242568, EPI_ISL_18243896, EPI_ISL_18247826-18247827, EPI_ISL_18253490, EPI_ISL_18261506, EPI_ISL_18271898, EPI_ISL_18279175, EPI_ISL_18279234, EPI_ISL_18285272, EPI_ISL_18285440, EPI_ISL_18294200, EPI_ISL_18300272, EPI_ISL_18338985, EPI_ISL_18342460, EPI_ISL_18354762, EPI_ISL_18354776, EPI_ISL_18362312, EPI_ISL_18370698, EPI_ISL_18370761, EPI_ISL_18371874, EPI_ISL_18372806, EPI_ISL_18373146, EPI_ISL_18373543, EPI_ISL_18376280, EPI_ISL_18376286, EPI_ISL_18377931, EPI_ISL_18382356, EPI_ISL_18382437, EPI_ISL_18382737, EPI_ISL_18385259, EPI_ISL_18387636, EPI_ISL_18390707, EPI_ISL_18390782, EPI_ISL_18390836, EPI_ISL_18397002, EPI_ISL_18402105, EPI_ISL_18402112, EPI_ISL_18411313, EPI_ISL_18413797, EPI_ISL_18413896`Back to Tasklist
Branch 18
Merged into HK.3
**Defining Mutations:** `EG.5.1.1` > `C22264T` > `G22927T(S:L455F)` **Query:** `G13627A, C22264T, G22927T` **Earliest seq:** 2023-07-30 (`EPI_ISL_18129236`, British Columbia, Canada) **Latest seq:** 2023-08-28 (`EPI_ISL_18213253`, Fujian, China) **Sampled Countries:** Canada (1, BC), China (1, Fujian), UK (1, England)Genomes:
`EPI_ISL_18129236, EPI_ISL_18142517, EPI_ISL_18213253`Back to Tasklist
Branch 19
Merged under HK.13, no longer tracking
**Defining Mutations:** `EG.5.1.1` > `C29167T` > `G1186A, T4871C(ORF1a:Y1536H), C7011T(ORF1a:A2249V), G17741A(ORF1b:R1425H), G22927C(S:L455F)` **Query:** `T4871C, G17741A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18160385`, New York, USA) **Latest seq:** 2023-08-19 (`EPI_ISL_18214905`, Ibaraki, Japan) **Sampled Countries:** China (1, Shanghai), Japan (1), USA (1, NY)Genomes:
`EPI_ISL_18160385, EPI_ISL_18208589, EPI_ISL_18214905`Back to Tasklist
Branch 20
Designated as HK.33
_Designated as HK.33 via cov-lineages/pango-designation@7ad122e_ **Defining Mutations:** `EG.5.1.1` > `C2644T` > `T7957C, G22927T(S:L455F), G29348T(N:A359S)` **Query:** `C2644T, G13627A, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18222131`, `SEA` airport, Washington, USA, travel history: UK) **Latest seq:** 2023-08-25 (`EPI_ISL_18208454`, Shanghai, China) **Sampled Countries:** USA (2, ex. UK), China (1, Shanghai)Genomes:
`EPI_ISL_18147035, EPI_ISL_18208454, EPI_ISL_18222131`Back to Tasklist
Branch 21, now pulled under HK.3.8
Pulled under HK.3.8
**Defining Mutations:** `EG.5.1.1` > `C18747T` > `C643T, T13060C, G19723T(ORF1b:V2086F), G22927T(S:L455F)` **Query:** `C643T, C18747T, G22927T` **Earliest seq:** 2023-08-11 (`EPI_ISL_18208543`, Shanghai) **Latest seq:** 2023-08-28 (`EPI_ISL_18232547`, Shanghai Customs, travel history to Japan **Sampled Countries:** China (3, SH)Genomes:
`EPI_ISL_18208543, EPI_ISL_18208548, EPI_ISL_18232547`Back to Tasklist
Branch 22, Now pulled under
HK.3.2>A708C(ORF1a:E148A)>C10969T, G23593T(S:Q677H), G28056A(ORF8:A55T), no longer tracking.Pulled under HK.3.2
**Defining Mutations:** `HK.5` > `G22927T(S:L455F)` **Query:** `spike_Q52H, spike_L455F, spike_Q677H` **Earliest seq:** 2023-08-13 (`EPI_ISL_18146068`, Hubei) **Latest seq:** 2023-08-24 (`EPI_ISL_18226161`, Virginia) **Sampled Countries:** USA (2, VA), China (1, HB)Genomes:
`EPI_ISL_18146068, EPI_ISL_18226161-18226162`Back to Tasklist
Branch 23
Transferred to main repo:
_Transferred to main repo cov-lineages/pango-designation#2319_ **Defining Mutations:** `HK.2` > `G22927T(S:L455F)` **Query:** `C6541T, G21604T, G22927T, -A518G, -C934T, -C1426T, -G3663A, -C5031T, -C7712T, -A7849G, -C8320T, -T16545G` **Earliest seq:** 2023-08-21 (`EPI_ISL_18141161`, Singapore) **Latest seq:** 2023-08-23 (`EPI_ISL_18232599`, Shanghai) **Sampled Countries:** Singapore (1), China (2, SH)Genomes:
`EPI_ISL_18141161, EPI_ISL_18232598-18232599`Back to Tasklist
Branch 24, Designated as
HK.20via cov-lineages/pango-designation@71cf97b ; follow-upS:G482R/G23006Cdesignated asHK.20.1Designated as HK.20 and HK.20.1
_Transferred to cov-lineages/pango-designation#2353_ **Defining Mutations:** `EG.5.1.1` > `C6695T(ORF1a:P2144S)` > `C9448A` > `C5575T, G22927T(S:L455F)` **Query:** `C6695T, C9448A, G22927T` **Earliest seq:** 2023-08-13 (`EPI_ISL_18114870`, Shanghai Customs, travel history to Japan) **Latest seq:** 2023-10-20 (`EPI_ISL_18448529`, Ontario, Canada) **Sampled Countries:** China (13, SH/6; SC/4; FJ/1; ex. Japan/1; ex. S. Korea/1), USA (12: CA/8; AZ/1; OH/1; TX/1; ex. Nepal/1), Singapore (6: Local/5; ex. China/1), Italy (5), UK (3: EN), Australia (2: NSW; QLD), Canada (2: ON), Japan (2), South Korea (2), Switzerland (2), Denmark (1), France (1), Spain (1)Genomes:
`EPI_ISL_18114870, EPI_ISL_18208555, EPI_ISL_18208592, EPI_ISL_18208601, EPI_ISL_18232643, EPI_ISL_18246292, EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192, EPI_ISL_18306956, EPI_ISL_18307066, EPI_ISL_18320793, EPI_ISL_18328004, EPI_ISL_18352555, EPI_ISL_18354001, EPI_ISL_18355023, EPI_ISL_18360344, EPI_ISL_18360616, EPI_ISL_18361723, EPI_ISL_18366403, EPI_ISL_18370066, EPI_ISL_18370200, EPI_ISL_18371411, EPI_ISL_18376528, EPI_ISL_18385607, EPI_ISL_18386446, EPI_ISL_18386489, EPI_ISL_18387133, EPI_ISL_18397207, EPI_ISL_18403093, EPI_ISL_18407761, EPI_ISL_18409112, EPI_ISL_18411495, EPI_ISL_18415804, EPI_ISL_18421982, EPI_ISL_18423702, EPI_ISL_18425050, EPI_ISL_18428715, EPI_ISL_18429030, EPI_ISL_18430106, EPI_ISL_18433978, EPI_ISL_18435244, EPI_ISL_18442967, EPI_ISL_18443714, EPI_ISL_18443742-18443744, EPI_ISL_18443746, EPI_ISL_18444154, EPI_ISL_18446641, EPI_ISL_18448416, EPI_ISL_18448529`Back to Tasklist
Branch 25: Mostly with
S:A684VDefining Mutations: EG.5.1.1 >
C29296T>G22927T(S:L455F)Query:C6541T, G22927T, C29296TEarliest seq: 2023-08-06 (EPI_ISL_18133933, Qinghai) Latest seq: 2023-08-30 (EPI_ISL_18245873, Gansu) Sampled Countries: China (4: SC/2; GS; QH)Genomes:
`EPI_ISL_18133933, EPI_ISL_18245873, EPI_ISL_18246316, EPI_ISL_18246328`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fec3_1b4b0.json?label=id:node_10825408
Back to Tasklist
Branch 26
Transferred to main repo
_Transferred to main repo cov-lineages/pango-designation#2320_ **Defining Mutations:** `HK.11` > `T13228C` > `T4789A` > `G22927T(S:L455F)` **Query:** `T4789A, T13228C, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18221467`, Halland, Sweden) **Latest seq:** 2023-08-21 (`EPI_ISL_18244247`, Denmark) **Sampled Countries:** Denmark (2), Sweden (1)Genomes:
`EPI_ISL_18221467, EPI_ISL_18244233, EPI_ISL_18244247`Back to Tasklist
Branch 27
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2342_ **Defining Mutations:** `EG.5.1.1` > `C25493A(ORF3a:T34K)` > `G28884C(N:G204P)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C25493A` **Earliest seq:** 2023-07-18 (`EPI_ISL_18245992`, Heilongjiang) **Latest seq:** 2023-10-10 (`EPI_ISL_18397223`, Singapore) **Sampled Countries:** China (18: HL/10; LN/2; SH/2; HB; SC; SX; YN), Singapore (14), Denmark (4), Italy (3), USA (3: CA/2; NY), France (2), Australia (1: NSW), Germany (1), South Korea (1), Sweden (1)Genomes:
`EPI_ISL_18138073, EPI_ISL_18232576, EPI_ISL_18244264, EPI_ISL_18245964, EPI_ISL_18245971, EPI_ISL_18245992, EPI_ISL_18246139, EPI_ISL_18246193, EPI_ISL_18282065, EPI_ISL_18300796, EPI_ISL_18306948, EPI_ISL_18306976, EPI_ISL_18306993, EPI_ISL_18307005-18307006, EPI_ISL_18307019, EPI_ISL_18307026, EPI_ISL_18313136, EPI_ISL_18320696, EPI_ISL_18324230, EPI_ISL_18329168, EPI_ISL_18330265, EPI_ISL_18339790, EPI_ISL_18352920, EPI_ISL_18356975, EPI_ISL_18361976, EPI_ISL_18362045, EPI_ISL_18376532, EPI_ISL_18376955, EPI_ISL_18377536, EPI_ISL_18377636, EPI_ISL_18382895, EPI_ISL_18384393, EPI_ISL_18384413, EPI_ISL_18384418, EPI_ISL_18384426, EPI_ISL_18384448, EPI_ISL_18384625, EPI_ISL_18384643, EPI_ISL_18391206-18391207, EPI_ISL_18397223, EPI_ISL_18397241, EPI_ISL_18397267, EPI_ISL_18397584, EPI_ISL_18401938, EPI_ISL_18405209, EPI_ISL_18406218`Back to Tasklist
Branch 28
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2398_ **Defining Mutations:** **EG.5.1.1** > `C5812T` > `G22927T(S:L455F)`, mostly with >> `A26565C(M:K15Q), C28770G(N:T166R)` **Query:** `C5812T, G22927T, C28770G` (for major `A26565C(M:K15Q), C28770G(N:T166R)` sub-branch only) **Earliest seq:** 2023-08-09 (`EPI_ISL_18214077`, South Korea) **Latest seq:** 2023-11-09 (`EPI_ISL_18547984`, Nevada, USA) **Sampled Countries:** South Korea (68), USA (5: NV/2; NC/1; ex. S. Korea/2), Australia (2: NSW; QLD), China (2: SC/1; ex. S. Korea/1), Denmark (2), Hungary (2), Finland (1), Japan (1)Genomes:
`EPI_ISL_18214077, EPI_ISL_18236938, EPI_ISL_18293068, EPI_ISL_18293497, EPI_ISL_18347905, EPI_ISL_18353940, EPI_ISL_18354370, EPI_ISL_18354403, EPI_ISL_18355265, EPI_ISL_18355547, EPI_ISL_18368528, EPI_ISL_18382157, EPI_ISL_18382304, EPI_ISL_18382505, EPI_ISL_18382615, EPI_ISL_18386641, EPI_ISL_18408701-18408702, EPI_ISL_18408814, EPI_ISL_18408878, EPI_ISL_18411301, EPI_ISL_18415920, EPI_ISL_18435710, EPI_ISL_18438964, EPI_ISL_18439203, EPI_ISL_18439262-18439263, EPI_ISL_18439368, EPI_ISL_18439436, EPI_ISL_18460639, EPI_ISL_18460726, EPI_ISL_18460826, EPI_ISL_18461023, EPI_ISL_18461030, EPI_ISL_18461109, EPI_ISL_18461117, EPI_ISL_18461139, EPI_ISL_18488790, EPI_ISL_18488878, EPI_ISL_18488904, EPI_ISL_18489119, EPI_ISL_18501908, EPI_ISL_18502007, EPI_ISL_18503617, EPI_ISL_18503624, EPI_ISL_18503755, EPI_ISL_18503952, EPI_ISL_18503974, EPI_ISL_18511170, EPI_ISL_18511222, EPI_ISL_18511248, EPI_ISL_18511257, EPI_ISL_18511484, EPI_ISL_18513699, EPI_ISL_18518361, EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535643-18535644, EPI_ISL_18535683, EPI_ISL_18539076, EPI_ISL_18539319, EPI_ISL_18539641, EPI_ISL_18539827, EPI_ISL_18540358, EPI_ISL_18544082, EPI_ISL_18547609, EPI_ISL_18547984, EPI_ISL_18550336, EPI_ISL_18552522, EPI_ISL_18559930, EPI_ISL_18564453, EPI_ISL_18564477, EPI_ISL_18564533, EPI_ISL_18564565, EPI_ISL_18564603, EPI_ISL_18564701, EPI_ISL_18564813, EPI_ISL_18564892, EPI_ISL_18564897, EPI_ISL_18565136`Back to Tasklist
Branch 29
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C16726T(ORF1b:H1087Y)` > `G9424T, A12472G, G22927T(S:L455F), T23030C(**S:F490P**), G27621T(ORF7a:Q76H)` **Query:** `A12472G, G22927T, G27621T` **Earliest seq:** 2023-08-25 (`EPI_ISL_18245860`, Fujian, China) **Latest seq:** 2023-09-06 (`EPI_ISL_18243501`, Singapore) **Sampled Countries:** Singapore (2), China (1, FJ)Genomes:
`EPI_ISL_18243491, EPI_ISL_18243501, EPI_ISL_18245860`Back to Tasklist
Branch 30
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C4423T` > `G22927T(S:L455F)` **Query:** `C4423T, G13627A, G22927T` **Earliest seq:** 2023-08-12 (`EPI_ISL_18246284`, Sichuan, China) **Latest seq:** 2023-08-25 (`EPI_ISL_18235973`, Chiba, Japan) **Sampled Countries:** China (2, SC), Japan (1)Genomes:
`EPI_ISL_18232772, EPI_ISL_18235973, EPI_ISL_18246284`Back to Tasklist
Branch 31
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2321_ **Defining Mutations:** **EG.5.1.1** > `C12020T(ORF1a:L3919F), T24496C` > `C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)` **Query:** `C6541T, C12020T, G22927T, -G6337T, -C8982A, -G18445A, -C28087T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18216560`, Galway, Ireland) **Latest seq:** 2023-09-04 (`EPI_ISL_18254216`, Hubei) **Sampled Countries:** China (1), Ireland (1), UK (1)Genomes:
`EPI_ISL_18216560, EPI_ISL_18244531, EPI_ISL_18254216`Back to Tasklist
Branch 32
Defining Mutations: EG.5.1.1 >
T4579A>G2329A, A8443G>G22927T(S:L455F)Query:T4579A, A8443G, G22927TEarliest seq: 2023-08-08 (EPI_ISL_18166186, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18254268, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18166186, EPI_ISL_18232746, EPI_ISL_18245861, EPI_ISL_18246325, EPI_ISL_18254268`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_647e_1a2900.json?label=id:node_6956460
Back to Tasklist
Branch 33
Designated as EG.5.1.19
_Designated as **EG.5.1.19** via cov-lineages/pango-designation@0807c23 , after transferred to cov-lineages/pango-designation#2322_ **Defining Mutations:** **EG.5.1** > `T26171A(ORF3a:M260K)` > `A17615G(ORF1b:K1383R), G22927T(S:L455F)` **Query:** `G21718T, G22927T, T26171A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18134871`, Daknam, Belgium) **Latest seq:** 2023-09-03 (`EPI_ISL_18252041`, `SEA` airport, Washington, with travel hisotry: Netherlands) **Sampled Countries:** Belgium (1), France (1), Romania (1), USA (1, ex. Netherlands)Genomes:
`EPI_ISL_18134871, EPI_ISL_18229094, EPI_ISL_18252041, EPI_ISL_18254718`Back to Tasklist
Branch 34, NOT FLip but with
S:L455SDefining Mutations: EG.5.1.3 >
G2946A(ORF1a:G894D), T15264C, T22926C(S:L455S)Query:C1889T, C2334T, T22926C, -A4340G, -A10703CEarliest seq: 2023-07-27 (EPI_ISL_18248425, Zagreb, Croatia) Latest seq: 2023-07-31 (EPI_ISL_18248430, Zagreb, Croatia) Sampled Countries: Croatia (4)Genomes:
`EPI_ISL_18248425, EPI_ISL_18248427, EPI_ISL_18248429-18248430`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ed45_24dab0.json?f_userOrOld=uploaded%20sample&label=id:node_10831638
Back to Tasklist
Branch 35, side-branch to JJ.1
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2354_ **Defining Mutations:** **EG.5.1.4** > `C26111T(ORF3:P240L)` > `C18555T` > `T17268C` > `G22927T(S:L455F)` **Query:** `T17268C, G22927T, C26111T` **Earliest seq:** 2023-08-08 (`EPI_ISL_18132133`, Newfoundland and Labrador) **Latest seq:** 2023-10-23 (`EPI_ISL_18448815`, Ontario, Canada) **Sampled Countries:** Canada (49: ON/22; NL/15; AB/10; BC/1; NS/1), US (7: CA/2; NY/2; AZ/1; UT/1; VA/1), France (1)Genomes:
`EPI_ISL_18132133, EPI_ISL_18256806, EPI_ISL_18258767, EPI_ISL_18258769-18258770, EPI_ISL_18258773, EPI_ISL_18258778, EPI_ISL_18291996, EPI_ISL_18291998, EPI_ISL_18292017, EPI_ISL_18292020-18292022, EPI_ISL_18292026-18292028, EPI_ISL_18333999, EPI_ISL_18344763, EPI_ISL_18357035, EPI_ISL_18372328, EPI_ISL_18372367, EPI_ISL_18383112, EPI_ISL_18383123-18383124, EPI_ISL_18383697, EPI_ISL_18388693, EPI_ISL_18395288, EPI_ISL_18395414, EPI_ISL_18395581, EPI_ISL_18404467, EPI_ISL_18425010, EPI_ISL_18425420, EPI_ISL_18425431, EPI_ISL_18425847, EPI_ISL_18425967, EPI_ISL_18426727, EPI_ISL_18427300, EPI_ISL_18427492, EPI_ISL_18427494, EPI_ISL_18427496, EPI_ISL_18427507, EPI_ISL_18427602, EPI_ISL_18431345, EPI_ISL_18436820, EPI_ISL_18437028, EPI_ISL_18437176, EPI_ISL_18438632, EPI_ISL_18438777, EPI_ISL_18448237, EPI_ISL_18448584-18448585, EPI_ISL_18448588, EPI_ISL_18448699-18448700, EPI_ISL_18448702, EPI_ISL_18448740, EPI_ISL_18448815`Back to Tasklist
Branch 36
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2399_ **Defining Mutations:** **EG.5.1.1** > `C22388T(S:L276L)` > `G22927T(S:L455F)`, mostly with >> `C1853T` sub-branch **Query:** `C1853T, G13627A, G22927T, -C4780T, -C5031T, -C6627T, -C8982A` (for major `C1853T` sub-branch only) **Earliest seq:** 2023-08-14 (`EPI_ISL_18224087`, Colorado, USA) **Latest seq:** 2023-11-20 (`EPI_ISL_18568071`, `SEA` airport, travel history: France) **Sampled Countries:** France (20), Norway (12), Germany (11), Switzerland (8), USA (6: CO/2; ex. France/2; ex.Germany/2), UK (4: EN), China (3: XJ/2; FJ/1), Denmark (3), Ukraine (3), Canada (2: NB; ON), Finland (2), Spain (2), Belgium (1), Italy (1), Japan (1), Singapore (1)Genomes:
`EPI_ISL_18224087, EPI_ISL_18224096, EPI_ISL_18233134, EPI_ISL_18239749, EPI_ISL_18263561, EPI_ISL_18263571, EPI_ISL_18263574, EPI_ISL_18263576, EPI_ISL_18272601-18272602, EPI_ISL_18280654, EPI_ISL_18280813, EPI_ISL_18290994, EPI_ISL_18291008, EPI_ISL_18291011, EPI_ISL_18308259, EPI_ISL_18313749, EPI_ISL_18326424, EPI_ISL_18326608, EPI_ISL_18327645, EPI_ISL_18337648, EPI_ISL_18337651, EPI_ISL_18338378, EPI_ISL_18373487, EPI_ISL_18373856, EPI_ISL_18380089, EPI_ISL_18380091, EPI_ISL_18388662, EPI_ISL_18388711, EPI_ISL_18411952, EPI_ISL_18412072, EPI_ISL_18421745, EPI_ISL_18421949, EPI_ISL_18428144, EPI_ISL_18428460, EPI_ISL_18428992, EPI_ISL_18433011, EPI_ISL_18441991, EPI_ISL_18451507, EPI_ISL_18464584, EPI_ISL_18464947, EPI_ISL_18468968, EPI_ISL_18476770, EPI_ISL_18485554, EPI_ISL_18486361, EPI_ISL_18486756, EPI_ISL_18493947, EPI_ISL_18494748, EPI_ISL_18495920, EPI_ISL_18496297, EPI_ISL_18496628, EPI_ISL_18496636, EPI_ISL_18496703, EPI_ISL_18499460, EPI_ISL_18505686, EPI_ISL_18505750, EPI_ISL_18519177-18519178, EPI_ISL_18525816, EPI_ISL_18530654, EPI_ISL_18530657-18530658, EPI_ISL_18530757, EPI_ISL_18530938, EPI_ISL_18530967, EPI_ISL_18538000, EPI_ISL_18540615, EPI_ISL_18540768, EPI_ISL_18540871, EPI_ISL_18540915, EPI_ISL_18544152, EPI_ISL_18552615, EPI_ISL_18553571, EPI_ISL_18556840, EPI_ISL_18568060, EPI_ISL_18568071, EPI_ISL_18568733-18568735, EPI_ISL_18570228`Back to Tasklist
Branch 37
⚠
C29095Tbecame homoplastic across the EG.5.1+L455F tree, no longer tracking.No longer tracking
**Defining Mutations:** **EG.5.1.1** > `C29095T` > `G22927T(S:L455F)` **Query:** `G13627A, G22927T, C29095T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18246374`, Sichuan, China) **Latest seq:** 2023-08-31 (`EPI_ISL_18264700`, Texas, USA) **Sampled Countries:** USA (2: TX), China (1: SC)Genomes:
`EPI_ISL_18246374, EPI_ISL_18264482, EPI_ISL_18264700`Back to Tasklist
Branch 38
Defining Mutations: EG.5.1.1 >
T24583C>G22927T(S:L455F)Query:C6541T, G22927T, T24583CEarliest seq: 2023-08-03 (EPI_ISL_18166149, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18268462Shanghai) Sampled Countries: China (3: SC/2; SH/1)Genomes:
`EPI_ISL_18166149, EPI_ISL_18232692, EPI_ISL_18268462`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f9a8_5a58c0.json?f_userOrOld=uploaded%20sample&label=id:node_10885352
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Branch 39
Defining Mutations: HK.1 (EG.5.1.1.1) >
G22927T(S:L455F)Query:C6541T, G13627A, G22332T, G22927T+C6541T, G13627A, G22332A, G22927TEarliest seq: 2023-08-09 (EPI_ISL_18146086, Hubei) Latest seq: 2023-08-28 (EPI_ISL_18254226, Hubei) Sampled Countries: China (7)Genomes:
`EPI_ISL_18146086, EPI_ISL_18146100, EPI_ISL_18254226-18254227, EPI_ISL_18268425, EPI_ISL_18138066, EPI_ISL_18254258`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cca6_5afd40.json?f_userOrOld=uploaded%20sample&label=id:node_6971951
Back to Tasklist
Branch 40
Defining Mutations: EG.5.1.1 >
C10615T>G22927T(S:L455F)>C1426T, G25691T(ORF3a:G100V)Query:C1426T, C10615T, G22927TEarliest seq: 2023-08-08 (EPI_ISL_18138249, Shanghai) Latest seq: 2023-08-25 (EPI_ISL_18268441, Shanghai) Sampled Countries: China (4: SH)Genomes:
`EPI_ISL_18138249, EPI_ISL_18208636, EPI_ISL_18268441, EPI_ISL_18268482`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20010_5b23f0.json?f_userOrOld=uploaded%20sample&label=id:node_6983332
Back to Tasklist
Branch 41
Defining Mutations: EG.5.1.1 >
C24023T>C2485T, G15025A(ORF1b:A520T), G22927C(S:L455F)Query:C6541T, G22927C, C24023TEarliest seq: 2023-08-14 (EPI_ISL_18239206, South Korea) Latest seq: 2023-08-24 (EPI_ISL_18254859, South Korea) Sampled Countries: South Korea (3)Genomes:
`EPI_ISL_18239206, EPI_ISL_18254859, EPI_ISL_18271926`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26c10_8252f0.json?f_userOrOld=uploaded%20sample&label=id:node_10885690
Back to Tasklist
Branch 42
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2355_ **Defining Mutations:** **EG.5.1.1** > `C22687T` > `G22927T(S:L455F)` **Query:** `C6541T, C22687T, G22927T, -T2145C, -A16482C, -C21191T` **Earliest seq:** 2023-08-14 (`EPI_ISL_18279039`, Singapore, travel history: China) **Latest seq:** 2023-09-01 (`EPI_ISL_18278560`, Alberta, Canada) **Sampled Countries:** China (21: GS/4; HB/3; XJ/3; AH/2; SC/2; SX/2; FJ/1; HK/1; QH/1; SH/1; YN/1), Australia (12: NSW/5; SA/4; QLD/1; TA/1; VIC/1), South Korea (8), Canada (6: AB), USA (3: AZ/1; ex. Australia/2), Singapore (2: Local/1; ex. China/1), Japan (1)Genomes:
`EPI_ISL_18146046, EPI_ISL_18213336, EPI_ISL_18217223, EPI_ISL_18278558, EPI_ISL_18278560, EPI_ISL_18279039, EPI_ISL_18289881, EPI_ISL_18293677, EPI_ISL_18293698, EPI_ISL_18311984, EPI_ISL_18312274, EPI_ISL_18312380, EPI_ISL_18313209, EPI_ISL_18327623, EPI_ISL_18327666, EPI_ISL_18346251, EPI_ISL_18346325, EPI_ISL_18347707, EPI_ISL_18350428, EPI_ISL_18360224, EPI_ISL_18361336, EPI_ISL_18361999, EPI_ISL_18365676, EPI_ISL_18365684, EPI_ISL_18365890, EPI_ISL_18366374, EPI_ISL_18382081, EPI_ISL_18382589, EPI_ISL_18382710, EPI_ISL_18384562, EPI_ISL_18388967, EPI_ISL_18389014, EPI_ISL_18389016, EPI_ISL_18390872, EPI_ISL_18396110, EPI_ISL_18401894, EPI_ISL_18401903, EPI_ISL_18401983, EPI_ISL_18404054, EPI_ISL_18408752, EPI_ISL_18411422, EPI_ISL_18411665, EPI_ISL_18411717, EPI_ISL_18411753, EPI_ISL_18425089, EPI_ISL_18427884, EPI_ISL_18435235, EPI_ISL_18438336, EPI_ISL_18438338, EPI_ISL_18438347, EPI_ISL_18439100, EPI_ISL_18447517, EPI_ISL_18447771`Back to Tasklist
Branch 43
now seems to be pulled under HK.3, no longer tracking
Pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C19524T` > `G22927T(S:L455F), A28254Δ` **Query:** `G13627A, C19524T, G22927T, -C5031T` **Earliest seq:** 2023-08-19 (`EPI_ISL_18246322`, Sichuan) **Latest seq:** 2023-09-07 (`EPI_ISL_18277156`, Fujian) **Sampled Countries:** China (3: FJ; HL; SC)Genomes:
`EPI_ISL_18246049, EPI_ISL_18246322, EPI_ISL_18277156`Back to Tasklist
Branch 44, "FLippeR"
Transferred to main Repo
_Transferred to cov-lineages/pango-designation#2296_ **Defining Mutations:** **EG.5.1** > `A22106C(S:K182Q)` > `C22995G(S:T478R), A25664G(ORF3a:Y91C)` > `C1613T(ORF1a:L450F), G20995T(ORF1b:G2510C), G22927C(S:L455F), C25803T, A27388C` **Query:** `A22106C, G22927C, C22995G` **Earliest seq:** 2023-08-14 (`EPI_ISL_18160020`, Denmark, or, `EPI_ISL_18278998`, Singapore) **Latest seq:** 2023-09-04 (`EPI_ISL_18243476`, Singapore) **Sampled Countries:** Singapore (2), Denmark (1)Genomes:
`EPI_ISL_18160020, EPI_ISL_18243476, EPI_ISL_18278998`Back to Tasklist
Branch 45
Transferred to main Repo
_Transferred to cov-lineages/pango-designation#2308_ **Defining Mutations:** `EG.5.1.1` > `C13968A, A15885G` > `T11449C` > `C10369T, G22927T(S:L455F), C29077T, G29140T(N:Q289H)` **Query:** `T11449C, C13968A, G22927T` **Earliest seq:** 2023-09-06 (`EPI_ISL_18273676`, England) **Latest seq:** 2023-09-07 (`EPI_ISL_18284457`, `IAD` Airport, DC, travel history: Italy) **Sampled Countries:** UK (2: EN) USA (2, ex. Italy)Genomes:
`EPI_ISL_18273676, EPI_ISL_18281373, EPI_ISL_18284072, EPI_ISL_18284457`Back to Tasklist
Branch 46 with a sub-lineage of
S:L452Q, designated as HK.22parental lineage of HK.22
_Branch 46 + S:L452Q designated as HK.22 via cov-lineages/pango-designation@2d3115a_ **Defining Mutations:** `EG.5.1.1` > `G25407T(ORF3a:M5I)` > `C2662T` > `G22927T(S:L455F)` **Query:** `C2662T, G22927T, G25407T` **Earliest seq:** 2023-08-06 (`EPI_ISL_18114750`, Shanghai) **Latest seq:** 2023-09-06 (`EPI_ISL_18284970`, Shanghai) **Sampled Countries:** China (4: SH)Genomes:
`EPI_ISL_18114750, EPI_ISL_18232688, EPI_ISL_18284888, EPI_ISL_18284970`Back to Tasklist
Branch 47
Defining Mutations:
EG.5.1.1>C7600T>G22927T(S:L455F)>T10216CQuery:C7600T, T10216C, G22927TEarliest seq: 2023-08-22 (EPI_ISL_18246331, Sichuan) Latest seq: 2023-09-04 (EPI_ISL_18284731, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18246331, EPI_ISL_18284731, EPI_ISL_18284776, EPI_ISL_18284783, EPI_ISL_18284960`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ad47_b108e0.json?f_userOrOld=uploaded%20sample&label=id:node_10899080
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Branch 48
Transferred to main repo
Transferred to cov-lineages/pango-designation#2360 ⚠️ Please check potential misplacement. **Defining Mutations:** `EG.5.1.1` > `A23539T(S:S659S)` > `G22927T(S:L455F)` **Query:** `G13627A, G22927T, A23539T, -T899C, -C2662T, -C10015T, -T12865C, -G22332A` **Earliest seq:** 2023-08-16 (`EPI_ISL_18141107`, Singapore) **Latest seq:** 2023-10-22 (`EPI_ISL_18440472`, Netherlands) **Sampled Countries:** Australia (32: NSW/14; SA/8; QLD/4; VIC/3; TAS/1; WA/1), China (10: SC/4; HB/2; SH/2; FJ/1; XJ/1), New Zealand (9), Singapore (4), Netherlands (3), USA (2), France (1)Genomes:
`EPI_ISL_18141107, EPI_ISL_18246326, EPI_ISL_18278997, EPI_ISL_18279955, EPI_ISL_18292475, EPI_ISL_18300669, EPI_ISL_18307132, EPI_ISL_18320781, EPI_ISL_18324527, EPI_ISL_18324537, EPI_ISL_18324951, EPI_ISL_18346779, EPI_ISL_18346805, EPI_ISL_18346818, EPI_ISL_18347516, EPI_ISL_18347639, EPI_ISL_18347703-18347704, EPI_ISL_18347710, EPI_ISL_18352381, EPI_ISL_18355046, EPI_ISL_18360352, EPI_ISL_18365605, EPI_ISL_18365672, EPI_ISL_18365874, EPI_ISL_18376439, EPI_ISL_18388898, EPI_ISL_18396188, EPI_ISL_18411419, EPI_ISL_18411467, EPI_ISL_18411551, EPI_ISL_18411564, EPI_ISL_18411674, EPI_ISL_18411695, EPI_ISL_18423924, EPI_ISL_18427871, EPI_ISL_18428112, EPI_ISL_18435043, EPI_ISL_18438373, EPI_ISL_18440466, EPI_ISL_18440472, EPI_ISL_18440476, EPI_ISL_18442757, EPI_ISL_18442774, EPI_ISL_18447732, EPI_ISL_18454463, EPI_ISL_18454489, EPI_ISL_18457508, EPI_ISL_18459380, EPI_ISL_18459604, EPI_ISL_18459721, EPI_ISL_18459855, EPI_ISL_18459912, EPI_ISL_18459940, EPI_ISL_18461585, EPI_ISL_18461782, EPI_ISL_18461792, EPI_ISL_18461895, EPI_ISL_18461916, EPI_ISL_18461956, EPI_ISL_18464115`Back to Tasklist
Branch 49
Now at least 3 smaller clusters seems pulled together a
S:L455Fbranch right under EG.5.1.4 polytomy, hard to catch by proper query now.Query failed
**Defining Mutations:** `EG.5.1.4` > `C8407T, C11008A(ORF1a:H3581Q), G22927T(S:L455F), G25538T(ORF3a:G49V), C25572T` **Query:** `A18492G, A21137G, G22927T, -C6120T, -G13627A, -C26111T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18284756`, Hubei) **Latest seq:** 2023-09-03 (`EPI_ISL_18284729`, Hubei) **Sampled Countries:** China (3)Genomes:
`EPI_ISL_18284721, EPI_ISL_18284729, EPI_ISL_18284756`Back to Tasklist
Branch 50
Defining Mutations:
EG.5.1.1>G28904T(N:A211S)>G22927T(S:L455F), G27261T, C28744TQuery:C6541T, G22927T, G28904TEarliest seq: 2023-08-30 (EPI_ISL_18268410, Shanghai) Latest seq: 2023-09-03 (EPI_ISL_18254255, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18254255, EPI_ISL_18268410, EPI_ISL_18289864, EPI_ISL_18289874, EPI_ISL_18289889`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_523af_c118f0.json?f_userOrOld=uploaded%20sample&label=id:node_6955662
Back to Tasklist
Branch 51
Transferred to main repo
_transferred to cov-lineages/pango-designation#2365_ **Defining Mutations:** EG.5.1.1 > `C10015T` > `G22927T(S:L455F)` **Query:** `C6541T, C10015T, G22927T, -C4586T` **Earliest seq:** 2023-07-31 (`EPI_ISL_18246153`, Heilongjiang) **Latest seq:** 2023-10-31 (`EPI_ISL_18473950`, Spain) **Sampled Countries:** China (20: SH/6; HL/5; LN/3; AH/1; BJ/1; GS/1; HB/1; SC/1; SX/1; XJ/1), Canada (10: ON/9; NS/1), Australia (5: NSW/4; QLD/1), Singapore (5), Spain (5), Croatia (4), USA (3: NY/2; HI/1), Denmark (2), Japan (2), Belgium (1), France (1), Italy (1), Switzerland (1)Genomes:
`EPI_ISL_18246153, EPI_ISL_18268220, EPI_ISL_18284760, EPI_ISL_18289806, EPI_ISL_18304238, EPI_ISL_18307185, EPI_ISL_18309728, EPI_ISL_18320892, EPI_ISL_18333882, EPI_ISL_18354453, EPI_ISL_18356455, EPI_ISL_18362071, EPI_ISL_18382338, EPI_ISL_18384364, EPI_ISL_18388937, EPI_ISL_18388943, EPI_ISL_18392626, EPI_ISL_18392641, EPI_ISL_18395616, EPI_ISL_18398918, EPI_ISL_18401900, EPI_ISL_18422863, EPI_ISL_18425076, EPI_ISL_18433557, EPI_ISL_18438020, EPI_ISL_18438314, EPI_ISL_18438838, EPI_ISL_18445101, EPI_ISL_18445501, EPI_ISL_18446144, EPI_ISL_18448315, EPI_ISL_18448907-18448908, EPI_ISL_18448913-18448914, EPI_ISL_18461557, EPI_ISL_18461608, EPI_ISL_18461684, EPI_ISL_18461722, EPI_ISL_18464481, EPI_ISL_18464633, EPI_ISL_18465094, EPI_ISL_18465113, EPI_ISL_18465171, EPI_ISL_18465395, EPI_ISL_18465403, EPI_ISL_18466062, EPI_ISL_18466326-18466327, EPI_ISL_18466420, EPI_ISL_18466590, EPI_ISL_18470572, EPI_ISL_18471609, EPI_ISL_18471611, EPI_ISL_18473319, EPI_ISL_18473421, EPI_ISL_18473950, EPI_ISL_18475156, EPI_ISL_18475172, EPI_ISL_18475181, EPI_ISL_18475190, EPI_ISL_18475453`Back to Tasklist
Branch 52, now pulled under HK.3.2
Now part of HK.3.2
**Defining Mutations:** `EG.5.1.1` > `C26029A(ORF3a:Q213K)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C26029A, -G24944T, -A26901G` **Earliest seq:** 2023-08-16 (`EPI_ISL_18146001`, Hubei, China) **Latest seq:** 2023-09-20 (`EPI_ISL_18340137`, Illinois, USA) **Sampled Countries:** China (5: HB/3; SC; YN) USA (3: IL; NY; WA), Oman (1)Genomes:
`EPI_ISL_18146001, EPI_ISL_18246341, EPI_ISL_18290983, EPI_ISL_18292780, EPI_ISL_18313122, EPI_ISL_18322921, EPI_ISL_18330205, EPI_ISL_18333620, EPI_ISL_18340137`Back to Tasklist
Branch 53
Transferred to main repo
_transferred to cov-lineages/pango-designation#2366_ **Defining Mutations:** `EG.5.1.1` > `C27741T` > `C1912T, C1968T(ORF1a:T568I), T7111C, A20010T(ORF1b:Q2181H), T20592C, G22927C(S:L455F), C28093T(ORF8:S67F)` **Query:** `C6541T, G22927C, C27741T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18345224`, Cork, Ireland) **Latest seq:** 2023-10-23 (`EPI_ISL_18471085`, Connecticut, USA) **Sampled Countries:** UK (17: EN/16; WS/1), USA (14: NY/3; NJ/2; TX/2; UT/2; AZ/1; CA/1; CT/1; MN/1; OH/1), Ireland (9), Canada (4: ON/3; BC/1), Denmark (2), France (2), China (2: SC/1; ex. Spain/1), Belgium (1), South Korea (1), Netherlands (1)Genomes:
`EPI_ISL_18250090, EPI_ISL_18284832, EPI_ISL_18290882, EPI_ISL_18290915, EPI_ISL_18308328, EPI_ISL_18308339, EPI_ISL_18315360, EPI_ISL_18321565, EPI_ISL_18332107, EPI_ISL_18332505, EPI_ISL_18345224, EPI_ISL_18354139, EPI_ISL_18362839, EPI_ISL_18362880-18362881, EPI_ISL_18362951, EPI_ISL_18375850, EPI_ISL_18377642, EPI_ISL_18385706, EPI_ISL_18385720, EPI_ISL_18385728, EPI_ISL_18385734, EPI_ISL_18388184, EPI_ISL_18388760-18388761, EPI_ISL_18389241, EPI_ISL_18398829, EPI_ISL_18399988, EPI_ISL_18400877, EPI_ISL_18403587, EPI_ISL_18403998, EPI_ISL_18407932, EPI_ISL_18416430, EPI_ISL_18416450, EPI_ISL_18420893, EPI_ISL_18420911, EPI_ISL_18422267, EPI_ISL_18427521, EPI_ISL_18429173, EPI_ISL_18429518, EPI_ISL_18430506, EPI_ISL_18433870, EPI_ISL_18438642, EPI_ISL_18442008, EPI_ISL_18443922, EPI_ISL_18448322, EPI_ISL_18452961, EPI_ISL_18456955, EPI_ISL_18467439, EPI_ISL_18467445, EPI_ISL_18467479, EPI_ISL_18471085, EPI_ISL_18475314`Back to Tasklist
Branch 54:
Defining Mutations:
EG.5.1.1>G24368T(S:D936Y)>G22927T(S:L455F)Query:G13627A, G22927T, G24368T, -G3567A, -C4012T, -C5031T, -T13234C, -C17976TEarliest seq: 2023-09-11 (EPI_ISL_18312655, South Korea) Latest seq: 2023-11-24 (EPI_ISL_18567787, Veneto, Italy) Sampled Countries: Finland (15), South Korea (15), USA (9: NY/7; UT/2), Italy (2), Singapore (2), Australia (1: QLD), Germany (1)Genomes:
`EPI_ISL_18312655, EPI_ISL_18343453, EPI_ISL_18347772, EPI_ISL_18347778, EPI_ISL_18347783, EPI_ISL_18347794, EPI_ISL_18347862, EPI_ISL_18354114, EPI_ISL_18394470, EPI_ISL_18408694, EPI_ISL_18411981, EPI_ISL_18411986, EPI_ISL_18412002, EPI_ISL_18412024, EPI_ISL_18412052, EPI_ISL_18412131, EPI_ISL_18439287, EPI_ISL_18439475, EPI_ISL_18445086, EPI_ISL_18445161, EPI_ISL_18449963, EPI_ISL_18458264, EPI_ISL_18458329, EPI_ISL_18460569, EPI_ISL_18502041, EPI_ISL_18503589, EPI_ISL_18511443, EPI_ISL_18533418, EPI_ISL_18533465, EPI_ISL_18533560, EPI_ISL_18533727, EPI_ISL_18534149, EPI_ISL_18539237, EPI_ISL_18539435, EPI_ISL_18539679, EPI_ISL_18539701, EPI_ISL_18539776, EPI_ISL_18541395, EPI_ISL_18541532, EPI_ISL_18544389, EPI_ISL_18547900, EPI_ISL_18554927, EPI_ISL_18555070, EPI_ISL_18564736, EPI_ISL_18567787`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28b3b_c482d0.json?label=id:node_3526683
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Branch 55
Designated with 2 levesl: HK.24 and HK.24.1
Designated as [HK.24](https://github.com/cov-lineages/pango-designation/commit/211018361b201eda9d492fdb25dc7fbcad217804) and [HK.24.1](https://github.com/cov-lineages/pango-designation/commit/77596389b8d6291450be40a5b8a7c1701c9e5309) **Defining Mutations:** `EG.5.1.1` > `G23522A(S:E654K)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, G23522A` **Earliest seq:** 2023-08-26 (`EPI_ISL_18284795`, Shanghai, China) **Latest seq:** 2023-09-24 (`EPI_ISL_18346833`, South Australia, Australia) **Sampled Countries:** Australia (6: QLD/2; WA/2; NSW; SA), China (3: SH), New Zealand (1)Genomes:
`EPI_ISL_18284795, EPI_ISL_18284982, EPI_ISL_18324864, EPI_ISL_18346833, EPI_ISL_18347678, EPI_ISL_18352382, EPI_ISL_18352389, EPI_ISL_18352581, EPI_ISL_18354460, EPI_ISL_18360253`Back to Tasklist
Branch 56
Defining Mutations:
EG.5.1.1>A22582G(S:E340)>G22927T(S:L455F)Query:G13627A, A22582G, G22927T, -G3153AEarliest seq: 2023-08-30 (EPI_ISL_18303241, Portugal) Latest seq: 2023-09-25 (EPI_ISL_18355054, Singapore) Sampled Countries: Portugal (2), Singapore (2), China (1: QH), UK (1: EN)Genomes:
`EPI_ISL_18268272, EPI_ISL_18274005, EPI_ISL_18303241, EPI_ISL_18303432, EPI_ISL_18307200, EPI_ISL_18355054`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450332
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Branch 57
Defining Mutations:
EG.5.1.1>A22582G(S:E340)>G3153A(ORF1a:G963D)>G22927T(S:L455F)Query:G3153A, A22582G, G22927TEarliest seq: 2023-08-14 (EPI_ISL_18146012, Hubei, China) Latest seq: 2023-09-26 (EPI_ISL_18350530, Basque, Spain) Sampled Countries: China (4: FJ; HB; HK; SH), Japan (2), South Korea (2), USA (2: ex. Greece), Spain (1)Genomes:
`EPI_ISL_18146012, EPI_ISL_18277143, EPI_ISL_18293356, EPI_ISL_18306220, EPI_ISL_18306632, EPI_ISL_18306769, EPI_ISL_18309318, EPI_ISL_18309324, EPI_ISL_18350530, EPI_ISL_18354289, EPI_ISL_18360277`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450116
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Branch 58, formerly singlet, thanks to @aviczhl2 for updated info
Defining Mutations:
EG.5.1>T26972C>C28909T>C2106A(ORF1a:T614N), G28423T(ORF9b:R47L)>A21759G(S:H66R), G22927T(S:L455F), G24004A(S:K814), C25572TQuery:A18492G, G22927T, C28909TEarliest seq: 2023-08-21 (EPI_ISL_18271704, S. Korea) Latest seq: 2023-09-19 (EPI_ISL_18355498, S. Korea) Sampled Countries: South Korea (6)Genomes:
`EPI_ISL_18271704, EPI_ISL_18354058, EPI_ISL_18354072, EPI_ISL_18354264, EPI_ISL_18355236, EPI_ISL_18355498`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26418_30eca0.json?label=id:node_3429102
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Branch 59: ⚠️ careful with potential dropout/misplacement.
Defining Mutations:
EG.5.1.1>G20134T(ORF1b:V2223L)>G22927T(S:L455F)Query:G13627A, G20134T, G22927TEarliest seq: 2023-09-04 (EPI_ISL_18300595, New South Wales) Latest seq: 2023-10-03 (EPI_ISL_18361370, NSW) Sampled Countries: Australia (17: NSW/16; QLD)Genomes:
`EPI_ISL_18300595, EPI_ISL_18300598, EPI_ISL_18300624, EPI_ISL_18300634, EPI_ISL_18300676-18300679, EPI_ISL_18300732, EPI_ISL_18300745-18300746, EPI_ISL_18300790, EPI_ISL_18324806, EPI_ISL_18352578, EPI_ISL_18361360-18361361, EPI_ISL_18361370`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4fa9_6ad320.json?label=id:node_3451611
Trivia:
Heilongjiang/HLJCDC-2004/2023|EPI_ISL_18245889|2023-07-25, please check potential HK.3-dropout/misplacement.Back to Tasklist
Branch 60: Formerly
Y144Fartifact branch now maskedDefining Mutations:
EG.5.1.1>T16545G>C1471T, G22927T(S:L455F)Query:G13627A, T16545G, G22927TEarliest seq: 2023-08-25 (EPI_ISL_18228384, Finland) Latest seq: 2023-10-04 (EPI_ISL_18362018, Singapore) Sampled Countries: Singapore (7), China (3: SH/2; HB), Finland (1)Genomes:
`EPI_ISL_18228384, EPI_ISL_18243407, EPI_ISL_18254180, EPI_ISL_18306951, EPI_ISL_18320869, EPI_ISL_18360325, EPI_ISL_18361717, EPI_ISL_18361964, EPI_ISL_18362005, EPI_ISL_18362018, EPI_ISL_18362077`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_108b5_6b1720.json?f_userOrOld=uploaded%20sample&label=id:node_3457632
Trivia:
Y144Fartifact sub-branch now seems masked, thanks to @FedeGueli for the quick analysis and query.Back to Tasklist
Branch 61
⚠️ Please check potential reversion/artifact/misplacement,
C26681Tis quite homoplastic in HK.3*, no longer trackingpotential HK.3 dropout
**Defining Mutations:** `EG.5.1.1` > `C26681T` > `T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)` **Query:** `T22032C, G22927T, C26681T` **Earliest seq:** 2023-09-03 (`EPI_ISL_18376557`, Sichuan) **Latest seq:** 2023-09-11 (`EPI_ISL_18376558`, Sichuan, _OR_ `EPI_ISL_18277141`, Fujian) **Sampled Countries:** China (5: SC/4; FJ)Genomes:
`EPI_ISL_18277141, EPI_ISL_18376556-18376559`Back to Tasklist
Branch 62: With a sub-branch of FLippeR
Defining Mutations:
EG.5.1.1>C18559T(ORF1b:L1698F)>T15927C, G22927T(S:L455F)Query:C6541T, C18559T, G22927TEarliest seq: 2023-08-31 (EPI_ISL_18285056, Sichuan, China) Latest seq: 2023-09-20 (EPI_ISL_18382134, South Korea) Sampled Countries: China (4: SC/2; SH/2), South Korea (1)Genomes:
`EPI_ISL_18285056-18285057, EPI_ISL_18320863, EPI_ISL_18360320, EPI_ISL_18382134`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_24de1_9159b0.json?label=id:node_3445922
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Branch 63
⚠️ Please check potential misplacement
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2400_ **Defining Mutations:** `EG.5.1.1` > `T14034C` > `T6556C` > `G22927T(S:L455F)` **Query:** `T6556C, T14034C, G22927T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18236022`, Chiba, Japan) **Latest seq:** 2023-11-16 (`EPI_ISL_18568493`, Ardèche, France) **Sampled Countries:** South Korea (66), Japan (11), France (7), China (2: Taiwan), Singapore (2), Germany (1), Ireland (1), UK (1: England)Genomes:
`EPI_ISL_18236022, EPI_ISL_18307101, EPI_ISL_18307183, EPI_ISL_18312967, EPI_ISL_18354179, EPI_ISL_18354386, EPI_ISL_18371409, EPI_ISL_18371437, EPI_ISL_18376385, EPI_ISL_18381917, EPI_ISL_18382077, EPI_ISL_18382170, EPI_ISL_18382306, EPI_ISL_18382313, EPI_ISL_18384744, EPI_ISL_18390972, EPI_ISL_18408733, EPI_ISL_18408999, EPI_ISL_18409046, EPI_ISL_18409110, EPI_ISL_18418096, EPI_ISL_18418099, EPI_ISL_18420466, EPI_ISL_18423347, EPI_ISL_18438958, EPI_ISL_18439063, EPI_ISL_18439157, EPI_ISL_18439221, EPI_ISL_18439371, EPI_ISL_18460530, EPI_ISL_18460541, EPI_ISL_18460589, EPI_ISL_18460966, EPI_ISL_18460978, EPI_ISL_18461033, EPI_ISL_18461094, EPI_ISL_18461485, EPI_ISL_18465933, EPI_ISL_18468665, EPI_ISL_18486472, EPI_ISL_18491815, EPI_ISL_18496187, EPI_ISL_18501996, EPI_ISL_18502046, EPI_ISL_18502053, EPI_ISL_18502059, EPI_ISL_18503696, EPI_ISL_18503846, EPI_ISL_18510036, EPI_ISL_18510038, EPI_ISL_18511034, EPI_ISL_18511095, EPI_ISL_18511104, EPI_ISL_18511108, EPI_ISL_18511172, EPI_ISL_18511241, EPI_ISL_18511380, EPI_ISL_18511416, EPI_ISL_18511461, EPI_ISL_18511469, EPI_ISL_18511480, EPI_ISL_18511508, EPI_ISL_18511521, EPI_ISL_18511532, EPI_ISL_18511557, EPI_ISL_18511580, EPI_ISL_18511661, EPI_ISL_18511670, EPI_ISL_18535606, EPI_ISL_18535663, EPI_ISL_18535697, EPI_ISL_18539307, EPI_ISL_18539369, EPI_ISL_18539422, EPI_ISL_18539428, EPI_ISL_18539447, EPI_ISL_18539483, EPI_ISL_18539547, EPI_ISL_18545014, EPI_ISL_18564392, EPI_ISL_18564436, EPI_ISL_18564462-18564463, EPI_ISL_18564564, EPI_ISL_18564669, EPI_ISL_18564752, EPI_ISL_18564926, EPI_ISL_18565014, EPI_ISL_18565195, EPI_ISL_18568493, EPI_ISL_18570360`Back to Tasklist
Branch 64
Defining Mutations:
EG.5.1.6>C28236T(ORF8:R115C)>C16092T>C10969T>G526T(ORF1a:E87D)>C23380T(S:N606)>A12485G(ORF1a:I4074V)>T877C, A15270T(ORF1b:E601D), G22927T(S:L455F)Query:G526T, A15270T, G22927TEarliest seq: 2023-10-08 (EPI_ISL_18404805, New Brunswick, Canada) Latest seq: 2023-10-15 (EPI_ISL_18427247, Ontario, Canada) Sampled Countries: Canada (4: ON/3; NB)Genomes:
`EPI_ISL_18404805, EPI_ISL_18426514, EPI_ISL_18426586, EPI_ISL_18427247`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21e1_9e19a0.json?label=id:node_3437762
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Branch 65
Defining Mutations:
EG.5.1>A3210G(ORF1a:D982G)>G26888A>G26227T(_TRS of Envelope_), C28720T(_TRS of ORF9c_)>T8909C>G22927T(S:L455F)Query:A3210G, T8909C, G22927TEarliest seq: 2023-09-07 (EPI_ISL_18419405, Sicily, Italy) Latest seq: 2023-09-18 (EPI_ISL_18329969, Denmark) Sampled Countries: Italy (13), Denmark (1)Genomes:
`EPI_ISL_18258788-18258789, EPI_ISL_18329969, EPI_ISL_18419405, EPI_ISL_18419417, EPI_ISL_18419442, EPI_ISL_18419446, EPI_ISL_18419449, EPI_ISL_18419451, EPI_ISL_18419459, EPI_ISL_18419472, EPI_ISL_18419474, EPI_ISL_18419478, EPI_ISL_18419484`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b9a_9e23b0.json?label=id:node_3428133
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Branch 66
Defining Mutations:
EG.5.1.1>C11779T>C12525T(ORF1a:T4087I)>G22927T(S:L455F)Query:C11779T, C12525T, G22927TEarliest seq: 2023-08-27 (EPI_ISL_18360191, England) Latest seq: 2023-10-09 (EPI_ISL_18421921, Belgium) Sampled Countries: South Korea (4), Canada (3: BC), Belgium (1), China (1: SH), New Zealand (1), Singapore (1), UK (1: EN)Genomes:
`EPI_ISL_18227053, EPI_ISL_18292157, EPI_ISL_18355538, EPI_ISL_18360191, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18397328, EPI_ISL_18408737, EPI_ISL_18421921, EPI_ISL_18430928, EPI_ISL_18431490, EPI_ISL_18431860`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34aaf_9ea630.json?label=id:node_3493682
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Branch 67
Defining Mutations:
EG.5.1.1>C25613T(ORF3a:S74F)>G22927C(S:L455F)Query:C6541T, G22927C, C25613T, -C26681T, -G26840AEarliest seq: 2023-10-12 (EPI_ISL_18428810, Singapore) Latest seq: 2023-10-16 (EPI_ISL_18428772, Singapore) Sampled Countries: Singapore (5)Genomes:
`EPI_ISL_18428766, EPI_ISL_18428769, EPI_ISL_18428771-18428772, EPI_ISL_18428810`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41fd2_a0fe0.json?label=id:node_3487648
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Branch 68
Defining Mutations:
EG.5.1.1>G16710A>G22927T(S:L455F)Query:G16710A, G13627A, G22927T, -G28904TEarliest seq: 2023-09-25 (EPI_ISL_18355035, Singapore) Latest seq: 2023-10-18 (EPI_ISL_18428623, Singapore) Sampled Countries: Singapore (11)Genomes:
`EPI_ISL_18355035, EPI_ISL_18361806, EPI_ISL_18361914, EPI_ISL_18361935, EPI_ISL_18362103, EPI_ISL_18397258, EPI_ISL_18397453, EPI_ISL_18428554, EPI_ISL_18428623, EPI_ISL_18428638, EPI_ISL_18428659`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c933_9f2590.json?label=id:node_3474466
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Branch 69
Defining Mutations:
EG.5.1.1>G1085T(ORF1a:V274L)>G1535A(ORF1a:V424I), G22927T(S:L455F)Query:G1085T, G13627A, G22927T, -A11000G, -C29375T, Earliest seq: 2023-10-02 (EPI_ISL_18361916, Singapore) Latest seq: 2023-10-16 (EPI_ISL_18428661, Singapore) Sampled Countries: Singapore (5)Genomes:
`EPI_ISL_18361916, EPI_ISL_18397376, EPI_ISL_18397599, EPI_ISL_18428562, EPI_ISL_18428661`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18f8d_9f5e00.json?label=id:node_3486178
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Branch 70
Defining Mutations:
EG.5.1.1>T21748C(S:V62)>A16225G(ORF1b:T920A), T25036C>G22927C(S:L455F)Query:A16225G, T21748C, G22927CEarliest seq: 2023-08-10 (EPI_ISL_18438105, Beijing, China) Latest seq: 2023-10-09 (EPI_ISL_18426675, Montana, USA) Sampled Countries: China (13: BJ/11; HB/1; HL/1), Netherlands (2), Singapore (1), USA (1: MT)Genomes:
`EPI_ISL_18254239, EPI_ISL_18331365, EPI_ISL_18362093, EPI_ISL_18384410, EPI_ISL_18386767, EPI_ISL_18426675, EPI_ISL_18438074-18438075, EPI_ISL_18438082, EPI_ISL_18438103, EPI_ISL_18438105, EPI_ISL_18438108, EPI_ISL_18438114, EPI_ISL_18438136, EPI_ISL_18438177-18438178, EPI_ISL_18438235`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4eb1c_b77620.json?label=id:node_3464035
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Branch 71
Defining Mutations:
EG.5.1.1>C6638T(ORF1a:H2125Y)>G22927T(S:L455F)Query:C6638T, G13627A, G22927T, -C14889TEarliest seq: 2023-09-11 (EPI_ISL_18313157, Hubei, China) Latest seq: 2023-10-09 (EPI_ISL_18438431, Hubei, China) Sampled Countries: China (5: HB), South Korea (1)Genomes:
`EPI_ISL_18313157-18313158, EPI_ISL_18382135, EPI_ISL_18438389, EPI_ISL_18438415, EPI_ISL_18438431`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b5b8_b7aee0.json?f_userOrOld=uploaded%20sample&label=id:node_3482675
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Branch 72
Defining Mutations:
EG.5.1.1>C11779T>G10261A>C9611T(ORF1a:L3116F), C18348T>G22927T(S:L455F)Query:C9611T, C11779T, G22927TEarliest seq: 2023-09-06 (EPI_ISL_18313115, Hubei, China) Latest seq: 2023-10-09 (EPI_ISL_18406324, Vienna, Austria) Sampled Countries: South Korea (6), Singapore (2), Austria (1), China (1: HB)Genomes:
`EPI_ISL_18313115, EPI_ISL_18355007, EPI_ISL_18355538, EPI_ISL_18376812, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18406324, EPI_ISL_18408737, EPI_ISL_18435658, EPI_ISL_18439298`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b3db_cbcfb0.json?label=id:node_3497922
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Branch 73
Defining Mutations:
EG.5.1.1>C19170T>G22927T(S:L455F)Query:G13627A, C19170T, G22927T, -C1909T, -C3736T, -C5031T, -C7504T, -A18153GEarliest seq: 2023-08-31 (EPI_ISL_18438072, Beijing) Latest seq: 2023-10-14 (EPI_ISL_18442753, Sichuan) Sampled Countries: China (6: SC/3; BJ/1; HB/1; SC/1), South Korea (1)Genomes:
`EPI_ISL_18320875, EPI_ISL_18360251, EPI_ISL_18360272, EPI_ISL_18438072, EPI_ISL_18438352, EPI_ISL_18439041, EPI_ISL_18442753`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26c5d_cced10.json?label=id:node_3466266
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Branch 74
Defining Mutations:
EG.5.1.3>A28032G(ORF8:I47V)>A1047C(ORF1a:K261T)>C3608A(ORF1a:L1115I), C18261T, G22927T(S:L455F)Query:A1047C, C1889T, G22927TEarliest seq: 2023-09-11 (EPI_ISL_18314192, France) Latest seq: 2023-10-12 (EPI_ISL_18441710, Netherlands) Sampled Countries: Belgium (2), France (2), Netherlands (1)Genomes:
`EPI_ISL_18314192, EPI_ISL_18337916, EPI_ISL_18338399, EPI_ISL_18399343, EPI_ISL_18441710`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38cb6_cd6010.json?f_userOrOld=uploaded%20sample&label=id:node_3458506
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Branch 75
Defining Mutations:
EG.5.1.1>C29253T(N:S327L)>G22927T(S:L455F)Query:G13627A, G22927T, C29253T, -G1067T, -C2110T, -A2730CEarliest seq: 2023-08-17 (EPI_ISL_18389043, Xinjiang, China) Latest seq: 2023-10-24 (EPI_ISL_18445150, Singapore, travel history: Malaysia) Sampled Countries: Denmark (3), China (2: XJ), Singapore (2)Genomes:
`EPI_ISL_18320957, EPI_ISL_18377581, EPI_ISL_18377610, EPI_ISL_18389043, EPI_ISL_18397195, EPI_ISL_18442952, EPI_ISL_18445150`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2e8_a8650.json?label=id:node_3492354
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Branch 76
Defining Mutations:
EG.5.1.1>T26609C>C5907T(ORF1a:T1881I), T17454A>G22927T(S:L455F)Query:G13627A, T17454A, G22927TEarliest seq: 2023-09-20 (EPI_ISL_18445852, Castilla y León, Spain) Latest seq: 2023-10-13 (EPI_ISL_18402965, Donostia-San Sebastián, Spain) Sampled Countries: Spain (9)Genomes:
`EPI_ISL_18402961, EPI_ISL_18402965, EPI_ISL_18419672, EPI_ISL_18421286, EPI_ISL_18445852, EPI_ISL_18445906, EPI_ISL_18445934, EPI_ISL_18446071-18446072`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b023_af570.json?label=id:node_3474073
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Branch 77
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2401_ **Defining Mutations:** `EG.5.1.6` > `C925T, C27161T` > `C14919A` > `G14559A` > `G22927T(S:L455F)` **Query:** `C5835T, G14559A, G22927T` **Earliest seq:** 2023-09-11 (`EPI_ISL_18381025`, British Columbia, Canada) **Latest seq:** 2023-11-21 (`EPI_ISL_18572342`, Israel) **Sampled Countries:** Canada (59: AB/25; BC/25; SK/7; ON/1; QC/1), Israel (5), USA (3: NY/2; CA), Finland (2), Sweden (2), Austria (1), Ireland (1), UK (1: EN)Genomes:
`EPI_ISL_18313726, EPI_ISL_18374552, EPI_ISL_18381025, EPI_ISL_18381642, EPI_ISL_18399548, EPI_ISL_18405416, EPI_ISL_18429724, EPI_ISL_18431316, EPI_ISL_18431484, EPI_ISL_18431577, EPI_ISL_18448820, EPI_ISL_18449315, EPI_ISL_18451058, EPI_ISL_18452675, EPI_ISL_18453011, EPI_ISL_18453157, EPI_ISL_18456002, EPI_ISL_18456201, EPI_ISL_18493062, EPI_ISL_18499142, EPI_ISL_18501414, EPI_ISL_18501469, EPI_ISL_18501539, EPI_ISL_18501675, EPI_ISL_18512520, EPI_ISL_18512575, EPI_ISL_18512726, EPI_ISL_18512904, EPI_ISL_18512975, EPI_ISL_18513012, EPI_ISL_18516832, EPI_ISL_18516837, EPI_ISL_18517029, EPI_ISL_18517372, EPI_ISL_18517374-18517375, EPI_ISL_18517477, EPI_ISL_18517505, EPI_ISL_18526773, EPI_ISL_18526937-18526938, EPI_ISL_18526942, EPI_ISL_18526999, EPI_ISL_18527195, EPI_ISL_18532450-18532451, EPI_ISL_18533407, EPI_ISL_18538515, EPI_ISL_18538528, EPI_ISL_18538535, EPI_ISL_18538740, EPI_ISL_18538774, EPI_ISL_18538986, EPI_ISL_18541507-18541508, EPI_ISL_18547665, EPI_ISL_18552699, EPI_ISL_18553923, EPI_ISL_18553948, EPI_ISL_18558921, EPI_ISL_18560813, EPI_ISL_18563933, EPI_ISL_18563975, EPI_ISL_18563992, EPI_ISL_18564064, EPI_ISL_18564086, EPI_ISL_18564088, EPI_ISL_18564119, EPI_ISL_18564154, EPI_ISL_18564182, EPI_ISL_18564194, EPI_ISL_18572342, EPI_ISL_18572380, EPI_ISL_18572384`Back to Tasklist
Branch 78
Defining Mutations:
EG.5.1.1>C18395T(ORF1b:A1643V)>G22927T(S:L455F)Query:C6541T, C18395T, G22927TEarliest seq: 2023-08-16 (EPI_ISL_18146006, Hubei, China) Latest seq: 2023-10-15 (EPI_ISL_18453170, British Columbia, Canada) Sampled Countries: Canada (7: BC), China (6: FJ/3; HB/2; GS/1), Japan (2)Genomes:
`EPI_ISL_18146006, EPI_ISL_18330196, EPI_ISL_18330296, EPI_ISL_18330311, EPI_ISL_18376315, EPI_ISL_18405472, EPI_ISL_18409239, EPI_ISL_18425055, EPI_ISL_18452695, EPI_ISL_18452923, EPI_ISL_18452979, EPI_ISL_18453059, EPI_ISL_18453168, EPI_ISL_18453170, EPI_ISL_18454186`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e744_1f9880.json?label=id:node_3476703
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Branch 79
Defining Mutations:
EG.5.1.1>T6736C>T23287C(S:A575)>C22075T(S:V171)>C8389T, A16668G, C17474T(ORF1b:T1336I), G22927T(S:L455F), G26416T(E:V58F)Query:T6736C, G13627A, G22927TEarliest seq: 2023-08-17 (EPI_ISL_18241549, Yunnan) Latest seq: 2023-10-14 (EPI_ISL_18454380, Yunnan) Sampled Countries: China (12: YN)Genomes:
`EPI_ISL_18241549, EPI_ISL_18384462, EPI_ISL_18384468, EPI_ISL_18384485, EPI_ISL_18384488, EPI_ISL_18384501, EPI_ISL_18384510, EPI_ISL_18384514, EPI_ISL_18384522, EPI_ISL_18454363, EPI_ISL_18454380, EPI_ISL_18454383`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6626_1fc330.json?label=id:node_3476751
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Branch 80
Defining Mutations:
EG.5.1.1>C8146T>G2035A, G6373T(ORF1a:M2036I), G22927T(S:L455F)Query:C8146T, G13627A, G22927T, -C27557TEarliest seq: 2023-08-28 (EPI_ISL_18289791, Anhui, China) Latest seq: 2023-10-07 (EPI_ISL_18454332, Yunnan, China) Sampled Countries: South Korea (6), China (3: AH, HB, YN)Genomes:
`EPI_ISL_18289791, EPI_ISL_18376503, EPI_ISL_18382123, EPI_ISL_18454332, EPI_ISL_18460781, EPI_ISL_18460783, EPI_ISL_18460821-18460822, EPI_ISL_18460834`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d9d0_762270.json?label=id:node_3494057
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Branch 81
Defining Mutations:
EG.5.1.1>C2857T>G22927T(S:L455F)Query:C2857T, G13627A, G22927T, -C5031T, -T17475CEarliest seq: 2023-09-14 (EPI_ISL_18388886, Hubei, China) Latest seq: 2023-10-13 (EPI_ISL_18461038, South Korea) Sampled Countries: China (7: TW/5; HB; SC), Belgium (1), Japan (1), South Korea (1)Genomes:
`EPI_ISL_18388886, EPI_ISL_18399792, EPI_ISL_18427833, EPI_ISL_18432501, EPI_ISL_18438519, EPI_ISL_18440359, EPI_ISL_18440668, EPI_ISL_18461038, EPI_ISL_18461507, EPI_ISL_18461514`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5f66_766bb0.json?label=id:node_3485431
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Branch 82
Defining Mutations:
EG.5.1.1>T16494C, T22307C>G22927C(S:L455F)Query:G13627A, T16494C, G22927CEarliest seq: 2023-09-12 (EPI_ISL_18376962, Singapore, Travel History: Malaysia) Latest seq: 2023-10-09 (EPI_ISL_18461687, New South Wales, Australia) Sampled Countries: Singapore (7), China (2: HL), Australia (1: NSW)Genomes:
`EPI_ISL_18355070, EPI_ISL_18355078, EPI_ISL_18355084, EPI_ISL_18355119, EPI_ISL_18376962, EPI_ISL_18397262, EPI_ISL_18397335, EPI_ISL_18461687, EPI_ISL_18465032, EPI_ISL_18465036`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice14_genome_1351a_73edc0.json?label=id:node_3508527
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Branch 83
Defining Mutations:
EG.5.1.1>C29358T(N:T362I)>T23803C(S:T747T)>C842T(ORF1a:P193S), C15141T, T16743C, C22450T(S:L296L), G22927T(S:L455F), C24442T(S:N960N), C25916T(ORF3a:T175I), C28232TQuery:G22927T, T23803C, C29358TEarliest seq: 2023-09-11 (EPI_ISL_18384535, Yunnan, China) Latest seq: 2023-10-31 (EPI_ISL_18473684, Singapore) Sampled Countries: Singapore (11), France (2), Australia (1: NSW), Canada (1: ON), China (1: YN), Germany (1)Genomes:
`EPI_ISL_18327437, EPI_ISL_18384535, EPI_ISL_18423274, EPI_ISL_18428663, EPI_ISL_18455125, EPI_ISL_18461961, EPI_ISL_18472175, EPI_ISL_18473491, EPI_ISL_18473552, EPI_ISL_18473557, EPI_ISL_18473565, EPI_ISL_18473584, EPI_ISL_18473600, EPI_ISL_18473608, EPI_ISL_18473617, EPI_ISL_18473635, EPI_ISL_18473684`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33d1_b55240.json?label=id:node_3483621
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Branch 84
Defining Mutations:
HK.19>C2455T>G22927T(S:L455F), C23533T(S:N657)Query:C2455T, C22033A, G22927T, -G25606AEarliest seq: 2023-09-20 (EPI_ISL_18327665,SEAairport, travel history: China) Latest seq: 2023-10-06 (EPI_ISL_18454355, Yunnan China) Sampled Countries: China (7)Genomes:
`EPI_ISL_18327626, EPI_ISL_18327665, EPI_ISL_18454355, EPI_ISL_18475173-18475174, EPI_ISL_18481030, EPI_ISL_18481032`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_14b93_98620.json?label=id:node_3515333
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Branch 85: Mostly with
ORF6:N34K/C27303ADefining Mutations:
EG.5.1.1>C7390T>G22927T(S:L455F)Query:C7390T, G13627A, G22927TEarliest seq: 2023-08-31 (EPI_ISL_18312335, South Korea) Latest seq: 2023-10-30 (EPI_ISL_18494555, Denmark) Sampled Countries: China (7: SC/3; HB/2; XJ/2), South Korea (4), Australia (2), Denmark (1), Spain (1)Genomes:
`EPI_ISL_18284798, EPI_ISL_18312335, EPI_ISL_18312767, EPI_ISL_18313150, EPI_ISL_18330217, EPI_ISL_18355417, EPI_ISL_18361365, EPI_ISL_18376681, EPI_ISL_18402975, EPI_ISL_18447796, EPI_ISL_18461975, EPI_ISL_18475119, EPI_ISL_18481228, EPI_ISL_18494555, EPI_ISL_18495106`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25e0e_b6750.json?label=id:node_3492892
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Branch 86: many with
S:N17T/A21612CDefining Mutations:
EG.5.1.1>G25855T(ORF3a:D155Y)>G22927T(S:L455F)Query:A21612C, G22927T, G25855TEarliest seq: 2023-08-31 (EPI_ISL_18284769, Sichuan, China) Latest seq: 2023-10-24 (EPI_ISL_18458002, Kuala Lumpur, Malaysia) Sampled Countries: China (9: YN/6; SC/3), Malaysia (3), Japan (1)Genomes:
`EPI_ISL_18284769, EPI_ISL_18324153, EPI_ISL_18324208, EPI_ISL_18324235, EPI_ISL_18384546, EPI_ISL_18419659, EPI_ISL_18419662, EPI_ISL_18454181, EPI_ISL_18458002, EPI_ISL_18475350, EPI_ISL_18481259, EPI_ISL_18488097, EPI_ISL_18488110`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_372c6_bbb70.json?label=id:node_3488769
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Branch 87
Defining Mutations:
EG.5.1>C15960T>C16260T>G22927T(S:L455F), C24771T(S:A1070V), C25658T(ORF3a:T89I)Query:C15960T, C16260T, A18492G, G22927TEarliest seq: 2023-09-01 (EPI_ISL_18384575, Yunnan, China) Latest seq: 2023-10-27 (EPI_ISL_18493260, Alberta, Canada) Sampled Countries: China (5: SH/3; SX; YN), Canada (3: AB), South Korea (2)Genomes:
`EPI_ISL_18384575, EPI_ISL_18426071, EPI_ISL_18436785, EPI_ISL_18460945-18460946, EPI_ISL_18475132, EPI_ISL_18481223, EPI_ISL_18493260, EPI_ISL_18495087, EPI_ISL_18495466`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice95_genome_43bfd_a83e0.json?label=id:node_3517572
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Branch 88
⚠️ sibling to Branch 32 please check potential misplacement
Defining Mutations:
EG.5.1.1>T4579A>A4576T>G22927T(S:L455F)Query:A4576T, G13627A, G22927TEarliest seq: 2023-08-18 (EPI_ISL_18239385, South Korea) Latest seq: 2023-10-30 (EPI_ISL_18520721, Saitama, Japan) Sampled Countries: South Korea (39), Japan (2), USA (2, ex. Japan), China (1, ex. S. Korea)Genomes:
`EPI_ISL_18239385, EPI_ISL_18313064, EPI_ISL_18320761, EPI_ISL_18354110, EPI_ISL_18355244, EPI_ISL_18355256, EPI_ISL_18355270, EPI_ISL_18355539, EPI_ISL_18368435, EPI_ISL_18368571, EPI_ISL_18382929, EPI_ISL_18408987, EPI_ISL_18411143, EPI_ISL_18432570, EPI_ISL_18439431, EPI_ISL_18460891, EPI_ISL_18460981, EPI_ISL_18461196, EPI_ISL_18503870, EPI_ISL_18510989, EPI_ISL_18511173, EPI_ISL_18511218, EPI_ISL_18511236, EPI_ISL_18511259, EPI_ISL_18511379, EPI_ISL_18511388, EPI_ISL_18511531, EPI_ISL_18511534, EPI_ISL_18511636, EPI_ISL_18511644, EPI_ISL_18511659, EPI_ISL_18511666, EPI_ISL_18511675, EPI_ISL_18511683, EPI_ISL_18520721, EPI_ISL_18535535, EPI_ISL_18539100, EPI_ISL_18539189, EPI_ISL_18539430, EPI_ISL_18539531, EPI_ISL_18539554, EPI_ISL_18539681, EPI_ISL_18539751, EPI_ISL_18539824`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2459b_3b16b0.json?f_userOrOld=uploaded%20sample&label=id:node_3488766
view from
EG.5.1.1>T4579Abranch, sibling to Branch 32?details
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Branch 89
Defining Mutations:
EG.5.1.1>C27406T(ORF7a:L5F)>G22927T(S:L455F)Query:C6541T, G13627A , G22927T, C27406TEarliest seq:2023-08-11(EPI_ISL_18145981, Hubei, China) Latest seq: 2023-10-18 (EPI_ISL_18487967, Henan, China) Sampled Countries: China (6: HA/2; HB/2; SC/2; BJ), South Korea (1)Genomes:
`EPI_ISL_18145981, EPI_ISL_18320871, EPI_ISL_18360327, EPI_ISL_18382216, EPI_ISL_18438321, EPI_ISL_18485262, EPI_ISL_18487967`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice16_genome_15d09_3ad150.json?label=id:node_3506957
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Branch 90
Defining Mutations:
EG.5.1.1>C13724T(ORF1a:A4487V), A25636T(ORF3a:N82Y)>T10750C, G22927T(S:L455F)Query:G13627A, C13724T, G22927T, -C5031TEarliest seq: 2023-08-22 (EPI_ISL_18272130, South Korea) Latest seq: 2023-10-19 (EPI_ISL_18451971,SEAairport, travel history: South Korea) Sampled Countries: South Korea (6), USA (2: ex. South Korea)Genomes:
`EPI_ISL_18272130, EPI_ISL_18376686, EPI_ISL_18376765, EPI_ISL_18451971, EPI_ISL_18460748, EPI_ISL_18488908-18488909, EPI_ISL_18492194`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_42b73_3bb260.json?label=id:node_3520099
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Branch 91
Defining Mutations:
EG.5.1.1>C22987T(S:A475A)>G22927T(S:L455F)>G19419A, G21974C(S:D138H)Query:G13627A, G19419A, G21974CEarliest seq: 2023-08-24 (EPI_ISL_18284675, Beijing, China) Latest seq: 2023-11-04 (EPI_ISL_18486471, Dublin, Ireland) Sampled Countries: China (6: SC/4; BJ; YN), Ireland (2), Greece (1)Genomes:
`EPI_ISL_18284675, EPI_ISL_18409255, EPI_ISL_18409302, EPI_ISL_18429520, EPI_ISL_18438109, EPI_ISL_18442759, EPI_ISL_18454352, EPI_ISL_18486471, EPI_ISL_18490986`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_6555_3bdc60.json?label=id:node_3502929
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Branch 92
Defining Mutations:
EG.5.1.1>C629T(ORF1a:L122F)>A1168G>C22987T(S:A475A)>T595C, C20148T, G22927T(S:L455F)Query:A1168G, G22927T, C22987TEarliest seq: 2023-09-08 (EPI_ISL_18330247, Hubei, China) Latest seq: 2023-10-30 (EPI_ISL_18539359, South Korea) Sampled Countries: South Korea (5), Japan (2), China (1, HB), USA (1: CA)Genomes:
`EPI_ISL_18330247, EPI_ISL_18435755, EPI_ISL_18443954, EPI_ISL_18446528, EPI_ISL_18502023, EPI_ISL_18503555, EPI_ISL_18511230, EPI_ISL_18520709, EPI_ISL_18539359`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6555_3bdc50.json?label=id:node_3498262
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Branch 93
Defining Mutations:
EG.5.1>G26051T(ORF3a:S220I)>G9269A(ORF1a:G3002S)>T1216C, A9034G, A12121T, A12519G(ORF1a:D4085G), G22927T(S:L455F)Query:G9269A, G22927T, G26051TEarliest seq: 2023-10-21 (EPI_ISL_18453659, South Australia) Latest seq: 2023-11-05 (EPI_ISL_18524643, Queensland) Sampled Countries: Australia (7: QLD/6; SA)Genomes:
`EPI_ISL_18453659, EPI_ISL_18489126, EPI_ISL_18501702, EPI_ISL_18501758, EPI_ISL_18524643, EPI_ISL_18524655, EPI_ISL_18524668`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice52_genome_199a5_39a640.json?label=id:node_3459700
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Branch 94
a sub-branch of #1074 proposed by @aviczhl2
Defining Mutations:
EG.5.1.13> _G670T_rev(ORF1a:R135S_rev)_ >T28861C>G8889A(ORF1a:R2875H)>C13381T>G22424T(S:A288S)>C25047T(S:P1162L)>G25855T(ORF3a:D155Y)>G22927T(S:L455F)Query:G8889A, C13381T, G22927TEarliest seq: 2023-10-10 (EPI_ISL_18486858, Temuco, Chile) Latest seq: 2023-11-26 (EPI_ISL_18582164, Ontario, Canada) Sampled Countries: Canada (14: ON/13; NS), Chile (3), USA (3: NY/2; PA)Genomes:
`EPI_ISL_18483588, EPI_ISL_18483657, EPI_ISL_18486858, EPI_ISL_18523437, EPI_ISL_18534577, EPI_ISL_18548162, EPI_ISL_18581551-18581554, EPI_ISL_18581688, EPI_ISL_18581705, EPI_ISL_18582159, EPI_ISL_18582162, EPI_ISL_18582164, EPI_ISL_18582914, EPI_ISL_18582921-18582922, EPI_ISL_18582983, EPI_ISL_18602138`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7d45_55cdd0.json?label=id:node_3474267
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Singlets
Guangdong/GDCDC_GZ_0568/2023|EPI_ISL_18033894|2023-06-28EG.5.1 > G1069A > C12005T > C9803T, A13707G, C14809T(ORF1b:R448C), C18348T, G22927C(S:L455F) [Query:C14809T, C18348T, G22927C, 07/24]Japan/PG-568093/2023|EPI_ISL_18279075|2023-09-05EG.5.1 > T15198A > C1191A(ORF1a:P309Q), A24999C(S:D1146A), A27642G > A21137G(ORF1a:K2557R) > T25851C > C6120T(ORF1a:S1952L), T13030C, G22927T(S:L455F) [Query:C1191A, T15198A, G22927T, 09/19]Canada/QC-L00671579001/2023|EPI_ISL_18478213|2023-10-30EG.5.1 > T15198A > G22317C(S:G252A) > C3267T(ORF1a:T1001I), T8421C(ORF1a:M2719T), G22927T(S:L455F), C22949T(S:P463S) [Query:T15198A, G22317C, G22927T, 11/08]Sichuan/NJCDC-0906-7/2023|EPI_ISL_18261486|2023-08-30EG.5.1.1 > A3069G(ORF1a:D935G) > C367T, A1197C(ORF1a:E311A), A6925G, G22927T(S:L455F), T27212C(ORF6:L4P) [Query:A3069G, C6541T, G22927T, 09/14]Shanghai/SCDC-HP-XG-0731-1/2023|EPI_ISL_18138078|2023-07-31EG.5.1.1 > G3242A(ORF1a:G993S) > G1595A(ORF1a:E444K), C6628T, G22927T(S:L455F), A27721G(ORF7a:I110V) [Query:G3242A, C6541T, G22927T, 08/25]Shanghai/SCDC-XG09-13670/2023|EPI_ISL_18285000|2023-09-07EG.5.1.1 > C3653T(ORF1a:L1130F) > G410T(ORF1a:G49C), C1498T, C2227A, C6395T, C11563T, G22927C(S:L455F), G27604T(ORF7a:V71L) [Query:C3653T, C6541T, G22927C, 09/19]South_Korea/KDCA262399/2023|EPI_ISL_18271956|2023-08-22EG.5.1.1 > C7764T(ORF1a:S2500F) > T5448C(ORF1a:V1728A), G22927T(S:L455F), C25539T [Query:C7764T, G13627A, G22927T, 09/18]Japan/TKYnat15208/2023|EPI_ISL_18285185|2023-09-01EG.5.1.1 > C13730T(ORF1b:A88V) > T12727C, G22927T(S:L455F) [Query:C6541T, C13730T, G22927T, -C11779T, 09/20]Australia/QLD0x01374B/2023|EPI_ISL_18122559|2023-08-09FLIP+346I+478R EG.5.1.1 > C16830T, C18348T, G22599T(S:R346I), G22927T(S:L455F), C22995G(S:T478R), T23176C [Query:C18348T, G22599T, G22927T, 08/22]South_Korea/KDCA262306/2023|EPI_ISL_18271874|2023-08-15EG.5.1.1 > C21588T(S:P9L) > G22927T(S:L455F), C28770T(N:T166I) [Query:G13627A, C21588T, G22927T, 09/18]Anhui/HCDC-176/2023|EPI_ISL_18289771|2023-09-04EG.5.1.1 > C24130T > G9177T(ORF1a:G2971V), T28705C > A10863C(ORF1a:E3533A), G22927T(S:L455F), G25522A(ORF3a:G44R), G27933A(ORF8:A14T) [Query:G9177T, G22927T, C24130T, 09/20]GZSCDC-GY07-14/2023|EPI_ISL_18074217|2023-07-18EG.5.1.1 > G24926T(S:V1122L) > C1960T, C12076T, T22926C(S:L455S), T27428A(ORF7a:L12H) [Query:G13627A, T22926C, G24926T, 08/07]England/CLIMB-CM7YRMOM/2023|EPI_ISL_18227115|2023-08-22EG.5.1.3 > A4340G(ORF1a:I1359V) > A2163G(ORF1a:E633G) > C23185T > T11932G, T14022C, T22926C(S:L455S) [Query:A2163G, A4340G, T22926C, 09/06]Sweden/W-49492298L6/2023|EPI_ISL_18249322|2023-08-23EG.5.1.3 > A10703C > C1314T(ORF1a:T350I), C9118T > G4907A(ORF1a:G1548S) > C6936G(ORF1a:S2224C), C18959T(ORF1b:A1831V), G22094T(S:D178Y), T22926C(S:L455S), G27160A(M:S213N) [Query:G4907A, C9118T, T22926C, 09/12]Spain/CT-HUGTiP-B1R154/2023|EPI_ISL_18281164|2023-09-13EG.5.1.3 > T14568C > T7651C, G27962T(ORF8:Q23H) > T4579A, C19017T, G22927T(S:L455F) [Query:C1889T, T7651C, G22927T, 09/19]Canada/ON-PHL-23-30576/2023|EPI_ISL_18277805|2023-09-11EG.5.1.4 > C26111T(ORF3a:P240L) > C21622A > C9430T > C20133T > G22927T(S:L455F) [Query:C9430T, C20133T, G22927T, 09/18]USA/NY-URMC-N6S1J239-1/2023|EPI_ISL_18247548|2023-08-27EG.5.1.4 > C26111T(ORF3:P240L) > G25563T(ORF3a:Q57H) > C1427T(ORF1a:H388Y) > G25494A > A21759G(S:H66R), G22927T(S:L455F) [Query:G22927T, G25494A, G25563T, 09/11]USA/MD-HP49490-PIDPVKAURD/2023|EPI_ISL_18432449|2023HV.1 (EG.5.1.6.1) > C2695T > C26964T(M:H148Y) > C27600T > C14376T > A5424G(ORF1a:K1720R) > C4752T(ORF1a:T1496I), G22927T(S:L455F) [Query:A5424G, C14376T, G22927T, 10/24]USA/OH-ODH-SC3032871/2023|EPI_ISL_18422243|2023-09-29HV.1 > A5021G(ORF1a:M1586V) > C6117T(ORF1a:A1951V), G22927T(S:L455F), C29028T(N:A252V) [Query:A5021G, C5835T, G22927T, 10/23]Back to Tasklist
Doublets
USA/NY-NYULH-16857/2023|EPI_ISL_18440726|2023-10-19andUSA/NY-CDC-VSX-A357619/2023|EPI_ISL_18534359|2023-10-26EG.5.1 > C2147T(ORF1a:L628F), T6115C > G18498T(ORF1b:M1677I) > C21811T, A22911T(S:N450I), G22927T(S:L455F) [Query:C2147T, G18498T, G22927T, 2 seqs, 11/22] (Another 3 seqs not on GISAID yetShanghai/SCDC-MH200506/2023|EPI_ISL_18114819|2023-07-30andLiaoning/LNCDC-360-1/2023|EPI_ISL_18330279|2023-09-12EG.5.1 > C6706T > C7482T(ORF1a:S2406L) > C2507T(ORF1a:P748S), C4543T, C8251T, G22927T(S:L455F) [Query:C6706T, C7482T, G22927T, 2 seqs, 09/30]Shanghai/SCDC-804/2023|EPI_ISL_18268355|2023-09-02andShanghai/SCDC-831/2023|EPI_ISL_18284896|2023-09-09EG.5.1.1 > A3021G(ORF1a:H919R), A21493C > C1913T(ORF1a:R550C), C4965T(ORF1a:T1567I), C17977T(ORF1b:L1504F), A19237C, G22927T(S:L455F), C27393T, C28791T(N:A173V) [Query:A3021G, A21493C, G22927T, 2 seqs, 09/19]Taiwan/CDC-W30906/2023|EPI_ISL_18164789|2023-07-29andUSA/HI-H2324424/2023|EPI_ISL_18283168|2023-08-29EG.5.1.1 > C6317T(ORF1a:P2018S) > C1567T, C8152T, C16192T(ORF1b:P909S), G22927C(S:L455F), G25606A(ORF3a:A72T) [Query:C6317T, C6541T, G22927C, 2 seqs, 09/19]Sichuan/YACDC-XGcx133/2023|EPI_ISL_18232742|2023-08-14andSichuan/YACDC-XGCX151/2023|EPI_ISL_18304270|2023-09-18EG.5.1.1 > C6327T(ORF1a:T2021I) > C1684A, A17008G(ORF1b:I1181V), G22927C(S:L455F), G27217T(ORF6:D6Y) [Query:C6327T, C6541T, G22927C, 2 seqs, 09/25]Hubei/HCDC-ES2799/2023|EPI_ISL_18254184|2023-08-30andEngland/CLIMB-CM7YEDUX/2023|EPI_ISL_18274069|2023-09-08EG.5.1.1 > C9142T > G22927T(S:L455F) [Query:C9142T, G13627A, G22927T, 2 seqs, 09/18]Shanghai/SCDC-XG08-12942/2023|EPI_ISL_18268428|2023-08-27andShanghai/SCDC-836/2023|EPI_ISL_18284901|2023-09-10EG.5.1.1 > C9996T(ORF1a:S3244L) > G22927T(S:L455F) [Query:C6541T, C9996T, G22927T, 2 seqs, 09/19]Sichuan/CDCDC-3-LZJ/2023|EPI_ISL_18166147|2023-07-29andSichuan/CDCDC-19-CX2806/2023|EPI_ISL_18246264|2023-08-20EG.5.1.1 > C11779T > C7420T > A12644G(ORF1a:I4127V), G16662A, G22927T(S:L455F), A27736T(ORF7a:T115S), C28585T [Query:C7420T, C11779T, G22927T, 2 seqs, 09/11]USA/OR-OSPHL08951/2023|EPI_ISL_18285283|2023-09-07andUSA/OR-OSPHL08953/2023|EPI_ISL_18285285|2023-09-10EG.5.1.1 > C11956T > C17746T(ORF1b:P1427S), T20252C(ORF1b:I2262T), G22927T(S:L455F) [Query:C11956T, G13627A, G22927T, 2 seqs, 09/20]Shanghai/SCDC-XG09-13443/2023|EPI_ISL_18284954|2023-08-30andSichuan/MYCDC-XGCX312/2023|EPI_ISL_18284766|2023-09-03EG.5.1.1 > C14571T > T16340C(ORF1b:I958T), T17736C, G22927T(S:L455F) [Query:C6541T, C14571T, G22927T, -A1051G, 2 seqs, 09/19]Germany/NW-RKI-I-1137155/2023|EPI_ISL_18131003|2023-08-02andUkraine/81521/2023|EPI_ISL_18539909|2023-10-12EG.5.1.3 > C1059T(ORF1a:T265I) > G22927C(S:L455F) [Query:C1059T, C1889T, G22927C, 2 seqs, 11/23]Canada/QC-L00650653001/2023|EPI_ISL_18252385|2023-08-28andCanada/QC-L00650647001/2023|EPI_ISL_18252388|2023-08-29EG.5.1.3 > C17718T > A17066G(ORF1b:Y1200C), A17622G, G22927T(S:L455F) [Query:C1889T, C17718T, G22927T, 2 seqs, 09/12]Canada/ON-PHL-23-36533/2023|EPI_ISL_18448204|2023-10-18andCanada/ON-PHL-23-36753/2023|EPI_ISL_18448385|2023-10-20HV.1 (EG.5.1.6.1) > C12513T(ORF1a:T4083M) > T17343C > G22918T(S:R452) > T22926C(S:L455S), C29784T [Query:C12513T, T17343C, T22926C, 2 seqs, 10/30]USA/HI-H2325918/2023|EPI_ISL_18487957|2023-10-26andUSA/HI-H2325960/2023|EPI_ISL_18535129|2023-11-03HV.1 > T23198C(S:L546L) > C29466T > T28417C(ORF9b:I45T) > C875T(ORF1a:L204F), G22927T(S:L455F) [Query:G22927T, T23198C, T28417C, 2 seqs, 11/22]Back to Tasklist
Triplets
Shanghai/SCDC-770/2023|EPI_ISL_18232641|2023-08-20;Shanghai/SCDC-802/2023|EPI_ISL_18268353|2023-08-31andGermany/NW-RKI-I-1138223/2023|EPI_ISL_18343384|2023-09-19EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G3091A > C13959T, T22020G(S:M153R), G22927T(S:L455F) [Query:G347A, G3091A, G22927T, 3 seqs, 10/04]Shanghai/SCDC-0823-3241/2023|EPI_ISL_18208400|2023-08-21;France/BRE-IPP21293/2023|EPI_ISL_18350826|2023-09-18andUSA/CA-GBW-H20-334-1265/2023|EPI_ISL_18357649|2023-09-26EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G22927T(S:L455F), A26117G(ORF3a:E242G) [Query:G347A, G22927T, T27956C, -G3091A, 3 seqs, 10/06]Yunnan/YNCDC-2364/2023|EPI_ISL_18166234|2023-08-02;Yunnan/YNCDC-2493/2023|EPI_ISL_18241493|2023-08-28andYunnan/YNCDC-2972/2023|EPI_ISL_18384579|2023-09-22EG.5.1.1 > C629T(ORF1a:L122F) > A1168G > T6640C > C18864T, G22927T(S:L455F), A25506G [Query:C629T, T6640C, G22927T, 3 seqs, 10/12]Xinjiang/XJCDCWLMQ-412/2023|EPI_ISL_18161044|2023-07-29;South_Korea/KDCA271622/2023|EPI_ISL_18511017|2023-10-20;Shanghai/SCDC-JD1024_1/2023|EPI_ISL_18495067|2023-10-21andDenmark/DCGC-663353/2023|EPI_ISL_18518786|2023-11-06EG.5.1.1 > C4832T > G22927T(S:L455F) [Query:C4832T, G13627A, G22927T, C27874T, 3 seqs, 11/18]Shanghai/SCDC-FX0906-018/2023|EPI_ISL_18284805|2023-09-03;Hubei/HCDC-JZ3118/2023|EPI_ISL_18376469|2023-09-25andHubei/HCDC-YC3307/2023|EPI_ISL_18438465|2023-09-27EG.5.1.1 > C26151T > C19524G, C20235T, G22927T(S:L455F), G29044A [Query:C19524G, G22927T, C26151T, 3 seqs, 10/26]Australia/SA708969/2023|EPI_ISL_18453685|2023-10-23;Australia/SA832208/2023|EPI_ISL_18536619|2023-11-14andAustralia/SA832209/2023|EPI_ISL_18536620|2023-11-14EG.5.1.3 > C1057T > G18462A > C6578T(ORF1a:L2105F) > G22927T(S:L455F), C26058T, T27210C [Query:C1057T, C6578T, G22927T, 3 seqs, 11/23] thanks to @FedeGueliSpain/CU-19903/2023|EPI_ISL_18294739|2023-08-22;Denmark/DCGC-661638/2023|EPI_ISL_18442881|2023-10-16andItaly/LOM_Unimi-3611-23/2023|EPI_ISL_18443629|2023-10-19EG.5.1.6 > C12513T(ORF1a:T4083M) > G22927T(S:L455F) [Query:C5835T, C12513T, G22927T, 3 seqs, 10/28]Back to Tasklist
Quadruplets
Shanghai/SCDC-826/2023|EPI_ISL_18284891|2023-09-07;Yunnan/YNCDC-3103/2023|EPI_ISL_18454372|2023-10-13;Sichuan/CDCDC-19-CX3446/2023|EPI_ISL_18457460|2023-10-22andHubei/HCDC-WH3507/2023|EPI_ISL_18485337|2023-10-25EG.5.1.1 > A2483G(ORF1a:I740V) > T15996C, G22927C(S:L455F) [Query:A2483G, G13627A, G22927C, 4, 11/08], many withS:R158K/G22035AandS:E554K/G23222ASouth_Korea/KDCA267746/2023|EPI_ISL_18408949|2023-09-18;South_Korea/KDCA268248/2023|EPI_ISL_18411258|2023-09-19;South_Korea/KDCA269573/2023|EPI_ISL_18460793|2023-10-04; andSouth_Korea/KDCA269703/2023|EPI_ISL_18460915|2023-10-09EG.5.1.1 > C3695T > G22927T(S:L455F) [Query:C3695T, G13627A, G22927T, -T2959C, 4 seq, 11/03]France/COR-HCL-723001296701/2023|EPI_ISL_18387770|2023-09-25;France/NAQ-HCL723001378601/2023|EPI_ISL_18423405|2023-10-09;Austria/AGES-1141981/2023|EPI_ISL_18485506|2023-10-18andGermany/BY-MVP-000022265/2023|EPI_ISL_18525885|2023-10-30EG.5.1.3 > C6151T > G2468A(ORF1a:A735T), T22926G(S:L455W) [Query:C6151T, T22926G, 4 seqs, 11/21]Back to Tasklist
Quintuplets
Fujian/FCDC-QZ08S024/2023|EPI_ISL_18145964|2023-08-18;England/CLIMB-CM7YJZ4C/2023|EPI_ISL_18392773|2023-10-05;Yunnan/YNCDC-3090/2023|EPI_ISL_18454344|2023-10-12;Yunnan/YNCDC-3139/2023|EPI_ISL_18488099|2023-10-12;Singapore/R78MR69/2023|EPI_ISL_18444918|2023-10-25;South_Korea/KDCA273761/2023|EPI_ISL_18535687|2023-10-31andUSA/MN-MDH-37408/2023|EPI_ISL_18510684|2023-11-01EG.5.1.1 > C25578T > G22927T(S:L455F) [Query:C8320T, G22927T, C25578T, 5 seqs, 11/23]Back to Tasklist