FedeGueli
commented
1 year ago Thank you for this one @NkRMnZr great work, please credit @borisuitham who was the first to notice the high homoplasy of L455F in EG.5.1 backbone.
Closed NkRMnZr closed 11 months ago
FedeGueli
commented
1 year ago Thank you for this one @NkRMnZr great work, please credit @borisuitham who was the first to notice the high homoplasy of L455F in EG.5.1 backbone.
BorisUitham
commented
1 year ago I dont have a lot of problems with credits or axknowledgements, we all find these separately :)
NkRMnZr
commented
1 year ago Tracking updates:
08-08, 1 sequence from Ontario, Canada on Branch 1: EPI_ISL_18076513; Adding Branch 3 from previously singlet Shanghai/SCDC-XG07-10066/2023|EPI_ISL_17994488|2023-07-04; Adding a few doublets.
08-11, Adding Branch 4 from former doublets: Shanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09(local case) and Shanghai/SCDC-HG0724-2748_2-2/2023|EPI_ISL_18075026|2023-07-22 (travel history: Thailand), 2 additional seqs from Ginkgo BioWorks with travel history to Japan, spotted by @FedeGueli
08-15, Branch 3, +14 (Shanghai, China); Adding Branch 5 & 6 from previously doublets and singlet
08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7
08-18, Branch 4, +2 (China); Branch 5, +1 (South Korea); Adding Branch 8, 9, 10 from former doublets
08-21, Branch 9, +2 (China); Branch 10, +1 (China)
08-22, Branch 1, +2 (China); Branch 2, +3 (USA); Branch 4, +1 (USA)
08-24, Branch 2 +1 (Japan); Adding Branch 11 (3 seqs, Japan)
08-25, Branch 1 +5 (China); Branch 4 +1 (China); Branch 10 +2 (China)
08-30, Branch 1 & 2 transferred to main repo; Branch 5, +1 (USA)
08-31, Branch 10, +1 (China); Branch 11, +2 (Japan); Adding Branch 14
09-01, Branch 7, +3 (China); Branch 10, +1 (China); Adding Branch 15
09-07, Branch 5, +1 (Singapore); Branch 8, +2 (China); Adding Branch 21~23
09-08, Branch 17, +2 (Japan)
09-12, Update on Branch 5, 6, 7, 10, 11, 12, 15, 17, 23, 24; Adding Branch 25~30
09-13, Update on Branch 5, 8, 10, 13, 17, 18; Adding Branch 31~33
09-15, Updates on Branch 10, 11 and 17; Adding Branch 35
09-16, Update on Branch 5-11, 13, 18, 23, 25, 26, 30, 31, 33; adding Branch 36~40
09-18, Branch 17 +1 (S. Korea); Adding Branch 41
09-19, Update on Branch 5, 10-12, 17, 23, 25, 31, 33, 36 and 40; Adding Branch 42-44
09-20, Update on Branch 5, 7-15, 17, 22-24, 27, 30-32, 38. Remove Branch 6. Adding Branch 45-49
09-21 Final update, clean up singlets/doublets, adding Branch 50-51, remove Branch 29
FedeGueli
commented
1 year ago propose in the main page (Pango) each of them when reaching 5
FedeGueli
commented
1 year ago I think two more intercepted by American airports: 18094969-18094946 i m checking
FedeGueli
commented
1 year ago
Shanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09andShanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09EG.5.1 > C12100G, G22927T(S:L455F) [Query:C12100G, G22927T, 2 seqs, 08/02]
Two samples imported in Usa from japan cluster with this Shanghai sequence ( i think you double counted it but it is the same!)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_381d3_6b7940.json?c=gt-S_455&label=id:node_6794559
They are four now: EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946, EPI_ISL_18094969
I would propose it in a separate issue.
xz-keg
commented
1 year ago Branch 3 explodes to 17 seqs
NkRMnZr
commented
1 year ago 08-15, Branch 3, +14 (Shanghai, China)：
EPI_ISL_18105750, EPI_ISL_18105752, EPI_ISL_18105756-18105765, EPI_ISL_18105768, EPI_ISL_18105818
Transferred Branch 3 to Main Repo cov-lineages/pango-designation#2194
Adding Branch 5 & 6 from previously doublets and singlet.
FedeGueli
commented
1 year ago Thank you @NkRMnZr
xz-keg
commented
1 year ago Branch 1 also reaches 5 now
NkRMnZr
commented
1 year ago 08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7
Branch 1, +2 (Fujian, Shanghai): EPI_ISL_18108313, EPI_ISL_18108479
Branch 4, +1 (Shanghai): EPI_ISL_18108375
Branch 5, +1 (Shanghai): EPI_ISL_18108346
Adding Branch 7 from previously singlet Adding a few singlets and doublets
FedeGueli
commented
1 year ago 08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7 Branch 1, +2 (Fujian, Shanghai):
EPI_ISL_18108313, EPI_ISL_18108479Branch 4, +1 (Shanghai):EPI_ISL_18108375Branch 5, +1 (Shanghai):EPI_ISL_18108346Adding Branch 7 from previously singlet Adding a few singlets and doublets
Great work thank you,
xz-keg
commented
1 year ago Branch 5 and 6 also reached 5. Shall do a lot of proposals.
NkRMnZr
commented
1 year ago 08-18, Branch 4, +2 (China); Branch 5, +1 (South Korea); Adding Branch 8, 9, 10 from former doublets
Branch 4: +2 China (Shanghai) EPI_ISL_18114693, EPI_ISL_18114890
Branch 5: +1 South Korea EPI_ISL_18111663
Adding Branch 8, 9, 10 from former Doublets A former singlet now became #644
NkRMnZr
commented
1 year ago 08-21, Branch 9, +2 (China); Branch 10, +1 (China)
Branch 9 +2 (Liaoning) EPI_ISL_18116287, EPI_ISL_18116314
Branch 10 +1 (Liaoning) EPI_ISL_18116311
xz-keg
commented
1 year ago Branch 2 reaches 5 too.
NkRMnZr
commented
1 year ago 08-22, Branch 1, +2 (China); Branch 2, +3 (USA); Branch 4, +1 (USA)
Branch 1, 2 seqs from Fujian: EPI_ISL_18127148, EPI_ISL_18127155
Branch 2, 3 seqs from SFO, California, with travel history to Switzerland: EPI_ISL_18124861, EPI_ISL_18124879, EPI_ISL_18125017
Branch 4, 1 more from New York: EPI_ISL_18126507
FedeGueli
commented
1 year ago What a work @NkRMnZr ! ( and @aviczhl2 too!) really grateful to you. ping @corneliusroemer : this is high level tracking!
FedeGueli
commented
1 year ago
Xinjiang/XJCDCWLMQ_369/2023|EPI_ISL_18108848|2023-07-04andXinjiang/XJCDCWLMQ-398/2023|EPI_ISL_18108876|2023-07-18HK.1 (EG.5.1.1.1) > G6320A(ORF1a:V2019I) > C11704T, C22482T(S:T307I), G22927C(S:L455F) [Query:G6320A, G22332T, G22927C, 2, 08/16]
this one has been proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/631
FedeGueli
commented
1 year ago @NkRMnZr when each of them reaches 10 propose in the main page.
NkRMnZr
commented
1 year ago 08-24, Branch 2 +1 (Japan); Adding Branch 11 (3 seqs, Japan)
Branch 2, +1 (Japan): EPI_ISL_18130075
Adding Branch 11 with 3 seqs from Japan
FedeGueli
commented
1 year ago Thank you @NkRMnZr was B11 a singlet before?
NkRMnZr
commented
1 year ago Thank you @NkRMnZr was B11 a singlet before?
nope, that's a triplet (you can tell from EPI_ISL accession, they are quite close)
BTW, how do I transfer other branches that goes above 10 seqs? Add them one by one to cov-lineages/pango-designation#2194 or start different issues?
NkRMnZr
commented
1 year ago 08-25, Branch 1 +5 (China); Branch 4 +1 (China); Branch 10 +2 (China)
Branch 1 +5 (Sichuan) EPI_ISL_18133988, EPI_ISL_18133990, EPI_ISL_18133993-18133995
Branch 4 +1 (Anhui) EPI_ISL_18133875
Branch 10 +2 (Sichuan, Qinghai) EPI_ISL_18133939, EPI_ISL_18133980
FedeGueli
commented
1 year ago Thank you @NkRMnZr was B11 a singlet before?
nope, that's a triplet (you can tell from EPI_ISL accession, they are quite close)
BTW, how do I transfer other branches that goes above 10 seqs? Add them one by one to cov-lineages/pango-designation#2194 or start different issues?
Thx sorry didnt check the EPi_ISl. Yes one by one on the Pango repo.
NkRMnZr
commented
1 year ago 08-26, Branch 4, +3 (China); Branch 9, +3 (England; Denmark); Branch 10, +1 (China); Adding Branch 12 from Singlets
EPI_ISL_18138157, EPI_ISL_18138216, EPI_ISL_18138268England/CLIMB-CM7YGJST/2023|2023-08-05, Denmark/DCGC-647756/2023|EPI_ISL_18130341|2023-08-07 and Denmark/DCGC-647847/2023|EPI_ISL_18135367|2023-08-14 (Danish seqs are with T19983C_reversion so unable to be caught by query)EPI_ISL_18138175FedeGueli
commented
1 year ago Please propose Branch 4 and Branch 9 separately on the main Pango page.
NkRMnZr
commented
1 year ago 08-28, Branch 2, +1 (Japan); Branch 7, +1 (China); Branch 8, +1 (Singapore); Branch 4 Transferred to main repo
Branch 2, +1 (Fukushima): EPI_ISL_18139669
Branch 4, +2 (Singapore): EPI_ISL_18141110, EPI_ISL_18141214
Branch 7, +1 (Taiwan): EPI_ISL_18139352
Branch 8, +1 (Singapore): EPI_ISL_18141095
Branch 4 Transferred to cov-lineages/pango-designation#2224
NkRMnZr
commented
1 year ago 08-29, Branch 1, +2 (China); Branch 2, +1 (Austria); Branch 5, +1 (China); Branch 7, +1 (China); Branch 9, +1 (China); Branch 10, +1 (China); Adding Branch 13
Branch 1, +2 (Fujian) EPI_ISL_18145944, EPI_ISL_18145952
Branch 2, +1 (Vienna) EPI_ISL_18141863
Branch 5, +1 (Liaoning) EPI_ISL_18146109
Branch 7, +1 (Fujian) EPI_ISL_18145951
Branch 9, +1 (Hubei) EPI_ISL_18146106
Branch 10, +1 (Hubei) EPI_ISL_18146058
Adding Branch 13 with 2 seqs from Hubei and 1 from Singapore
NkRMnZr
commented
1 year ago 08-30 Branch 1 & 2 transferred to main repo; Branch 5, +1 (USA)
Branch 1 now transferred to cov-lineages/pango-designation#2230 Branch 2 now transferred to cov-lineages/pango-designation#2229
Branch 5, +1 (New York) EPI_ISL_18160385
Branch 9 seems to be different lineages pulled together, one follows EG.5.1.1 > C19983T > G22927T(S:L455F) as it is proposed with 6 seqs, but there's another one with T19983C_reversion, I don't think they are the same lineage, it could be just HK.3 misplaced, so number of seqs of Branch 9 revert back to 6.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1aa80_f37790.json?c=gt-nuc_19983&label=id:node_6943008
FedeGueli
commented
1 year ago Branch 9 seems to be different lineages pulled together, one follows EG.5.1.1 > C19983T > G22927T(S:L455F) as it is proposed with 6 seqs, but there's another one with T19983C_reversion, I don't think they are the same lineage, it could be just HK.3 misplaced, so number of seqs of Branch 9 revert back to 6. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1aa80_f37790.json?c=gt-nuc_19983&label=id:node_6943008
Weird this reversion , it has both before it and after it defining mutations of the branch so unlikely it is some sort of recombination, the branch following the mutation reverted is unique . But there was a fe.1.2 plus S:809S in Denmark and Ireland (4 seqs) but still i dont see how bring back pieces together a microrecombiantion? i see that the larger branch without 455F has more sample with that reversion not sure what this means.
NkRMnZr
commented
1 year ago 08-31, Branch 10, +1 (China); Branch 11, +2 (Japan); Adding Branch 14
Branch 10, +1 (Yunnan) EPI_ISL_18166202
Branch 11, +2 (Japan) EPI_ISL_18164881, EPI_ISL_18165247
Adding former doublet to Branch 14 with 1 more sequence from Sichuan
FedeGueli
commented
1 year ago Branch 1 got designated HK.8 via https://github.com/cov-lineages/pango-designation/commit/9527e15afb0acedf720e1042d5da347a4c0abd7d
FedeGueli
commented
1 year ago Very happy you got recognized your unbelievable work! you have the praise of all the variant community @NkRMnZr !
FedeGueli
commented
1 year ago Branch 9 designated HK.10 via https://github.com/cov-lineages/pango-designation/commit/f6556710dd5e198e827b227bd3db24ae11b45c74
Being a problematic branch i explained the whole thing in the commit. Lets see if @corneliusroemer and @angiehinrichs could help and check this designation.
NkRMnZr
commented
1 year ago 09-01, Branch 7, +3 (China); Branch 10, +1 (China); Adding Branch 15
Branch 7, +3 (Shanghai): EPI_ISL_18208395, EPI_ISL_18208450, EPI_ISL_18208478
Branch 10, +1 (Shanghai): EPI_ISL_18208650
Adding Branch 15 from former doublet with 1 more sequence from Shanghai
FedeGueli
commented
1 year ago 09-01, Branch 7, +3 (China); Branch 10, +1 (China); Adding Branch 15
Branch 7, +3 (Shanghai):
EPI_ISL_18208395, EPI_ISL_18208450, EPI_ISL_18208478Branch 10, +1 (Shanghai):EPI_ISL_18208650Adding Branch 15 from former doublet with 1 more sequence from Shanghai
Thank you, i dont really never see anything like this : 63 independent emergence of Flip in one backbone. Ok lets say that 2/3 are artifacts still a lot still unprecedented.
FedeGueli
commented
1 year ago Please propose Branche 5 and Branch 10 having reached 10seqs both @NkRMnZr
Over-There-Is
commented
1 year ago Not only the Danish sequences, also the British sequence England/CLIMB-CM7YGJST does not have C19983T, it has Ns on 19790~20042. It is reasonable to believe that these sequences are from a HK.3 subbranch. (or descendant of EG.5.1.1> C934T?)
Over-There-Is
commented
1 year ago I can't understand it anymore.
EG.5.1.1> C6695T> C9448A> C5575T, G22927T> G23006C?
I don't know how Shanghai/SCDC-HG0815-3112/2023|EPI_ISL_18114870|2023-08-13 get C19983T.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_16083_2d5990.json?c=gt-nuc_19983&f_userOrOld=uploaded%20sample&gmax=20983&gmin=18983&label=id:node_6940696
FedeGueli
commented
1 year ago I can't understand it anymore. EG.5.1.1> C6695T> C9448A> C5575T, G22927T> G23006C? I don't know how Shanghai/SCDC-HG0815-3112/2023|EPI_ISL_18114870|2023-08-13 get C19983T. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_16083_2d5990.json?c=gt-nuc_19983&f_userOrOld=uploaded%20sample&gmax=20983&gmin=18983&label=id:node_6940696
Is this a downsampled tree?
xz-keg
commented
1 year ago A lot of new research show that blood samples from patients infected with EG.5.1 doesn't neutralize EG.5.1 well(which means they're easy to get a second EG.5.1*), so we may be expected to see a lot of mini-recombinations of maybe 2 branches of EG.5.1.1s I guess.
FedeGueli
commented
1 year ago A lot of new research show that blood samples from patients infected with EG.5.1 doesn't neutralize EG.5.1 well(which means they're easy to get a second EG.5.1*), so we may be expected to see a lot of mini-recombinations of maybe 2 branches of EG.5.1.1s I guess.
source?
xz-keg
commented
1 year ago A lot of new research show that blood samples from patients infected with EG.5.1 doesn't neutralize EG.5.1 well(which means they're easy to get a second EG.5.1*), so we may be expected to see a lot of mini-recombinations of maybe 2 branches of EG.5.1.1s I guess.
source?
Yunlong Cao's new research? XBB(mostly EG.5.1 consider the proportion in China) BTI infection doesn't neutralize well with Flip, https://twitter.com/yunlong_cao/status/1697318194976010446
FedeGueli
commented
1 year ago A lot of new research show that blood samples from patients infected with EG.5.1 doesn't neutralize EG.5.1 well(which means they're easy to get a second EG.5.1*), so we may be expected to see a lot of mini-recombinations of maybe 2 branches of EG.5.1.1s I guess.
source?
Yunlun Cao's new research? XBB(mostly EG.5.1 consider the proportion in China) BTI infection doesn't neutralize well with Flip, https://twitter.com/yunlong_cao/status/1697318194976010446
yeah i would prefer to stick with the paper: Flips (not eg.5.1 only ) not being neutralized well by XBB infected plasma.
FedeGueli
commented
1 year ago Please everyone had a closed issue on the main page reactivate the tracking here. we will raise the threshold to 50sequences before transferring. Hope we will be still able to track all this mess.
Over-There-Is
commented
1 year ago A lot of new research show that blood samples from patients infected with EG.5.1 doesn't neutralize EG.5.1 well(which means they're easy to get a second EG.5.1*), so we may be expected to see a lot of mini-recombinations of maybe 2 branches of EG.5.1.1s I guess.
source?
Yunlong Cao's new research? XBB(mostly EG.5.1 consider the proportion in China) BTI infection doesn't neutralize well with Flip, https://twitter.com/yunlong_cao/status/1697318194976010446
But in the 2nd quarter, the XBBs in China are mainly FL, XBB.1.16, FU.1, FY.3, GW.1 and XBB.1.5. EG.5 didn't reach a 50% proportion of XBB* until mid-July.
FedeGueli
commented
1 year ago HK.10 has been withdrawn.
NkRMnZr
commented
1 year ago 09-05, Branch 7, +1 (Malaysia); Branch 8 & 11, +1 (Japan); Branch 13, +2 (China); Adding Branch 16~19 from former doublets.
Branch 7, +1 (Kuala Lumpur) EPI_ISL_18215034
Branch 8, +1 (Osaka) EPI_ISL_18214769
Branch 11, +1 (Gifu) EPI_ISL_18217906
Branch 13, +2 (Hubei) EPI_ISL_18217222, EPI_ISL_18217236
Adding Branch 16 with a triplet from Hubei
Adding Branch 17 from former doublet with 2 seqs from Osaka
Adding Branch 18 from former doublet with 1 sequence from Fujian, be careful with potential artifact/misplacement, due to a reversion, stated before https://github.com/cov-lineages/pango-designation/issues/2194#issuecomment-1702973887
Adding Branch 19 from former doublet with 1 sequence from Ibaraki
FedeGueli
commented
1 year ago 09-05, Branch 7, +1 (Malaysia); Branch 8 & 11, +1 (Japan); Branch 13, +2 (China); Adding Branch 16~19 from former doublets.
Branch 7, +1 (Kuala Lumpur)
EPI_ISL_18215034Branch 8, +1 (Osaka)EPI_ISL_18214769Branch 11, +1 (Gifu)EPI_ISL_18217906Branch 13, +2 (Hubei)EPI_ISL_18217222, EPI_ISL_18217236Adding Branch 16 with a triplet from Hubei Adding Branch 17 from former doublet with 2 seqs from Osaka Adding Branch 18 from former doublet with 1 sequence from Fujian, be careful with potential artifact/misplacement, due to a reversion, stated before cov-lineages/pango-designation#2194 (comment) Adding Branch 19 from former doublet with 1 sequence from Ibaraki
Great work. Thank you.
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
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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
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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
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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
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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
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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
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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
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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
Back to Tasklist
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
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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