Closed NkRMnZr closed 11 months ago
krosa1910
commented
1 year ago No offense and I appreciate people's work to locate and designate those variants, yet may I ask why those are calculated as individual branches, instead of being several big "flip" branches with distinct orf mutations. A lot of those mutations are more or less confined to only 1 branch each so I think the latter model is more accurate.
FedeGueli
commented
1 year ago No offense and I appreciate people's work to locate and designate those variants, yet may I ask why those are calculated as individual branches, instead of being several big "flip" branches with distinct orf mutations. A lot of those mutations are more or less confined to only 1 branch each so I think the latter model is more accurate.
@angiehinrichs could you answer you please? we have more of 60 independently(according to Usher) acquisition of L455F on EG.5.1* family, the question on the table , is possible that exist, to say, just 6-7 big branches among EG.5.1 EG.5.1.1 and others and what we are seeing is just temporarily misplacements? My feeling is no. but you are the master of the whole tree so your opinion will be welcomed. Also cause if there are 60+ lineages (and we already have 19 with 3+ sequences and all of them are doubling at least as fast as the dominant lineages around) in one month means Cornelius will designate 50 very similar lineages all together. And also choosing not to designate you will have 50 undesignated fastest lineages around . So i see only mess coming and i think it is relevant cause in two months they all or in part will be the dominant co-dominant lineages.
FedeGueli
commented
1 year ago Minor correction we are already above 70. (cc @corneliusroemer never seen something similar the 444-460 combo era was a joke in comparison )
xz-keg
commented
1 year ago @AngieHinrichs could you answer you please? we have more of 60 independently(according to Usher) acquisition of L455F on EG.5.1* family, the question on the table , is possible that exist, to say, just 6-7 big branches among EG.5.1 EG.5.1.1 and others and what we are seeing is just temporarily misplacements? My feeling is no. but you are the master of the whole tree so your opinion will be welcomed. Also cause if there are 60+ lineages (and we already have 19 with 3+ sequences and all of them are doubling at least as fast as the dominant lineages around) in one month means Cornelius will designate 50 very similar lineages all together. And also choosing not to designate you will have 50 undesignated fastest lineages around . So i see only mess coming and i think it is relevant cause in two months they all or in part will be the dominant co-dominant lineages.
I guess we have experienced similar issues with XBB.1+S:486P?
FedeGueli
commented
1 year ago @AngieHinrichs could you answer you please? we have more of 60 independently(according to Usher) acquisition of L455F on EG.5.1* family, the question on the table , is possible that exist, to say, just 6-7 big branches among EG.5.1 EG.5.1.1 and others and what we are seeing is just temporarily misplacements? My feeling is no. but you are the master of the whole tree so your opinion will be welcomed. Also cause if there are 60+ lineages (and we already have 19 with 3+ sequences and all of them are doubling at least as fast as the dominant lineages around) in one month means Cornelius will designate 50 very similar lineages all together. And also choosing not to designate you will have 50 undesignated fastest lineages around . So i see only mess coming and i think it is relevant cause in two months they all or in part will be the dominant co-dominant lineages.
I guess we have experienced similar issues with XBB.1+S:486P?
not at this levels and in a short timeframe.
xz-keg
commented
1 year ago @AngieHinrichs could you answer you please? we have more of 60 independently(according to Usher) acquisition of L455F on EG.5.1* family, the question on the table , is possible that exist, to say, just 6-7 big branches among EG.5.1 EG.5.1.1 and others and what we are seeing is just temporarily misplacements? My feeling is no. but you are the master of the whole tree so your opinion will be welcomed. Also cause if there are 60+ lineages (and we already have 19 with 3+ sequences and all of them are doubling at least as fast as the dominant lineages around) in one month means Cornelius will designate 50 very similar lineages all together. And also choosing not to designate you will have 50 undesignated fastest lineages around . So i see only mess coming and i think it is relevant cause in two months they all or in part will be the dominant co-dominant lineages.
I guess we have experienced similar issues with XBB.1+S:486P?
not at this levels and in a short timeframe.
There are 27 XBB*+S:486P designated lineages. I guess this one may eventually end up designating similar number of lineages if half of the 60+ are artefacts.
Or there maybe one scale larger and get 50-100. Given there are two ways to achieve L455F.
xz-keg
commented
1 year ago not at this levels and in a short timeframe.
Maybe we shall do some math here.
Around 800 million Chinese get infected with XBB* in 2023.5-7, of them around 20% are EG.5.1, so shall be 160 million chances to get S:L455F. Patients from other countries, especially SE Asia also contribute, total maybe ~200 million.
For non-486P XBB, it took around ~3% of global share(5% peak) at that time, at a "variant soup" period(2022.9-2023.1) where ~30% of the global non-China population get infected, which should be ~60 million XBB* infections. We get 27 S:486P lineages from that.
Assume chance for non-486P XBB to get 486P is the same as EG.5.1 getting L455F (and become advanturous enough to cause some spread eligible for designation), we shall get 80~100 EG.5.1+L455F lineages.
That's only a rough estimation, number of lineages also affected by monitor systems, actual single-nuc relative advantage, immune backgrounds etc. Also there are 2 ways to get L455F. So just a very rough estimation based on estimated number of infections only.
NkRMnZr
commented
1 year ago 09-06, Branch 17, +1 (Japan); Branch 18, +2 (USA); Adding Branch 20; Removing former singlets now merged into designated branches.
Branch 17, +1 (Osaka) EPI_ISL_18226559
Branch 18, +2 (New Jersey) EPI_ISL_18225873, EPI_ISL_18225907
Adding Branch 20 from former doublet, a SEA Airport sample with travel history to UK.
Quite a few singlets purged from tracking list, they are now seemingly slot onto already designated branches (largely HK.3), but there are still quite a lot 'lone branches' left to track with.
Found a potential EG.5.1 and GK.1 recombinant
NkRMnZr
commented
1 year ago Well the potential recombinant of EG.5.1.1 and GK.1.1 is quite complex, query: A15436G, T22609G, C28519T, either with multiple (2 or 3?) breakpoints, or it's simply a contaminated sample, I'll just leave them here to see if more samples coming in.
USA/WA-GBW-H10-016-2490/2023|EPI_ISL_18222057|2023-08-24
USA/NJ-GBW-H10-016-3711/2023|EPI_ISL_18222077|2023-08-22view from XBB.1.5.70 polytomy
Phylogenetic order XBB.1.5 [T17124C > T23018C] > C27059T > C28005T(ORF8:P38S) > T22928C(S:F456L) > C1973T, G22927T(S:L455F) > C22624T, A25045G > C9693T(ORF1a:A3143V), C17124T_reversion, C23280T(S:T573I), C25658T(ORF3a:T89I) > T1973C_reversion, C2334T(ORF1a:A690V), C6541T, C12789T(ORF1a:T4175I), G13627A(ORF1b:D54N), A15436G(ORF1b:M657V), A16878T, A18492G, T22609G, C23673T(S:S704L), C26735T, C28519T
xz-keg
commented
1 year ago Well the potential recombinant of EG.5.1.1 and GK.1.1 is quite complex, query:
A15436G, T22609G, C28519T, either with multiple (2 or 3?) breakpoints, or it's simply a contaminated sample, I'll just leave them here to see if more samples coming in.USA/WA-GBW-H10-016-2490/2023|EPI_ISL_18222057|2023-08-24 USA/NJ-GBW-H10-016-3711/2023|EPI_ISL_18222077|2023-08-22view from XBB.1.5.70 polytomy
Phylogenetic order XBB.1.5 [T17124C > T23018C] > C27059T > C28005T(ORF8:P38S) > T22928C(S:F456L) > C1973T, G22927T(S:L455F) > C22624T, A25045G > C9693T(ORF1a:A3143V), C17124T_reversion, C23280T(S:T573I), C25658T(ORF3a:T89I) > T1973C_reversion, C2334T(ORF1a:A690V), C6541T, C12789T(ORF1a:T4175I), G13627A(ORF1b:D54N), A15436G(ORF1b:M657V), A16878T, A18492G, T22609G, C23673T(S:S704L), C26735T, C28519T
This deserves to be proposed independently on a new issue?
NkRMnZr
commented
1 year ago This deserves to be proposed independently on a new issue?
@aviczhl2 feel free to make proposal if you have spared time. To me this could be potential contaminated sample for it would have 2 or 3 breakpoints for a recombinant, I'd wait for more seqs to see if those missing definitions from both donors are dropouts.
FedeGueli
commented
1 year ago This deserves to be proposed independently on a new issue?
@aviczhl2 feel free to make proposal if you have spared time. To me this could be potential contaminated sample for it would have 2 or 3 breakpoints for a recombinant, I'd wait for more seqs to see if those missing definitions from both donors are dropouts.
they doesnt seem to me the the same recombinant. lets see if more samples will be added.
FedeGueli
commented
1 year ago 09-06, Branch 17, +1 (Japan); Branch 18, +2 (USA); Adding Branch 20; Removing former singlets now merged into designated branches.
Branch 17, +1 (Osaka)
EPI_ISL_18226559Branch 18, +2 (New Jersey)EPI_ISL_18225873, EPI_ISL_18225907Adding Branch 20 from former doublet, a
SEAAirport sample with travel history to UK.Quite a few singlets purged from tracking list, they are now seemingly slot onto already designated branches (largely HK.3), but there are still quite a lot 'lone branches' left to track with.
Found a potential EG.5.1 and GK.1 recombinant
thx we are at 60 independent acquisition of L455F
FedeGueli
commented
1 year ago maths
Lets count everything at the end.
AngieHinrichs
commented
1 year ago I looked at all of the branches (>= two sequences) with G22927T in EG.5.1, expecting to find lots of cases where G22927T was placed after some other mutation for dubious reasons like Ns etc. But instead I was really struck by how often the many different mutation(s) preceding G22927T were seen in sequences back in May or June (or were seen later, but along with additional new mutations which could plausibly follow the shared mutation) -- and then in August (sometimes July) there was suddenly a burst of sequences that gained G22927T. In other words, almost all of the branches looked pretty real to me.
There were a few that I wasn't so sure about, so I'll try my usual prune/re-optimize/re-place trick, but even out of those I expect some to be pulled back into place by multiple shared mutations (unless there are Ns). Will see what happens in the 2023-09-07 version of the tree late tomorrow.
krosa1910
commented
1 year ago @AngieHinrichs Is any of these branches about T14988C and C25546A? I discovered it as a by-product of another issue, and I wanted to search its "parent" here. Yet I checked this issue and did not find any. If it is missing, then I would happily include it here, which already gained 14 seqs , all pretty new (I mean fucking new, non is earlier than Aug 11, all submitted less than 10 days from now). Or I could start a new issue about it. （or change the one I am currently using)
NkRMnZr
commented
1 year ago 09-07, Branch 5, +1 (Singapore); Branch 8, +2 (China); Adding Branch 21~23
Branch 5, +1 (Singapore) EPI_ISL_18233162
Branch 8, +2 (Shanghai) EPI_ISL_18232515, EPI_ISL_18232656
Adding Branch 21 from former doublets with 1 sequence from Shanghai
Adding Branch 22 from former singlet with 2 seqs from Virginia
Adding Branch 23 from former singlet with 2 seqs from Shanghai
NkRMnZr
commented
1 year ago @AngieHinrichs Is any of these branches about T14988C and C25546A? I discovered it as a by-product of another issue, and I wanted to search its "parent" here. Yet I checked this issue and did not find any. If it is missing, then I would happily include it here, which already gained 14 seqs , all pretty new (I mean fucking new, non is earlier than Aug 11, all submitted less than 10 days from now). Or I could start a new issue about it. （or change the one I am currently using)
Those are now (mis-)placed under 'reversion' parts of Branch 18, so probably wait a bit for the tree to sort them out, or forcing them to other part of the tree.
FedeGueli
commented
1 year ago @krosa1910 please dont share Gisaid contents .
FedeGueli
commented
1 year ago @AngieHinrichs Is any of these branches about T14988C and C25546A? I discovered it as a by-product of another issue, and I wanted to search its "parent" here. Yet I checked this issue and did not find any. If it is missing, then I would happily include it here, which already gained 14 seqs , all pretty new (I mean fucking new, non is earlier than Aug 11, all submitted less than 10 days from now). Or I could start a new issue about it. （or change the one I am currently using)
Those are now (mis-)placed under 'reversion' parts of Branch 18, so probably wait a bit for the tree to sort them out, or forcing them to other part of the tree.
So this is not caught by branch 18 query right?
FedeGueli
commented
1 year ago @NkRMnZr very weird branch 22 with the right query it finds just the Hubei sample: G23593C, G22927T, G13627A , i didnt get why. resolved cause the VA subbranch has a silent mutation C23593T instead of C23593G so nuc mutations only is unuseful here! crazy!
FedeGueli
commented
1 year ago I looked at all of the branches (>= two sequences) with G22927T in EG.5.1, expecting to find lots of cases where G22927T was placed after some other mutation for dubious reasons like Ns etc. But instead I was really struck by how often the many different mutation(s) preceding G22927T were seen in sequences back in May or June (or were seen later, but along with additional new mutations which could plausibly follow the shared mutation) -- and then in August (sometimes July) there was suddenly a burst of sequences that gained G22927T. In other words, almost all of the branches looked pretty real to me.
There were a few that I wasn't so sure about, so I'll try my usual prune/re-optimize/re-place trick, but even out of those I expect some to be pulled back into place by multiple shared mutations (unless there are Ns). Will see what happens in the 2023-09-07 version of the tree late tomorrow.
Thank you!!
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.
After the kind and super useful answer from @AngieHinrichs i think we will stick to this rule : over 50 seqs > proposal. I just a bit worried about @NkRMnZr to keep track of such a high volume of very similar lineages . when you lack time or you re tired of i can help. ( hard to do two people together cause the thing is too big )
AngieHinrichs
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?)
Thanks @Over-There-Is -- fixed in 2023-09-07 tree.
NkRMnZr
commented
1 year ago @FedeGueli So this is not caught by branch 18 query right?
nope, they got C22264T reversed, so they should be HK.3 or some sort misplaced on Branch 18. Don't think this needs to be tracked unless it appears somewhere else in the tree, and the follow-up A475V can be tracked on another issue
@FedeGueli resolved cause the VA subbranch has a silent mutation C23593T instead of C23593G so nuc mutations only is unuseful here! crazy!
yeah, it's a further mutation of HK.5 defining G23593C, so I'll have to use aa query instead of nuc ones.
NkRMnZr
commented
1 year ago 09-08, Branch 17, +2 (Chiba, Fukushima), EPI_ISL_18235760, EPI_ISL_18236014
ryhisner
commented
1 year ago I don't know which of the 5 million undesignated EG.5.1 + L455F branches this one sits on, but a USA branch with seven sequences on it has picked up S:T95I. Five are from Hawaii, two from California. Collection dates are all between August 3 and August 22.
The branch immediately preceding this one has C12100G, an extremely rare synonymous mutation present only in 34 other sequences throughout the entire pandemic.
EPI_ISL_18160065, EPI_ISL_18222980, EPI_ISL_18225065, EPI_ISL_18235062, EPI_ISL_18241263, EPI_ISL_18241289, EPI_ISL_18241380
NkRMnZr
commented
1 year ago @ryhisner I don't know which of the 5 million undesignated EG.5.1 + L455F branches this one sits on, but a USA branch with seven sequences on it has picked up S:T95I. Five are from Hawaii, two from California. Collection dates are all between August 3 and August 22.
The branch immediately preceding this one has C12100G, an extremely rare synonymous mutation present only in 34 other sequences throughout the entire pandemic.
see cov-lineages/pango-designation#2224
NkRMnZr
commented
1 year ago 09-09, Branch 5, +3 (Canada); Branch 9 +1 (US); Branch 17, +2 (Japan); Branch 18, +5 (Canada); Adding Branch 24
Branch 5, +3 (Canada) EPI_ISL_18240022, EPI_ISL_18240041, EPI_ISL_18240510
Branch 9, +1 (USA) EPI_ISL_18239976
Branch 17, +2 (Japan) EPI_ISL_18235760, EPI_ISL_18236014
Branch 18, +5 (Canada) EPI_ISL_18240051, EPI_ISL_18240055, EPI_ISL_18240061, EPI_ISL_18240137, EPI_ISL_18240218
Adding Branch 24 from former singlet and doublet which merged into one branch
FedeGueli
commented
1 year ago EPI_ISL_18227115 EG.5.1.3 from England with S:L455S Query: T11932G, T14022C, T22926C
FedeGueli
commented
1 year ago Branch 4 got designated EG.5.1.8 from https://github.com/cov-lineages/pango-designation/issues/2224 via https://github.com/cov-lineages/pango-designation/commit/072c887d266647163602965c26d74a389ae8175a
NkRMnZr
commented
1 year ago 09-12, Update on Branch 5, 6, 7, 10, 11, 12, 15, 17, 23, 24; Adding Branch 25~30
Branch 5, +10 (Liaoning, Sichuan, Singapore, Tasmania) EPI_ISL_18243318, EPI_ISL_18243348, EPI_ISL_18243470, EPI_ISL_18243555, EPI_ISL_18246233, EPI_ISL_18246282-18246283, EPI_ISL_18246287, EPI_ISL_18246334, EPI_ISL_18248118
Branch 6, +1 (Heilongjiang) EPI_ISL_18246092
Branch 7, +2 (Fujian) EPI_ISL_18245833, EPI_ISL_18245852
Branch 10, +7 (Fujian, Liaoning, Sichuan, Singapore) EPI_ISL_18243494, EPI_ISL_18245834, EPI_ISL_18246228, EPI_ISL_18246273, EPI_ISL_18246285-18246286, EPI_ISL_18246309
Branch 11, +1 (Fujian) EPI_ISL_18245832
Branch 12, +1 (Singapore) EPI_ISL_18243476
Branch 15, +1 (Singapore) EPI_ISL_18243416
Branch 17, +2 (Nara, Tokyo) EPI_ISL_18242568, EPI_ISL_18243896
Branch 23, +3 (Singapore) EPI_ISL_18243407, EPI_ISL_18243535, EPI_ISL_18243547
Branch 24, +1 (Sichuan) EPI_ISL_18246292
Adding Branch 25 from former singlet with 3 extra seqs from Gansu and Sichuan Adding Branch 26 from former singlet with 2 extra seqs from Denmark Adding Branch 27 from former doublet with 6 extra seqs from Heilongjiang and Denmark Adding Branch 28 from former singlet with 1 more sequence from Sichuan Adding Branch 29 with a triplet from Fujian and Singapore Adding Branch 30 from former doublet with 1 more sequence from Sichuan
NkRMnZr
commented
1 year ago 09-13, Update on Branch 5, 8, 10, 13, 17, 18; Adding Branch 31~34
Branch 5, +2 (Gunma, Hubei) EPI_ISL_18253492, EPI_ISL_18254274
Branch 8, +3 (Hubei) EPI_ISL_18254181, EPI_ISL_18254187, EPI_ISL_18254259
Branch 10, +1 (Hubei) EPI_ISL_18254261
Branch 13, +1 (Hubei) EPI_ISL_18254205
Branch 17, +3 (Kanagawa, Tokyo) EPI_ISL_18247826-18247827, EPI_ISL_18253490
Branch 18, +1 (Québec) EPI_ISL_18252372
Adding Branch 31 from former doublet with 1 sequence from Hubei
Adding Branch 32 from former doublet with 3 seqs from Fujian, Sichuan and Hubei
Adding Branch 33 from former doublet with 1 sequence from Bucharest and Washington
Adding Branch 34 (S:L455S) with a quartlet from Croatia.
FedeGueli
commented
1 year ago @NkRMnZr i ve added this one using your "scrript":
Canada/NL- PHML-640907/2023|EPI_ISL_18132133|2023-08-08 EG.5.1.4 > C26111T(ORF3:P240L) > C18555T > T17268C > G22927T(S:L455F) [Query: T17268C, G22927T, C26111T, 08/24]
is now 6 on usher (7 on Gisaid with your query)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice6_genome_2637b_412f30.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_10879031
If you want i can add by myself to branches but i want not to mess your things !
FedeGueli
commented
1 year ago Adding branch 35 from Canada 7seqs
NkRMnZr
commented
1 year ago 09-15, updates on Branch 10, 11 and 17; Adding Branch 35
Branch 10, +4 (Sichuan) EPI_ISL_18261471-18261472, EPI_ISL_18261475, EPI_ISL_18261479
Branch 11, +1 (Shizuoka) EPI_ISL_18257101
Branch 17, +1 (Fukui) EPI_ISL_18261506
Adding Branch 35 from former doublet with 5 seqs from Newfoundland and Labrador (thanks @FedeGueli )
NkRMnZr
commented
1 year ago 09-16, update on Branch 5-11, 13, 18, 23, 25, 26, 30, 31, 33; adding Branch 36~40
Branch 5, +14 (Hubei, Iowa, Liaoning, Shanghai) EPI_ISL_18268155, EPI_ISL_18268187, EPI_ISL_18268198, EPI_ISL_18268200, EPI_ISL_18268203-18268204, EPI_ISL_18268290, EPI_ISL_18268305, EPI_ISL_18268357, EPI_ISL_18268360, EPI_ISL_18268454, EPI_ISL_18268469, EPI_ISL_18268474, EPI_ISL_18269356
Branch 6, +2 (Shanghai) EPI_ISL_18268478, EPI_ISL_18268504
Branch 7, +4 (Shanghai) EPI_ISL_18268331, EPI_ISL_18268365, EPI_ISL_18268430, EPI_ISL_18268478
Branch 8, +1 (Shanghai) EPI_ISL_18268451
Branch 9, +1 (Shanghai) EPI_ISL_18268330
Branch 10, +2 (Liaoning, Shanghai) EPI_ISL_18268212, EPI_ISL_18268407
Branch 11, +2 (Denmark, Iowa) EPI_ISL_18263990, EPI_ISL_18269291
Branch 13, +4 (Hubei and Qinghai) EPI_ISL_18268148-18268149, EPI_ISL_18268153, EPI_ISL_18268244
Branch 18, +1 (Delaware) EPI_ISL_18266425
Branch 23, +1 (Shanghai) EPI_ISL_18268289
Branch 25, +1 (Hubei) EPI_ISL_18268164
Branch 26, +3 (Denmark, Texas, Viken) EPI_ISL_18263586, EPI_ISL_18264001, EPI_ISL_18264572
Branch 30, +1 (Liaoning) EPI_ISL_18268211
Branch 31, +3 (Cork) EPI_ISL_18263700, EPI_ISL_18263710, EPI_ISL_18263712
Branch 33, +1 (Bayern) EPI_ISL_18264973
Adding Branch 36 from 2 of former doublets that joint together with 4 seqs from Viken Adding Branch 37 from former singlet with 2 seqs from Texas Adding Branch 38 from former doublet with 1 sequence from Shanghai Adding Branch 39 from 2 of former doublets that pulled together, also having difficulties with query for it further mutate HK.1 defining S:G257V(G22332T) to S:G257D(G22332A) Adding Branch 40 from former doublet with 2 seqs from Shanghai
FedeGueli
commented
1 year ago Please update branch 5 on the pango repo. it is fast as or more than HK.3
FedeGueli
commented
1 year ago Branch 17 seems fast. lets wait. Branch 16-19-20-21-22 slow.
NkRMnZr
commented
1 year ago 09-18, Branch 17 +1 (S. Korea); Adding Branch 41
Branch 17, +1 (S. Korea) EPI_ISL_18271898
Adding Branch 41 from former doublet with 1 more sequence from South Korea
BTW, I figured out how to use some kind of wildcard trick on GISAID, taking example of Branch 22, now has the query of G13627A, G22927T, G23593, that G23593 probably means "anything but Guanine at nuc_23593", that could be helpful for something that further changed on a same nucleotide, like Branch 39. @FedeGueli
NkRMnZr
commented
1 year ago 09-19, Update on Branch 5, 10-12, 17, 23, 25, 31, 33, 36 and 40; Adding Branch 42-44; Removing Branch 18
Branch 5, +4 (England) EPI_ISL_18273958, EPI_ISL_18274001, EPI_ISL_18274118, EPI_ISL_18281539
Branch 10, +2 (New York; Ronchin) EPI_ISL_18273291, EPI_ISL_18277184
Branch 11, +1 (Ontario) EPI_ISL_18277805
Branch 12, +1 (Singapore) EPI_ISL_18278998
Branch 17, +2 (Gifu; Nara) EPI_ISL_18279175, EPI_ISL_18279234
Branch 23, +1 (Fujian) EPI_ISL_18277142
Branch 25, +1 (Cataluña) EPI_ISL_18281760
Branch 31, +3 (England; Florida) EPI_ISL_18273572, EPI_ISL_18273769, EPI_ISL_18275799
Branch 33, +1 (Ontario) EPI_ISL_18277398
Branch 36, +2 (Reims; Hénin-Beaumont) EPI_ISL_18280654, EPI_ISL_18280813
Branch 40, +1 (Fujian) EPI_ISL_18277142
No longer track Branch 18 which merged into HK.3 @krosa1910
Adding Branch 42 from former singlet and doublet pulled toghether, with 3 seqs from Canada and Singapore Adding Branch 43 from former doublet, with 1 more sequence from Fujian. Note this branch contains an end of ORF8 deletion causing some kind of frameshift, which UShER doens't seem to handle it well, so it is split into 2 parts on the tree. Adding Branch 44 (FLippeR) from former doublet, with 1 more sequence from Singapore
FedeGueli
commented
1 year ago Thank you for the head uo for B18 @NkRMnZr great work as usual.
krosa1910
commented
1 year ago No longer track Branch 18 which merged into HK.3 @krosa1910
OK, I could take care of that myself if it helps relieve some pressure from you. I did not have the will to start some grouping for a 100ish large clade, and your task here s 10 times larger.
NkRMnZr
commented
1 year ago No longer track Branch 18 which merged into HK.3 @krosa1910
OK, I could take care of that myself if it helps relieve some pressure from you. I did not have the will to start some grouping for a 100ish large clade, and your task here s 10 times larger.
Ta. To be honest, no one would have thought it could end up like this, when I propose this I thought it could be some 30-ish branches at most, look how wrong I am now, this is one of the most stupid thing I've done. I had a feeling each provinces in China could have its own version of HK.3 impersonator, many just haven't submit their seqs yet. This can also happen in many Asian countries as well, and subsequently all over the world, and if that shall happen I would have to quit this folly.
NkRMnZr
commented
1 year ago 09-20, Update on Branch 5, 7-15, 17, 22-24, 27, 30-32, 38. Remove Branch 6. Adding Branch 45-49
Branch 5, +6 (England, Hubei, Queensland, Shanghai, Western Australia) EPI_ISL_18284610, EPI_ISL_18284718, EPI_ISL_18284857, EPI_ISL_18284891, EPI_ISL_18284967, EPI_ISL_18285915
Branch 7, +3 (Shanghai, Sichuan) EPI_ISL_18284773, EPI_ISL_18284874, EPI_ISL_18284923
Branch 8, +2 (Hubei, Shanghai) EPI_ISL_18284714, EPI_ISL_18284809
Branch 9, +2 (Sichuan, Shanghai) EPI_ISL_18284697, EPI_ISL_18284918
Branch 10, +6 (Shanghai, Sichuan) EPI_ISL_18284700, EPI_ISL_18284819, EPI_ISL_18284933, EPI_ISL_18284992, EPI_ISL_18285023, EPI_ISL_18285060
Branch 11, +1 (Saitama) EPI_ISL_18285397
Branch 12, +3 (Sichuan, Shanghai) EPI_ISL_18284885, EPI_ISL_18284898, EPI_ISL_18285080
Branch 13, +2 (Hubei) EPI_ISL_18284712, EPI_ISL_18284755
Branch 14, +2 (Sichuan) EPI_ISL_18285083-18285084
Branch 15, +5 (Shanghai, Sichuan) EPI_ISL_18284693, EPI_ISL_18284883, EPI_ISL_18284945, EPI_ISL_18285015, EPI_ISL_18285039
Branch 17, +2 (Chiba, Saitama) EPI_ISL_18285272, EPI_ISL_18285440
Branch 22, +1 (IAD airport, DC) EPI_ISL_18284072
Branch 23, +6 (Hubei, Shanghai, Sichuan) EPI_ISL_18284673, EPI_ISL_18284676, EPI_ISL_18284734, EPI_ISL_18284754, EPI_ISL_18284792, EPI_ISL_18284928
Branch 24, +3 (Shanghai, Sichuan, Tokyo) EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192
Branch 27, +1 (Hérault) EPI_ISL_18282065
Branch 30, +1 (Chiba) EPI_ISL_18285202
Branch 31, +7 (Dublin, England) EPI_ISL_18281553, EPI_ISL_18281559, EPI_ISL_18281563, EPI_ISL_18281565-18281566, EPI_ISL_18281571, EPI_ISL_18286405
Branch 32, +1 (Shanghai) EPI_ISL_18284833
Branch 38, +2 (Shanghai) EPI_ISL_18284797, EPI_ISL_18284801
No longer tracking Branch 6, many sequences are pulled back to HK.3, and the reversion seems caused by dropout rather than potential recombinant.
Adding Branch 45 from former doublet with 2 seqs from IAD, DC, ex. Italy
Adding Branch 46 from former doublet with 2 seqs from Shanghai
Adding Branch 47 from former singlet with 4 seqs from Hubei, Shanghai and Sichuan
Adding Branch 48 from former doublet with 2 seqs from Singapore and South Australia
Adding Branch 49 with 3 seqs from Hubei
krosa1910
commented
1 year ago Ta. To be honest, no one would have thought it could end up like this, when I propose this I thought it could be some 30-ish branches at most, look how wrong I am now, this is one of the most stupid thing I've done. I had a feeling each provinces in China could have its own version of HK.3 impersonator, many just haven't submit their seqs yet. This can also happen in many Asian countries as well, and subsequently all over the worlds, and if that shall happen I would have to quit this folly.
I would suggest you to largely limit your focus to the large branches(>10 seq) with international or at least inter-provincial with non-neighboring provinces in China spread from now on, then use large trash bag lineages like HK.3 to keep track of the rest. Because a lot of those branches are indeed too similar now according to our knowledge of the virus, and I guess most of those would be limited to local China province sequencers to discover them.
FedeGueli
commented
1 year ago No longer track Branch 18 which merged into HK.3 @krosa1910
OK, I could take care of that myself if it helps relieve some pressure from you. I did not have the will to start some grouping for a 100ish large clade, and your task here s 10 times larger.
Ta. To be honest, no one would have thought it could end up like this, when I propose this I thought it could be some 30-ish branches at most, look how wrong I am now, this is one of the most stupid thing I've done. I had a feeling each provinces in China could have its own version of HK.3 impersonator, many just haven't submit their seqs yet. This can also happen in many Asian countries as well, and subsequently all over the world, and if that shall happen I would have to quit this folly.
I think this issue is the best example of tracking we had from the start of the pandemic. But i think it is not bearable for you anymore i suggest to quit, i will follow up tracking pvt the 45 branches ( oh wiat they are 49 already crazy edited)you queried if someone new will pop up also other spotters will see for sure and i will care to track them back to this issue if spotted first here. SO take some relief and close this issue down.
FedeGueli
commented
1 year ago Consider also that now competition in China is wild . if something is faster than others we will see it for sure. Closed the issue. I will make a public thread to praise your efforts. edited : here: https://x.com/siamosolocani/status/1704801167639728295?s=20
FedeGueli
commented
1 year ago Said that Branch 48 seems very interesting with S:659S and already 3 countries and two continents
xz-keg
commented
1 year ago No longer track Branch 18 which merged into HK.3 @krosa1910
OK, I could take care of that myself if it helps relieve some pressure from you. I did not have the will to start some grouping for a 100ish large clade, and your task here s 10 times larger.
Ta. To be honest, no one would have thought it could end up like this, when I propose this I thought it could be some 30-ish branches at most, look how wrong I am now, this is one of the most stupid thing I've done. I had a feeling each provinces in China could have its own version of HK.3 impersonator, many just haven't submit their seqs yet. This can also happen in many Asian countries as well, and subsequently all over the world, and if that shall happen I would have to quit this folly.
I think this issue is the best example of tracking we had from the start of the pandemic. But i think it is not bearable for you anymore i suggest to quit, i will follow up tracking pvt the 45 branches ( oh wiat they are 49 already crazy edited)you queried if someone new will pop up also other spotters will see for sure and i will care to track them back to this issue if spotted first here. SO take some relief and close this issue down.
This thread is really useful! The problem is that when size of EG.5.1.1 becomes larger than 5000 usher starts to show downsampled trees and hence lineages on EG.5.1.1 become very difficult to track. Usher may show a number but without designation no one knows which number of EG.5.1.1 belongs to which branch.
S:L455Fin EG.5.1 backbone. Checking updates.C66T,C346T,G598A,G1820A,C4423T,C6843T,A10323G(ORF1a:K3353R),C12651T(ORF1a:T4129I),C13860T,A15159G,C19983T,C22096T(S:D178D),C22264T(S:N234N),C22792T(S:I410I),C22998T(S:P479L),C26681T,C27059T,C27507T,C27884T,A29700GBranch 1:
Transferred to main repo. Designated as HK.8
**Designated as HK.8 (EG.5.1.1.8) via cov-lineages/pango-designation@9527e15** _Transferred to cov-lineages/pango-designation#2230_ **Defining Mutations:** `EG.5.1.1` > `C11779T` > `G22927T(S:L455F)` **Query:** `C6541T, C11779T, G22927T` **Earliest seq:** 2023-06-27 (`EPI_ISL_18060870`, Yibin, Sichuan, China) **Latest seq:** 2023-07-17 (`EPI_ISL_18060877`, Zi'yang, Sichuan, China) **Sampled Countries:** China (2, Sichuan)Genomes:
`EPI_ISL_18060870, EPI_ISL_18060877`Back to Tasklist
Branch 2:
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2229_ **Defining Mutations:** `EG.5.1.1` > `C12053T(ORF1a:L3930F)` > `C503T(ORF1a:P80S)` > `C7732T, C18175T(ORF1b:P1570S), G22927T(S:L455F)` **Query:** `C503T, C6541T, G22927T` **Earliest seq:** 2023-07-15 (`EPI_ISL_18060497`, Tokyo, Japan) **Latest seq:** 2023-07-18 (`EPI_ISL_18065046`, Miyagi, Japan) **Sampled Countries:** Japan (2)Genomes:
`EPI_ISL_18060497, EPI_ISL_18065046`Back to Tasklist
Branch 3
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2194_ **Defining Mutations:** `EG.5.1.1` > `C11779T` > `C6781T, C17802T, G22927C(S:L455F)` **Query:** `C6781T, C17802T, G22927C` **Earliest seq:** 2023-07-04 (`EPI_ISL_17994488`, Shanghai, China) **Latest seq:** 2023-07-18 (`EPI_ISL_18074754`, Shanghai, China) **Sampled Countries:** China (3, Shanghai)Genomes:
`EPI_ISL_17994488, EPI_ISL_18074751, EPI_ISL_18074754`Back to Tasklist
Branch 4
Transferred to main repo
Transferred to cov-lineages/pango-designation#2224 **Defining Mutations:** `EG.5.1` > `C12100G, G22927T`(**S:L455F**) **Query:** `C12100G, G22927T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18060822`, Shanghai, China) **Latest seq:** 2023-07-31 (`EPI_ISL_18094969`, Washington, USA with Travel History to: Japan) **Sampled Countries:** China (2, Shanghai, 1 ex. Thailand), USA (2, Washington, ex. Japan)Genomes:
`EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946, EPI_ISL_18094969`Back to Tasklist
Branch 5
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2250_ **Defining Mutations:** `EG.5.1.1` > `G22927C`(**S:L455F**, different to **HK.3**'s `G22927T`) **Query:** `C6541T, G22927C, -C3653T, -C6317T, -C6327T, -A6659G, -T7111C, -C8074T, -G8768A, -C10702T, -C11779T, -C13968A, -T17811C, -A21137G, -T21748C, -C22482T, -C24023T, -C27741T, -G29734T` **Earliest seq:** 2023-07-08 (`EPI_ISL_18012368`, Sichuan, China) **Latest seq:** 2023-07-27 (`EPI_ISL_18105834`, Shanghai, China) **Sampled Countries:** China (3: Shanghai/2; Sichuan/1)Genomes:
`EPI_ISL_18012368, EPI_ISL_18074450, EPI_ISL_18105834`Back to Tasklist
Branch 6
Many sequences pulled back to HK.3, the reversion probably due to dropout rather than recombinant
**Defining Mutations:** `EG.5.1.1` > _T22480C_Reversion_ > `G22927T`(**S:L455F**) **Query:** `C6541T, G13627A, G22927T, -C7948T, -C22480T` **Earliest seq:** 2023-07-05 (`EPI_ISL_17988079`, Xiangyang, Hubei) **Latest seq:** 2023-08-07 (`EPI_ISL_18105560`, Xiangyang, Hubei) **Sampled Countries:** China (4, Hubei)Genomes:
`EPI_ISL_17988079, EPI_ISL_18105559-18105560, EPI_ISL_18105562`Back to Tasklist
Branch 7
Defining Mutations:
EG.5.1.1>C6627T(ORF1a:T2121I)>T17147C(ORF1b:I1227T)>G22927T(S:L455F) Query:C6627T, T17147C, G22927TEarliest seq: 2023-07-06 (EPI_ISL_18074610, Shanghai) Latest seq: 2023-08-05 (EPI_ISL_18108436, Shanghai, Travel history: Singapore) Sampled Countries: China (3: Shanghai)Genomes:
`EPI_ISL_18074610, EPI_ISL_18108436, EPI_ISL_18108490`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1999b_eabba0.json?f_userOrOld=uploaded%20sample&label=id:node_10741278
Back to Tasklist
Branch 8
Defining Mutations:
EG.5.1.1>C5284T>T14655C>C15951T, G22927T(S:L455F) Query:C5284T, T14655C, G22927TEarliest seq: 2023-07-23 (EPI_ISL_18105571, Shanghai) Latest seq: 2023-08-11 (EPI_ISL_18114886, Shanghai) Sampled Countries: China (3, Shanghai)Genomes:
`EPI_ISL_18105571, EPI_ISL_18108625, EPI_ISL_18114886`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28a92_b9eb0.json?f_userOrOld=uploaded%20sample&label=id:node_6895881
Back to Tasklist
Branch 9
Defining Mutations:
EG.5.1.1>C19983T>G22927T(S:L455F) Query:C6541T, G13627A, C19983T, G22927T, -C6695T **Earliest seq:** 2023-06-30 (EPI_ISL_18074254, Liaoning, China) **Latest seq:** 2023-08-27 (EPI_ISL_18239976`, Utah, USA) Sampled Countries: China (3: Liaoning/2; Shanghai/1)Genomes:
`EPI_ISL_18074249, EPI_ISL_18074254`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2cc80_bc030.json?f_userOrOld=uploaded%20sample&label=id:node_6895986
Back to Tasklist
Branch 10
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2251_ **Defining Mutations:** EG.5.1.1 > C11173T > G22927T(**S:L455F**) **Query:** `C11173T, G13627A, G22927T, -T22228C, -C27406T, -T28157C` **Earliest seq:** 2023-07-16 (`EPI_ISL_18049850`, Qinghai) **Latest seq:** 2023-08-01 (`EPI_ISL_18114762`, Shanghai) **Sampled Countries:** China (3, Qinghai, Shanghai, Xinjiang)Genomes:
`EPI_ISL_18049850, EPI_ISL_18108872, EPI_ISL_18114762`Back to Tasklist
Branch 11
Defining Mutations:
EG.5.1>C9430T>T1939C, C10039T, C20873G(ORF1b:A2469G), G22927T(S:L455F)Query:C9430T, G21718T, G22927T, -C1889T, -G13627A, -C21622AEarliest seq: 2023-07-31 (EPI_ISL_18127303, Tokyo, Japan) Latest seq: 2023-08-07 (EPI_ISL_18127606, Kanagawa, Japan) Sampled Countries: Japan (3: Tokyo/2; Kanagawa/1)Genomes:
`EPI_ISL_18127215, EPI_ISL_18127303, EPI_ISL_18127606`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_1293d_792f00.json?f_userOrOld=uploaded%20sample
Back to Tasklist
Branch 12:
Designated EG.5.1.17
_Designated as **EG.5.1.17** via cov-lineages/pango-designation@5a8103c_ **Defining Mutations:** `EG.5.1` > `G22927C(S:L455F)` **Query:** `C2334T, A18492G, G22927C, -G1069A, -A22106C, -C22570T, -C25572T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18108295`, Anhui, China) **Latest seq:** 2023-08-15 (`EPI_ISL_18138165`, Shanghai, China) **Sampled Countries:** China (4: Shanghai/3; Anhui/1)Genomes:
`EPI_ISL_18108295, EPI_ISL_18114797, EPI_ISL_18138165, EPI_ISL_18138282`Back to Tasklist
Branch 13:
Transferred to main repo
_transferred to cov-lineages/pango-designation#2364_ **Defining Mutations:** `EG.5.1.1` > `C19011T` > `C8991T(ORF1a:A2909V)` > `G22927T(S:L455F)` **Query:** `C8991T, C19011T, G22927T` **Earliest seq:** 2023-08-14 (`EPI_ISL_18146054`, Hubei, China) **Latest seq:** 2023-10-31 (`EPI_ISL_18473645`, Singapore, travel history: India) **Sampled Countries:** China (38: HB/23; SH/4; AH/3; BJ/2; YN/2; GS/1; HA/1; QH/1; XJ/1), Singapore (5: Local/2; ex. China/2; ex. India/1), Netherlands (3), Australia (2: NSW), Austria (1), Croatia (1), France (1), Laos (1)Genomes:
`EPI_ISL_18141179, EPI_ISL_18146054, EPI_ISL_18146087, EPI_ISL_18217222, EPI_ISL_18217236, EPI_ISL_18254205, EPI_ISL_18268148-18268149, EPI_ISL_18268153, EPI_ISL_18268244, EPI_ISL_18284712, EPI_ISL_18284755, EPI_ISL_18306934, EPI_ISL_18313098, EPI_ISL_18313105, EPI_ISL_18313198, EPI_ISL_18313226, EPI_ISL_18349877, EPI_ISL_18354962, EPI_ISL_18363349, EPI_ISL_18376465, EPI_ISL_18376494, EPI_ISL_18384477, EPI_ISL_18384508, EPI_ISL_18388887, EPI_ISL_18388889, EPI_ISL_18388891, EPI_ISL_18438085, EPI_ISL_18438311, EPI_ISL_18438356, EPI_ISL_18438359, EPI_ISL_18438427, EPI_ISL_18441693, EPI_ISL_18442727, EPI_ISL_18442730, EPI_ISL_18447747, EPI_ISL_18457659, EPI_ISL_18461703, EPI_ISL_18461971, EPI_ISL_18463327, EPI_ISL_18463426, EPI_ISL_18464919, EPI_ISL_18464984, EPI_ISL_18465193, EPI_ISL_18465381, EPI_ISL_18465391, EPI_ISL_18466345, EPI_ISL_18473414, EPI_ISL_18473645, EPI_ISL_18475163, EPI_ISL_18475178`Back to Tasklist
Branch 14
Defining Mutations:
EG.5.1.1>A8443G>G22927T(S:L455F)Query:C6541T, A8443G, G22927TEarliest seq: 2023-07-22 (EPI_ISL_18060879Ziyang, Sichuan) Latest seq: 2023-08-09 (EPI_ISL_18146071, Xiaogan, Hubei) Sampled Countries: China (3: Sichuan/2; Hubei/1)Genomes:
`EPI_ISL_18060879, EPI_ISL_18146071, EPI_ISL_18166195`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_140e3_db750.json?f_userOrOld=uploaded%20sample
Back to Tasklist
Branch 15
Designated with levels: HK.23, HK.23.1 and HK.23.1.1
Designated as three levels: [HK.23](https://github.com/cov-lineages/pango-designation/commit/12691b30210c9ab9b68ebfe04bda957d9a09b806), [HK.23.1](https://github.com/cov-lineages/pango-designation/commit/b83d9aa28a32b8a70a6e049b29986577cf07f23a) and [HK.23.1.1](https://github.com/cov-lineages/pango-designation/commit/b47c3ca2d6369c236951efde3b954e9ac022e5b7) _Transferred to cov-lineages/pango-designation#2340_ **Defining Mutations:** `EG.5.1.1` > `C28087T(ORF8:A65V)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C28087T, -A4306G, -G4444A, -A6889G, -G8171A, -T8305C, -C10039T, -C19185T, -C25207T` **Earliest seq:** 2023-08-10 (`EPI_ISL_18138246`, Shanghai) **Latest seq:** 2023-08-14 (`EPI_ISL_18208534`, Shanghai) **Sampled Countries:** China (3: Shanghai)Genomes:
`EPI_ISL_18138040, EPI_ISL_18138246, EPI_ISL_18208534`Back to Tasklist
Branch 16
Defining Mutations:
EG.5.1.1>C8074T > T17811C>C7604T, C10789T, C10834T, C12815T, G20348T(ORF1b:S2294I), G22927C(S:L455F), A25998GQuery:C6541T, C8074T, G22927CEarliest seq: 2023-08-22 (EPI_ISL_18217203, Hubei, China) Latest seq: 2023-08-22 (EPI_ISL_18217204, Hubei, China) Sampled Countries: China (3)Genomes:
`EPI_ISL_18217202-18217204`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2cf_6feba0.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_6949824
Back to Tasklist
Branch 17
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2341_ **Defining Mutations:** `EG.5.1.1` > `C9118T` > `G22927T(S:L455F)` **Query:** `C6541T, C9118T, G22927T, -C25546A` **Earliest seq:** 2023-08-14 (`EPI_ISL_18214798`, Osaka, Japan) **Latest seq:** 2023-10-02 (`EPI_ISL_18373543`, England, UK) **Sampled Countries:** Japan (37), USA (4: TX/2; NJ; SC), South Korea (2), UK (2: EN), Australia (1: WA), Canada (1: ON), France (1)Genomes:
`EPI_ISL_18162837, EPI_ISL_18166739, EPI_ISL_18214798, EPI_ISL_18214838, EPI_ISL_18226559, EPI_ISL_18235760, EPI_ISL_18236014, EPI_ISL_18242568, EPI_ISL_18243896, EPI_ISL_18247826-18247827, EPI_ISL_18253490, EPI_ISL_18261506, EPI_ISL_18271898, EPI_ISL_18279175, EPI_ISL_18279234, EPI_ISL_18285272, EPI_ISL_18285440, EPI_ISL_18294200, EPI_ISL_18300272, EPI_ISL_18338985, EPI_ISL_18342460, EPI_ISL_18354762, EPI_ISL_18354776, EPI_ISL_18362312, EPI_ISL_18370698, EPI_ISL_18370761, EPI_ISL_18371874, EPI_ISL_18372806, EPI_ISL_18373146, EPI_ISL_18373543, EPI_ISL_18376280, EPI_ISL_18376286, EPI_ISL_18377931, EPI_ISL_18382356, EPI_ISL_18382437, EPI_ISL_18382737, EPI_ISL_18385259, EPI_ISL_18387636, EPI_ISL_18390707, EPI_ISL_18390782, EPI_ISL_18390836, EPI_ISL_18397002, EPI_ISL_18402105, EPI_ISL_18402112, EPI_ISL_18411313, EPI_ISL_18413797, EPI_ISL_18413896`Back to Tasklist
Branch 18
Merged into HK.3
**Defining Mutations:** `EG.5.1.1` > `C22264T` > `G22927T(S:L455F)` **Query:** `G13627A, C22264T, G22927T` **Earliest seq:** 2023-07-30 (`EPI_ISL_18129236`, British Columbia, Canada) **Latest seq:** 2023-08-28 (`EPI_ISL_18213253`, Fujian, China) **Sampled Countries:** Canada (1, BC), China (1, Fujian), UK (1, England)Genomes:
`EPI_ISL_18129236, EPI_ISL_18142517, EPI_ISL_18213253`Back to Tasklist
Branch 19
Merged under HK.13, no longer tracking
**Defining Mutations:** `EG.5.1.1` > `C29167T` > `G1186A, T4871C(ORF1a:Y1536H), C7011T(ORF1a:A2249V), G17741A(ORF1b:R1425H), G22927C(S:L455F)` **Query:** `T4871C, G17741A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18160385`, New York, USA) **Latest seq:** 2023-08-19 (`EPI_ISL_18214905`, Ibaraki, Japan) **Sampled Countries:** China (1, Shanghai), Japan (1), USA (1, NY)Genomes:
`EPI_ISL_18160385, EPI_ISL_18208589, EPI_ISL_18214905`Back to Tasklist
Branch 20
Designated as HK.33
_Designated as HK.33 via cov-lineages/pango-designation@7ad122e_ **Defining Mutations:** `EG.5.1.1` > `C2644T` > `T7957C, G22927T(S:L455F), G29348T(N:A359S)` **Query:** `C2644T, G13627A, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18222131`, `SEA` airport, Washington, USA, travel history: UK) **Latest seq:** 2023-08-25 (`EPI_ISL_18208454`, Shanghai, China) **Sampled Countries:** USA (2, ex. UK), China (1, Shanghai)Genomes:
`EPI_ISL_18147035, EPI_ISL_18208454, EPI_ISL_18222131`Back to Tasklist
Branch 21, now pulled under HK.3.8
Pulled under HK.3.8
**Defining Mutations:** `EG.5.1.1` > `C18747T` > `C643T, T13060C, G19723T(ORF1b:V2086F), G22927T(S:L455F)` **Query:** `C643T, C18747T, G22927T` **Earliest seq:** 2023-08-11 (`EPI_ISL_18208543`, Shanghai) **Latest seq:** 2023-08-28 (`EPI_ISL_18232547`, Shanghai Customs, travel history to Japan **Sampled Countries:** China (3, SH)Genomes:
`EPI_ISL_18208543, EPI_ISL_18208548, EPI_ISL_18232547`Back to Tasklist
Branch 22, Now pulled under
HK.3.2>A708C(ORF1a:E148A)>C10969T, G23593T(S:Q677H), G28056A(ORF8:A55T), no longer tracking.Pulled under HK.3.2
**Defining Mutations:** `HK.5` > `G22927T(S:L455F)` **Query:** `spike_Q52H, spike_L455F, spike_Q677H` **Earliest seq:** 2023-08-13 (`EPI_ISL_18146068`, Hubei) **Latest seq:** 2023-08-24 (`EPI_ISL_18226161`, Virginia) **Sampled Countries:** USA (2, VA), China (1, HB)Genomes:
`EPI_ISL_18146068, EPI_ISL_18226161-18226162`Back to Tasklist
Branch 23
Transferred to main repo:
_Transferred to main repo cov-lineages/pango-designation#2319_ **Defining Mutations:** `HK.2` > `G22927T(S:L455F)` **Query:** `C6541T, G21604T, G22927T, -A518G, -C934T, -C1426T, -G3663A, -C5031T, -C7712T, -A7849G, -C8320T, -T16545G` **Earliest seq:** 2023-08-21 (`EPI_ISL_18141161`, Singapore) **Latest seq:** 2023-08-23 (`EPI_ISL_18232599`, Shanghai) **Sampled Countries:** Singapore (1), China (2, SH)Genomes:
`EPI_ISL_18141161, EPI_ISL_18232598-18232599`Back to Tasklist
Branch 24, Designated as
HK.20via cov-lineages/pango-designation@71cf97b ; follow-upS:G482R/G23006Cdesignated asHK.20.1Designated as HK.20 and HK.20.1
_Transferred to cov-lineages/pango-designation#2353_ **Defining Mutations:** `EG.5.1.1` > `C6695T(ORF1a:P2144S)` > `C9448A` > `C5575T, G22927T(S:L455F)` **Query:** `C6695T, C9448A, G22927T` **Earliest seq:** 2023-08-13 (`EPI_ISL_18114870`, Shanghai Customs, travel history to Japan) **Latest seq:** 2023-10-20 (`EPI_ISL_18448529`, Ontario, Canada) **Sampled Countries:** China (13, SH/6; SC/4; FJ/1; ex. Japan/1; ex. S. Korea/1), USA (12: CA/8; AZ/1; OH/1; TX/1; ex. Nepal/1), Singapore (6: Local/5; ex. China/1), Italy (5), UK (3: EN), Australia (2: NSW; QLD), Canada (2: ON), Japan (2), South Korea (2), Switzerland (2), Denmark (1), France (1), Spain (1)Genomes:
`EPI_ISL_18114870, EPI_ISL_18208555, EPI_ISL_18208592, EPI_ISL_18208601, EPI_ISL_18232643, EPI_ISL_18246292, EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192, EPI_ISL_18306956, EPI_ISL_18307066, EPI_ISL_18320793, EPI_ISL_18328004, EPI_ISL_18352555, EPI_ISL_18354001, EPI_ISL_18355023, EPI_ISL_18360344, EPI_ISL_18360616, EPI_ISL_18361723, EPI_ISL_18366403, EPI_ISL_18370066, EPI_ISL_18370200, EPI_ISL_18371411, EPI_ISL_18376528, EPI_ISL_18385607, EPI_ISL_18386446, EPI_ISL_18386489, EPI_ISL_18387133, EPI_ISL_18397207, EPI_ISL_18403093, EPI_ISL_18407761, EPI_ISL_18409112, EPI_ISL_18411495, EPI_ISL_18415804, EPI_ISL_18421982, EPI_ISL_18423702, EPI_ISL_18425050, EPI_ISL_18428715, EPI_ISL_18429030, EPI_ISL_18430106, EPI_ISL_18433978, EPI_ISL_18435244, EPI_ISL_18442967, EPI_ISL_18443714, EPI_ISL_18443742-18443744, EPI_ISL_18443746, EPI_ISL_18444154, EPI_ISL_18446641, EPI_ISL_18448416, EPI_ISL_18448529`Back to Tasklist
Branch 25: Mostly with
S:A684VDefining Mutations: EG.5.1.1 >
C29296T>G22927T(S:L455F)Query:C6541T, G22927T, C29296TEarliest seq: 2023-08-06 (EPI_ISL_18133933, Qinghai) Latest seq: 2023-08-30 (EPI_ISL_18245873, Gansu) Sampled Countries: China (4: SC/2; GS; QH)Genomes:
`EPI_ISL_18133933, EPI_ISL_18245873, EPI_ISL_18246316, EPI_ISL_18246328`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fec3_1b4b0.json?label=id:node_10825408
Back to Tasklist
Branch 26
Transferred to main repo
_Transferred to main repo cov-lineages/pango-designation#2320_ **Defining Mutations:** `HK.11` > `T13228C` > `T4789A` > `G22927T(S:L455F)` **Query:** `T4789A, T13228C, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18221467`, Halland, Sweden) **Latest seq:** 2023-08-21 (`EPI_ISL_18244247`, Denmark) **Sampled Countries:** Denmark (2), Sweden (1)Genomes:
`EPI_ISL_18221467, EPI_ISL_18244233, EPI_ISL_18244247`Back to Tasklist
Branch 27
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2342_ **Defining Mutations:** `EG.5.1.1` > `C25493A(ORF3a:T34K)` > `G28884C(N:G204P)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C25493A` **Earliest seq:** 2023-07-18 (`EPI_ISL_18245992`, Heilongjiang) **Latest seq:** 2023-10-10 (`EPI_ISL_18397223`, Singapore) **Sampled Countries:** China (18: HL/10; LN/2; SH/2; HB; SC; SX; YN), Singapore (14), Denmark (4), Italy (3), USA (3: CA/2; NY), France (2), Australia (1: NSW), Germany (1), South Korea (1), Sweden (1)Genomes:
`EPI_ISL_18138073, EPI_ISL_18232576, EPI_ISL_18244264, EPI_ISL_18245964, EPI_ISL_18245971, EPI_ISL_18245992, EPI_ISL_18246139, EPI_ISL_18246193, EPI_ISL_18282065, EPI_ISL_18300796, EPI_ISL_18306948, EPI_ISL_18306976, EPI_ISL_18306993, EPI_ISL_18307005-18307006, EPI_ISL_18307019, EPI_ISL_18307026, EPI_ISL_18313136, EPI_ISL_18320696, EPI_ISL_18324230, EPI_ISL_18329168, EPI_ISL_18330265, EPI_ISL_18339790, EPI_ISL_18352920, EPI_ISL_18356975, EPI_ISL_18361976, EPI_ISL_18362045, EPI_ISL_18376532, EPI_ISL_18376955, EPI_ISL_18377536, EPI_ISL_18377636, EPI_ISL_18382895, EPI_ISL_18384393, EPI_ISL_18384413, EPI_ISL_18384418, EPI_ISL_18384426, EPI_ISL_18384448, EPI_ISL_18384625, EPI_ISL_18384643, EPI_ISL_18391206-18391207, EPI_ISL_18397223, EPI_ISL_18397241, EPI_ISL_18397267, EPI_ISL_18397584, EPI_ISL_18401938, EPI_ISL_18405209, EPI_ISL_18406218`Back to Tasklist
Branch 28
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2398_ **Defining Mutations:** **EG.5.1.1** > `C5812T` > `G22927T(S:L455F)`, mostly with >> `A26565C(M:K15Q), C28770G(N:T166R)` **Query:** `C5812T, G22927T, C28770G` (for major `A26565C(M:K15Q), C28770G(N:T166R)` sub-branch only) **Earliest seq:** 2023-08-09 (`EPI_ISL_18214077`, South Korea) **Latest seq:** 2023-11-09 (`EPI_ISL_18547984`, Nevada, USA) **Sampled Countries:** South Korea (68), USA (5: NV/2; NC/1; ex. S. Korea/2), Australia (2: NSW; QLD), China (2: SC/1; ex. S. Korea/1), Denmark (2), Hungary (2), Finland (1), Japan (1)Genomes:
`EPI_ISL_18214077, EPI_ISL_18236938, EPI_ISL_18293068, EPI_ISL_18293497, EPI_ISL_18347905, EPI_ISL_18353940, EPI_ISL_18354370, EPI_ISL_18354403, EPI_ISL_18355265, EPI_ISL_18355547, EPI_ISL_18368528, EPI_ISL_18382157, EPI_ISL_18382304, EPI_ISL_18382505, EPI_ISL_18382615, EPI_ISL_18386641, EPI_ISL_18408701-18408702, EPI_ISL_18408814, EPI_ISL_18408878, EPI_ISL_18411301, EPI_ISL_18415920, EPI_ISL_18435710, EPI_ISL_18438964, EPI_ISL_18439203, EPI_ISL_18439262-18439263, EPI_ISL_18439368, EPI_ISL_18439436, EPI_ISL_18460639, EPI_ISL_18460726, EPI_ISL_18460826, EPI_ISL_18461023, EPI_ISL_18461030, EPI_ISL_18461109, EPI_ISL_18461117, EPI_ISL_18461139, EPI_ISL_18488790, EPI_ISL_18488878, EPI_ISL_18488904, EPI_ISL_18489119, EPI_ISL_18501908, EPI_ISL_18502007, EPI_ISL_18503617, EPI_ISL_18503624, EPI_ISL_18503755, EPI_ISL_18503952, EPI_ISL_18503974, EPI_ISL_18511170, EPI_ISL_18511222, EPI_ISL_18511248, EPI_ISL_18511257, EPI_ISL_18511484, EPI_ISL_18513699, EPI_ISL_18518361, EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535643-18535644, EPI_ISL_18535683, EPI_ISL_18539076, EPI_ISL_18539319, EPI_ISL_18539641, EPI_ISL_18539827, EPI_ISL_18540358, EPI_ISL_18544082, EPI_ISL_18547609, EPI_ISL_18547984, EPI_ISL_18550336, EPI_ISL_18552522, EPI_ISL_18559930, EPI_ISL_18564453, EPI_ISL_18564477, EPI_ISL_18564533, EPI_ISL_18564565, EPI_ISL_18564603, EPI_ISL_18564701, EPI_ISL_18564813, EPI_ISL_18564892, EPI_ISL_18564897, EPI_ISL_18565136`Back to Tasklist
Branch 29
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C16726T(ORF1b:H1087Y)` > `G9424T, A12472G, G22927T(S:L455F), T23030C(**S:F490P**), G27621T(ORF7a:Q76H)` **Query:** `A12472G, G22927T, G27621T` **Earliest seq:** 2023-08-25 (`EPI_ISL_18245860`, Fujian, China) **Latest seq:** 2023-09-06 (`EPI_ISL_18243501`, Singapore) **Sampled Countries:** Singapore (2), China (1, FJ)Genomes:
`EPI_ISL_18243491, EPI_ISL_18243501, EPI_ISL_18245860`Back to Tasklist
Branch 30
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C4423T` > `G22927T(S:L455F)` **Query:** `C4423T, G13627A, G22927T` **Earliest seq:** 2023-08-12 (`EPI_ISL_18246284`, Sichuan, China) **Latest seq:** 2023-08-25 (`EPI_ISL_18235973`, Chiba, Japan) **Sampled Countries:** China (2, SC), Japan (1)Genomes:
`EPI_ISL_18232772, EPI_ISL_18235973, EPI_ISL_18246284`Back to Tasklist
Branch 31
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2321_ **Defining Mutations:** **EG.5.1.1** > `C12020T(ORF1a:L3919F), T24496C` > `C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)` **Query:** `C6541T, C12020T, G22927T, -G6337T, -C8982A, -G18445A, -C28087T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18216560`, Galway, Ireland) **Latest seq:** 2023-09-04 (`EPI_ISL_18254216`, Hubei) **Sampled Countries:** China (1), Ireland (1), UK (1)Genomes:
`EPI_ISL_18216560, EPI_ISL_18244531, EPI_ISL_18254216`Back to Tasklist
Branch 32
Defining Mutations: EG.5.1.1 >
T4579A>G2329A, A8443G>G22927T(S:L455F)Query:T4579A, A8443G, G22927TEarliest seq: 2023-08-08 (EPI_ISL_18166186, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18254268, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18166186, EPI_ISL_18232746, EPI_ISL_18245861, EPI_ISL_18246325, EPI_ISL_18254268`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_647e_1a2900.json?label=id:node_6956460
Back to Tasklist
Branch 33
Designated as EG.5.1.19
_Designated as **EG.5.1.19** via cov-lineages/pango-designation@0807c23 , after transferred to cov-lineages/pango-designation#2322_ **Defining Mutations:** **EG.5.1** > `T26171A(ORF3a:M260K)` > `A17615G(ORF1b:K1383R), G22927T(S:L455F)` **Query:** `G21718T, G22927T, T26171A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18134871`, Daknam, Belgium) **Latest seq:** 2023-09-03 (`EPI_ISL_18252041`, `SEA` airport, Washington, with travel hisotry: Netherlands) **Sampled Countries:** Belgium (1), France (1), Romania (1), USA (1, ex. Netherlands)Genomes:
`EPI_ISL_18134871, EPI_ISL_18229094, EPI_ISL_18252041, EPI_ISL_18254718`Back to Tasklist
Branch 34, NOT FLip but with
S:L455SDefining Mutations: EG.5.1.3 >
G2946A(ORF1a:G894D), T15264C, T22926C(S:L455S)Query:C1889T, C2334T, T22926C, -A4340G, -A10703CEarliest seq: 2023-07-27 (EPI_ISL_18248425, Zagreb, Croatia) Latest seq: 2023-07-31 (EPI_ISL_18248430, Zagreb, Croatia) Sampled Countries: Croatia (4)Genomes:
`EPI_ISL_18248425, EPI_ISL_18248427, EPI_ISL_18248429-18248430`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ed45_24dab0.json?f_userOrOld=uploaded%20sample&label=id:node_10831638
Back to Tasklist
Branch 35, side-branch to JJ.1
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2354_ **Defining Mutations:** **EG.5.1.4** > `C26111T(ORF3:P240L)` > `C18555T` > `T17268C` > `G22927T(S:L455F)` **Query:** `T17268C, G22927T, C26111T` **Earliest seq:** 2023-08-08 (`EPI_ISL_18132133`, Newfoundland and Labrador) **Latest seq:** 2023-10-23 (`EPI_ISL_18448815`, Ontario, Canada) **Sampled Countries:** Canada (49: ON/22; NL/15; AB/10; BC/1; NS/1), US (7: CA/2; NY/2; AZ/1; UT/1; VA/1), France (1)Genomes:
`EPI_ISL_18132133, EPI_ISL_18256806, EPI_ISL_18258767, EPI_ISL_18258769-18258770, EPI_ISL_18258773, EPI_ISL_18258778, EPI_ISL_18291996, EPI_ISL_18291998, EPI_ISL_18292017, EPI_ISL_18292020-18292022, EPI_ISL_18292026-18292028, EPI_ISL_18333999, EPI_ISL_18344763, EPI_ISL_18357035, EPI_ISL_18372328, EPI_ISL_18372367, EPI_ISL_18383112, EPI_ISL_18383123-18383124, EPI_ISL_18383697, EPI_ISL_18388693, EPI_ISL_18395288, EPI_ISL_18395414, EPI_ISL_18395581, EPI_ISL_18404467, EPI_ISL_18425010, EPI_ISL_18425420, EPI_ISL_18425431, EPI_ISL_18425847, EPI_ISL_18425967, EPI_ISL_18426727, EPI_ISL_18427300, EPI_ISL_18427492, EPI_ISL_18427494, EPI_ISL_18427496, EPI_ISL_18427507, EPI_ISL_18427602, EPI_ISL_18431345, EPI_ISL_18436820, EPI_ISL_18437028, EPI_ISL_18437176, EPI_ISL_18438632, EPI_ISL_18438777, EPI_ISL_18448237, EPI_ISL_18448584-18448585, EPI_ISL_18448588, EPI_ISL_18448699-18448700, EPI_ISL_18448702, EPI_ISL_18448740, EPI_ISL_18448815`Back to Tasklist
Branch 36
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2399_ **Defining Mutations:** **EG.5.1.1** > `C22388T(S:L276L)` > `G22927T(S:L455F)`, mostly with >> `C1853T` sub-branch **Query:** `C1853T, G13627A, G22927T, -C4780T, -C5031T, -C6627T, -C8982A` (for major `C1853T` sub-branch only) **Earliest seq:** 2023-08-14 (`EPI_ISL_18224087`, Colorado, USA) **Latest seq:** 2023-11-20 (`EPI_ISL_18568071`, `SEA` airport, travel history: France) **Sampled Countries:** France (20), Norway (12), Germany (11), Switzerland (8), USA (6: CO/2; ex. France/2; ex.Germany/2), UK (4: EN), China (3: XJ/2; FJ/1), Denmark (3), Ukraine (3), Canada (2: NB; ON), Finland (2), Spain (2), Belgium (1), Italy (1), Japan (1), Singapore (1)Genomes:
`EPI_ISL_18224087, EPI_ISL_18224096, EPI_ISL_18233134, EPI_ISL_18239749, EPI_ISL_18263561, EPI_ISL_18263571, EPI_ISL_18263574, EPI_ISL_18263576, EPI_ISL_18272601-18272602, EPI_ISL_18280654, EPI_ISL_18280813, EPI_ISL_18290994, EPI_ISL_18291008, EPI_ISL_18291011, EPI_ISL_18308259, EPI_ISL_18313749, EPI_ISL_18326424, EPI_ISL_18326608, EPI_ISL_18327645, EPI_ISL_18337648, EPI_ISL_18337651, EPI_ISL_18338378, EPI_ISL_18373487, EPI_ISL_18373856, EPI_ISL_18380089, EPI_ISL_18380091, EPI_ISL_18388662, EPI_ISL_18388711, EPI_ISL_18411952, EPI_ISL_18412072, EPI_ISL_18421745, EPI_ISL_18421949, EPI_ISL_18428144, EPI_ISL_18428460, EPI_ISL_18428992, EPI_ISL_18433011, EPI_ISL_18441991, EPI_ISL_18451507, EPI_ISL_18464584, EPI_ISL_18464947, EPI_ISL_18468968, EPI_ISL_18476770, EPI_ISL_18485554, EPI_ISL_18486361, EPI_ISL_18486756, EPI_ISL_18493947, EPI_ISL_18494748, EPI_ISL_18495920, EPI_ISL_18496297, EPI_ISL_18496628, EPI_ISL_18496636, EPI_ISL_18496703, EPI_ISL_18499460, EPI_ISL_18505686, EPI_ISL_18505750, EPI_ISL_18519177-18519178, EPI_ISL_18525816, EPI_ISL_18530654, EPI_ISL_18530657-18530658, EPI_ISL_18530757, EPI_ISL_18530938, EPI_ISL_18530967, EPI_ISL_18538000, EPI_ISL_18540615, EPI_ISL_18540768, EPI_ISL_18540871, EPI_ISL_18540915, EPI_ISL_18544152, EPI_ISL_18552615, EPI_ISL_18553571, EPI_ISL_18556840, EPI_ISL_18568060, EPI_ISL_18568071, EPI_ISL_18568733-18568735, EPI_ISL_18570228`Back to Tasklist
Branch 37
⚠
C29095Tbecame homoplastic across the EG.5.1+L455F tree, no longer tracking.No longer tracking
**Defining Mutations:** **EG.5.1.1** > `C29095T` > `G22927T(S:L455F)` **Query:** `G13627A, G22927T, C29095T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18246374`, Sichuan, China) **Latest seq:** 2023-08-31 (`EPI_ISL_18264700`, Texas, USA) **Sampled Countries:** USA (2: TX), China (1: SC)Genomes:
`EPI_ISL_18246374, EPI_ISL_18264482, EPI_ISL_18264700`Back to Tasklist
Branch 38
Defining Mutations: EG.5.1.1 >
T24583C>G22927T(S:L455F)Query:C6541T, G22927T, T24583CEarliest seq: 2023-08-03 (EPI_ISL_18166149, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18268462Shanghai) Sampled Countries: China (3: SC/2; SH/1)Genomes:
`EPI_ISL_18166149, EPI_ISL_18232692, EPI_ISL_18268462`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f9a8_5a58c0.json?f_userOrOld=uploaded%20sample&label=id:node_10885352
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
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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
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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
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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