Open FedeGueli opened 3 weeks ago
19522299, LP.8 from Taiwan, it has mutations of both B1 and B2(M153I,L176F,A475V, R190S). Likely B2 getting R190S convergently.
EPI_ISL_19522303 also gets S:T22N, which is popular recently (seems the first LP.8+S:T22N)
EPI_ISL_19522303 also gets S:T22N, which is popular recently (seems the first LP.8+S:T22N)
Thank you, added to main proposal now. sorry @xz-keg and @HynnSpylor i was concentrated to make an issue that was a minimum readable and forgot to add credits for the sub branches you found, now i have added credits, please check if something more has to be credited pls let me know
By the way with 22N that singlet shows a triple N Glycan N22 N30 N188
57 for Br.1 with samples from Ontario NSW 8 for Br.2 with 2 super recent samples from Hong Kong.
@corneliusroemer i suggest a rapid designation of the two branches. My suggestion is to start Branch 2 from ORF1b:P1452L (C17822T because there is a mini branch from Hong Kong and Australia with it but without 153I and 176F :
Tree updated in the main proposal
BR.1 +2 Rhode Island
Branch 1 designated LP.8.1 via https://github.com/cov-lineages/pango-designation/commit/218759a01875ccbfd331629e36c593e547d86755
Branch 2 designated LP.8.2 via https://github.com/cov-lineages/pango-designation/commit/218759a01875ccbfd331629e36c593e547d86755
Thx @xz-keg for updating the proposal. Thx @DailyCovidCases for spotting the designations
One more LP.8.1+S:K679R seq from Canada, with additional S:P85S.
suggested to alter the Query of K679R to A23598G, G22132T, C22120A (3 seqs)
Also S:P85Q branch in LP.8.2.
LP.8.2 + 475V went to 6 with two GBW from one patient travelling from Thailand
One more LP.8.1+S:K679R seq from Canada, with additional S:P85S.
suggested to alter the Query of K679R to A23598G, G22132T, C22120A (3 seqs)
Many thx updated
LP.8.2 + 475V went to 6 with two GBW from one patient travelling from Thailand with additional S:V622A
Also S:P85Q branch in LP.8.2.
thx added. LP.8 seems flying. cc @corneliusroemer i would designate further LP.8.2 + 475V
It is crazy how fast LP.8 accumulates Spike mutations. In addition to all mentioned above, there are 5 Canadian LP.8.1 seqs with both S:A942T (G24386A) and S:A1087S (G24821T). The latter is next to K1086R, which was introduced already in KP.1
7, California for LB.8.2 + 475V that is growing fast
One Canadian LP.8.2+475V has additional T478E EPI_ISL_19544054
LP.8.1.: 1x Qatar
LP.8.1+679R branch went to 4 adding Australia and Canada LP.8.2+475V went to 8 with Canada (plu 478E as highlighted by @cvejris
Japan vanilla LP.8.1 + 6 seqs, 8 total
LP.8.1+679R branch went to 4 adding Australia and Canada LP.8.2+475V went to 8 with Canada (plu 478E as highlighted by @cvejris
One more LP.8.1+679R from GBW, ex Phillipines
10 for LP.8.1 + 679R 9 for LP.8.2 +475V
@corneliusroemer i suggest to designate it , in HK LP.8 went from around 10% to around 20% last two weeks of October vs November, also looking to older stats in CovSpectrum LP.8 is now showing solid advantage in at least three countries including Australia.
10 for LP.8.1 + 679R 9 for LP.8.2 +475V
@corneliusroemer i suggest to designate it , in HK LP.8 went from around 10% to around 20% last two weeks of October vs November, also looking to older stats in CovSpectrum LP.8 is now showing solid advantage in at least three countries including Australia.
Agree. Of note, the sporadically appearing A475V in LP.8.1 are convergent. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_22d79_f06e00.json?branchLabel=Spike%20mutations&c=gt-S_475,679&f_userOrOld=uploaded%20sample&gmax=25384&gmin=21563&label=id:node_2547213
Also convergent is furin-adjacent S:Q677H, one seq in each LP.8.1 and LP.8.2 (see tree above)
LP.8.1+S:A475V(C22986T)+S:P217L(C22212T)+S:A653V(C23520T)+S:NK679R(A23598G): 3x Canada BC One has to love LP.8, it´s just unhinged.
The other 5 seqs from lates Canada BC upload are: LP.8.1+G1462A+C6927T(ORF1a:P2221L)+S:NK679R(A23598G)+Orf3a:T89I(C25658T)
C22986T)+S:P217L(C22212T)+S:A653V(C23520T
thx i m checking adding these branches @cvejris
Added and tree now updated as Nov 23
Also convergent is furin-adjacent S:Q677H, one seq in each LP.8.1 and LP.8.2 (see tree above)
there is also a I670M+S680A from Queensland, the apparent success of 679R maybe could point toward a potential "tuning" coming from mutation in the FCS area, but too early to be sure
K679R CA-BC+8
LP.8.2+475V: +1 seq Israel
LP.8.1+S:K679R+S:P85S: 3 more from Canada, ON (one lacks coverage at 85, but is otherwise identical)
LP.8.1+S:K679R+S:P85S: 3 more from Canada, ON (one lacks coverage at 85, but is otherwise identical)
Thx . it is becoming a bit messy this issue. I think we should propose the LP.8.1+679R + Subs on Pango as also the LP.8.2 + 475V and using this for eventually new sublineages. cc @xz-keg @cvejris @HynnSpylor please propose them.
LP.8.1+S:K679R+S:P85S: 3 more from Canada, ON (one lacks coverage at 85, but is otherwise identical)
Thx . it is becoming a bit messy this issue. I think we should propose the LP.8.1+679R + Subs on Pango as also the LP.8.2 + 475V and using this for eventually new sublineages. cc @xz-keg @cvejris @HynnSpylor please propose them.
With S:P217L,A475V,A653V and S:P85S sublineages of LP.8.1+K679R, I think we should wait once (if) they spread outside Canada.
LP.8 has been designated from https://github.com/cov-lineages/pango-designation/issues/2811
It has two main branches:
Branch 1, Designated LP.8.1 found by @xz-keg LP.8 >> S:R190S (G22132T) Query for LP.8.1: C23039G,C4999T,G22132T,C25925T,-22088 (by @aviczhl2 ) Samples: 174 Places: Including Philippines (GBW)
LP.8.1 + 679R >> S:P217L,A475V,A653V LP.8.1 >> T5122C, ORF1a:L3667F (G11266T), ,Orf1a:T2846I (C8802T),Orf1b:V1649I (G18412A), S:K679R (A23598G), N:A152V (C28728T) >> S:P217L (C22212T), S:A475V (C22986T), S:A653V (C23520T) Query for LP.8.1 + 679R: A23598G, G22132T, C22120A [new by @xz-keg (old: T5122C, G11266T,C8802T)] Samples: 20 Singapore, Canada,Australia, New Zealand , Philippined with a sub branch found by @cvejris with S:P217L,S:A475V,S:A653V* Query for 679R,217L,475V,653V: C22212T,C22986T, C23520T Samples: 3 British Columbia
LP.8.1 +475V found by @HynnSpylor LP.8.1>> C13536T > T23407C (S:V615V) > S:A475V (C22986T) Query for LP.8.1+ 475V : C13536T , T23407C,C22986T Samples: 2 Singapore
LP.8.1 + T22N found by @HynnSpylor [ Triple N Glycan N22 N30 N188 ] LP.8.1 > S:T22N (C21627A),A28792T Query for LP.8.1+ 22N : A28792T,C21627A,G1954A Samples: 1 Taiwan infected while traveling
Branch 2, Designated LP.8.2 LP.8 >> ORF1b:P1452L (C17822T) > S:M153I (G22021C),S:L176F (C22088T) Query for LP.8.2:C17822T, G22021C ,C22088T Samples: 17 Countries: US-2 States, Israel, Singapore, Taiwan, Italy, Thailand, Hong Kong, South Korea, Canada
LP.8.2 + 475V LP.8.2 >> Orf1a:T1246I (C4002T), S:A475V (C22986T) Query for LP.8.2 + 475V : C4002T,22986T, G22021C Samples: 10 Places: Singapore, NY,Minnesota, Taiwan, Hong Kong, Thailand, California, Canada (with 478E by @cvejris ),Israel
LP.8.2 + 475V +190S found by @xz-keg LP.8.2 >> Orf1a:T1246I (C4002T), S:A475V (C22986T)> ORF1a:S984G (A3215G), T10771C, S:R190S (G22132T), C23896T,G29781C Query for LB.8.2 +475V + 190S : A3215G, T10771C Samples: 1 Places: Taiwan
LP.8.2 + S:P85Q found by @xz-keg LB.8.2 >> ORF1b:A373V (T12283C),C14585T, S:P85Q (C21816A), G29260A
Query for LB.8.2 +85Q: T12283C,C14585T, C21816A Samples: 3 Places: South Korea, NY, Virginia
Tree updated as of November 23:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_25759_181e30.json?label=id:node_7406712