Spike diversity: LP.8.1 and LP.8.2

[FedeGueli]

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

[xz-keg]

19522299, LP.8 from Taiwan, it has mutations of both B1 and B2(M153I,L176F,A475V, R190S). Likely B2 getting R190S convergently.

[HynnSpylor]

EPI_ISL_19522303 also gets S:T22N, which is popular recently (seems the first LP.8+S:T22N)

[FedeGueli]

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

[FedeGueli]

By the way with 22N that singlet shows a triple N Glycan N22 N30 N188

[FedeGueli]

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 :

[FedeGueli]

Tree updated in the main proposal

[FedeGueli]

BR.1 +2 Rhode Island

[DailyCovidCases]

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

[FedeGueli]

Thx @xz-keg for updating the proposal. Thx @DailyCovidCases for spotting the designations

[xz-keg]

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)

[xz-keg]

Also S:P85Q branch in LP.8.2.

[FedeGueli]

LP.8.2 + 475V went to 6 with two GBW from one patient travelling from Thailand

[FedeGueli]

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

[FedeGueli]

LP.8.2 + 475V went to 6 with two GBW from one patient travelling from Thailand with additional S:V622A

[FedeGueli]

Also S:P85Q branch in LP.8.2.

thx added. LP.8 seems flying. cc @corneliusroemer i would designate further LP.8.2 + 475V

[cvejris]

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

[FedeGueli]

7, California for LB.8.2 + 475V that is growing fast

[cvejris]

One Canadian LP.8.2+475V has additional T478E EPI_ISL_19544054

[cvejris]

LP.8.1.: 1x Qatar

[FedeGueli]

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

[cvejris]

Japan vanilla LP.8.1 + 6 seqs, 8 total

[cvejris]

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

[FedeGueli]

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.

[cvejris]

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

[cvejris]

Also convergent is furin-adjacent S:Q677H, one seq in each LP.8.1 and LP.8.2 (see tree above)

[cvejris]

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.

[cvejris]

The other 5 seqs from lates Canada BC upload are: LP.8.1+G1462A+C6927T(ORF1a:P2221L)+S:NK679R(A23598G)+Orf3a:T89I(C25658T)

[FedeGueli]

C22986T)+S:P217L(C22212T)+S:A653V(C23520T

thx i m checking adding these branches @cvejris

Added and tree now updated as Nov 23

[FedeGueli]

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

[Over-There-Is]

K679R CA-BC+8

[cvejris]

LP.8.2+475V: +1 seq Israel

[cvejris]

LP.8.1+S:K679R+S:P85S: 3 more from Canada, ON (one lacks coverage at 85, but is otherwise identical)

[FedeGueli]

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.

[cvejris]

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.