sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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Spike diversity: LP.8.1 and LP.8.2 #2199

Open FedeGueli opened 3 weeks ago

FedeGueli commented 3 weeks ago

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:

Screenshot 2024-11-23 alle 08 49 44 Screenshot 2024-11-23 alle 08 49 58 Screenshot 2024-11-23 alle 08 50 15

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_25759_181e30.json?label=id:node_7406712

xz-keg commented 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.

HynnSpylor commented 3 weeks ago

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

FedeGueli commented 3 weeks ago

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 commented 3 weeks ago

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

FedeGueli commented 2 weeks ago

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 :

Screenshot 2024-11-06 alle 12 51 58
FedeGueli commented 2 weeks ago

Tree updated in the main proposal

FedeGueli commented 2 weeks ago

BR.1 +2 Rhode Island

DailyCovidCases commented 2 weeks ago

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 commented 2 weeks ago

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

xz-keg commented 2 weeks ago

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 commented 2 weeks ago

Also S:P85Q branch in LP.8.2.

image

FedeGueli commented 2 weeks ago

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

FedeGueli commented 2 weeks ago

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 commented 2 weeks ago

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

FedeGueli commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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

cvejris commented 1 week ago

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

cvejris commented 1 week ago

LP.8.1.: 1x Qatar

FedeGueli commented 1 week ago

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 commented 1 week ago

Japan vanilla LP.8.1 + 6 seqs, 8 total

cvejris commented 1 week ago

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 commented 6 days ago

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 commented 5 days ago

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 commented 5 days ago

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

cvejris commented 4 days ago

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 commented 4 days ago

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

FedeGueli commented 3 days ago

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

thx i m checking adding these branches @cvejris

Added and tree now updated as Nov 23

FedeGueli commented 3 days ago

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 commented 3 days ago

K679R CA-BC+8

cvejris commented 2 days ago

LP.8.2+475V: +1 seq Israel

cvejris commented 1 day ago

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

FedeGueli commented 1 day ago

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 commented 23 hours ago

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.