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Spike diversity: LP.8.1 and LP.8.2 (updated as of Jan 27) #2199

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FedeGueli opened this issue Nov 3, 2024 · 215 comments
Open

Spike diversity: LP.8.1 and LP.8.2 (updated as of Jan 27) #2199

FedeGueli opened this issue Nov 3, 2024 · 215 comments

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@FedeGueli
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FedeGueli commented Nov 3, 2024

LP.8 has been designated from cov-lineages/pango-designation#2811
@xz-keg made a model on future mutations: LP.8.1 predicted spike diversity(training data before 10-01): S:A688V, S:A475V, S:T22N, S:Q677H, S:H49Y, S:G257S.

LP.8 has two main branches:

Tracked Branches

LP.8.1

LP.8.1.6 + 679R found by @cvejris
Query for 679R : A9328G,23598G
Samples: 2 ( 1 with this query)Australia, Taiwan

LP.8.1.6 + 475V found by @cvejris
Query for 475V:G27604T,C22986T,C1221T,
Samples: 1 Delaware

LP.8.1.6 + 478E
LP.8.1.6 >> A9328G > A14850G, , S:K478E (A22994G), ORF3a:G49V (G25538T), ORF3a:L94F (C25672T), ORF8:V5F
Query: A9328G ,A14850G
Samples: 1 Denmaark

**LP.8.1.7 (Orf1b:V980I ,Orf10:Q29stop) + S:A475V(IV)**now proposed in #2220

Query:T28582C, C29642T,22986T
Samples:10 (Aus,Virginia,NY,NZL,Spain, Israel,Philippines)

LP.8.1.8 + S:A475V(V)
LP.8.1.8 [N:A134V (C28674T)]> T12247C, ORF1b:L80S (T13706C), T19896G,S:A475V (C22986T),N:Q242L(A28998T)
Query:T12247C, T13706C, T19896G
Samples: 23 Ontario (Cluster)

LP.8.1 + S:N477D by @cvejris
LP.8.1 > Orf1a:S944L (C3096T),Orf1b:S997P (T16456C),S:19-20del(21617-21622), S:N477D (A22991G)
Query:C3096T, 22991G,T16456C
Samples:1 (Sweden)

LP.8.1 + S:T500A
LP.8.1 >> ORF1a:Q985K (C3218A),ORF1b:T1274I (C17288T), C18654T, S:T500A(A23060G), T28067C
Query:C3218A,C17288T,T3565C
Samples: 2 Canada

LP.8.1 + S:I68T + S:S256L found by @cvejris
LP.8.1 >> G29706A > C11986T, T14313C S:I68T (T21771C),S:S256L (C22329T)
Query:G29706A,T21771C,C22329T
Samples:3 (Singapore)

LP.8.1.8 + S:K478E (I) found by @cvejris
LP.8.1.8 [N:A134V (C28674T)] > S:K478E (A22994G)
Query: C28674T,A22994G,C22120A
Samples:2 HK

LP.8.1 + S:K478E (II)
LP.8.1 >> Orf1a:H110Y (C593T), C829T, Orf1a:E553K (G1922A), Orf1b:G977S (G16396A), C17733T, S:K478E (A22994G)
Query: C829T, C17733T,G1922A (NEW edited)
Samples: 4 Philippines,US

LP.8.1 + S:K478E (III)
LP.8.1 >> N:T362I (C29358T) > ORF1a:T4302I (C13170T), G17562A, S:K478E (A22994G), T24850C,ORF3a:L101I (C25693A), T26777C, N:A155V(C28737T)
Query:G17562A, C25693A, T26777C
Samples: 1 Philippines

LP.8.1.5 (Orf1a:K3353R) + S:K679R (I) [Note this could be also seen as sublineage of LP.8.1.1>Orf1a:K3353R]
LP.8.1.5>> Orf1a:K3353R (A10323G) > S:K679R (A23598G)
Query: A10323G,A23598G,G1954A,-C829T
Samples: 3 Canada,Singapore ,Italy
found by @cvejris

LP.8.1.5 (Orf1a:K3353R) + S:K679R (II)
LP.8.1.5>> Orf1a:K3353R (A10323G) > C18744T > C829T, G1186A, S:K679R (A23598G)
Query:C829T, G1186A, T3565C
Samples: 1 Taiwan

LP.8.1 + Orf1a:T999I + S:K679R (III) found by @cvejris
LP.8.1>> Orf1a:T999I (C3261T), S:K679R (A23598G)
Query: C25925T,23598G, C3261T
Samples: 2 ( 9 ON USHER) Canada, England, US

LP.8.1 + S:S680F spotted by @cvejris
LP.8.1 >> C13536T > T23407C > S:S680F (C23601T), C26735T
Query: T23407C, C23601T, C26735T
Samples: 12 Singapore

LP.8.1 + S:K481Q found by @cvejris
LP.8.1 >> C27630T > C20133T, T28918C > C4331T, T5779C,C10778T,T16224C, S:K481Q(A23003C), M:H155Y(C26985T), ORF7a:T28I (C27476T), C29762T
Query:23003C,C20133T, T28918C
Samples:1 Singapore

LP.8.1.5 + S:A435S
LP.8.1.5 (Orf1a:K3353R) > T3028C, T6880C, T14787C, S:A435S (G22865T)
Query:T3028C, T6880C, T3565C Samples: 1 Philippines

LP.8.1 + S:G476S
LP.8.1> T3124C > S:G476S (G22988A)
Query: 22988A, T3124C
Samples: 1 Aus

LP.8.1 + S:S680A
LP.8.1 > S:S680A (T23600G)
Query: T23600G,G22132T,C22120A
Samples: 7
Places : 7

LP.8.1.4 + S:A522P found by @cvejris and @HynnSpylor
LP.8.1.4 [C16308T] > S:A522P (G23126C), C27128T
Query: G23126C, C27128T
Samples: 12
with a putatitve S:L452R sample (could be artifact) to be checked

LP.8.1 + S:D287E
LP.8.1 >> G4255A > C8320T, Orf1b:T284I (C14318T), S:D287E (T22423A)
Query: G4255A , C8320T, C14318T
Samples: 1 California

LP.8.1.1

NY.2 + 475V (II) found by @cvejris
NY.2 [Orf1a:T2846I (C8802T)] > S:A475V (C22986T), Orf7a:t28I (C27476T), N:L230F(C28961T)
Query: C28961T ,C22986T, C27476T
Samples: 15 British Columbia (CLUSTER)

NY.5 + 475V. (III) found by @cvejris
NY.5 [ORF1a:F843Y (T2793A)] > C21736T > A142T, C14220T, S:A475V (C22986T)
Query:T2793A, C14220T,C4999T
Samples: 6 US (2 states)

LP.8.1.1 + S:N487D found by @cvejris
LP.8.1.1 >>C14235T> S:N487D (A23021G)
Query: A23598G,C14235T,A23021G
Samples: 1 Singapore

LP.8.1.1 + S:N487D (II) found by @cvejris
LP.8.1.1 > Orf1a:S994N (G3246A), N:A173V (C28791T) > S:N487D (A23021G)
Query: G3246A,C28791T
Samples: 7 NY,MN, Illinois, Philippines ( this has dropout at 487 , very likely having it), Singapore

LP.8.1.1 + S:K478E (III) found by @cvejris
LP.8.1.1 > S:K478E (A22994G),
Query: ,22994G,A23598G,C25925T,-A11923G,-C7521T,-C14235T
Samples: 4 Singapore,Australia, Canada

NY.4 + S:A344T found by @cvejris
NY.4 [ Orf1b:V1649I (G18412A)] > S:A344T (G22592A), C29762T
Query:G18412A,G22592A, C29762T
Samples: 1 Singapore

LP.8.1.1 + S:L335F
LP.8.1.1 >> C23638T > S:L335F (G22567C), T22846C, G26951C
Query:G22567C ,T22846C, G26951C
Samples:1 Minnesota

LP.8.1.1 + S:P384S
LP.8.1.1 >> Orf3a:Q213K (C26029A) > C21646T, S:P384S (C22712T), C27429T,N:D288N (G29135A)
Query:C21646T, C22712T, C27429T
Samples: 1 Australia

LP.8.1.1 + S:F32L + S:A672V by @cvejris
LP.8.1.1 >> C29545T > ORF1a:T2836I (C8772T), ORF1b:T1336I (C17474T), S:F32L (C21658G), T22156C,S:A672V (C23577T) ,Orf3a:L106F(C25708T), C29485T
Query:C21658G,C23577T
Samples: 7 British Columbia (CLUSTER)

LP.8.1.1 + S:N477D (I)
LP.8.1.1>> T11104C ,S:S>N477D (A22991G)
Query:T11104C ,A22991G
Samples: 1 South Korea

LP.8.1.1 + S:N477D (II) found by @cvejris
LP.8.1.1. > Orf3a:L106F(C25708T) > Orf1a:E933G (A3063G) > S:N477D (A22991G)
Samples: 2 Canada

LP.8.1.1 + S:R214H
LP.8.1.1 > C4021T, T9352C, ORF1a:A4642V (C14189T) , C26313T > C7834T, T10423C, Orf1a:L3808F (C11687T), S:R214H (G22203A)
Query: C26313T ,C7834T, T10423C
Samples: 6
10 Iowa, Colorado, Ohio, Ontario

NY.4+ S:G476S (spotted by @cvejris)
NY.4 [ Orf1b:V1649I (G18412A)] > S:G476S (G22988A),Orf8:V62L (G28077T)
Query:G22988A, G28077T,G18412A
Samples: 2 Philippines (GBW)

LP.8.1.1 + S:A67V
LP.8.1.1 >> S:A67V (C21762T)
Query:C21762T,G22132T, C22120A
Query: 4 England, California,US-CT, Japan

LP.8.1.1 + S:S446N found by @cvejris
LP.8.1.1 >> ORF1a:Q3777R (A11595G), S:S446N (G22899A)
Query: A11595G, 22899A,t3565C
Samples: 1
Canada

LP.8.1.1 + S:I434V by @cvejris
LP.8.1.1>> Orf1a:I2286T (T7122C), S:L5F (C21575T), S:I434V (A22862G )
Query: C22120A,A22862G
Samples: 2 Ohio,NY

LP.8.1.1 + S:N185D
Lp.8.1.1 >> S:N185D (A22115G)
Query: A22115G,C22120A,G22132T
Samples: 3 Scotland

LP.8.1.1 + S:N148T
LP.8.1.1 > S:N148T (A22005C)
Query: A22005C,23598G,C25925T,C22120A
Samples: 2 Canada

LP.8.1.1 + S:N370D
LP.8.1.1 >> T2896C, C18807T, S:N370D (A22670G)
Query:C18807T,A22670G
Samples: 1 NZL

LP.8.1.1 + S:R357K
LP.8.1.1 > C25708T,A3063G, A22991G, Orf1b:S1159G (C19269T), N:P383S (C29420T) > S:R357K (G22632A)
Query: C19269T,C29420T,G22632A
Samples: 1 NZL

NY.1 +S:K478E
A1124G, C5365T, C19017T
Samples: 1 Jap

NY.1 + S:T500A found by @cvejris
Query for T500A branch: C6968T, A23060G, C23683T
Samples:1 Singapore

NY.2 + S:M177I
NY.2 [Orf1a:T2846I (C8802T)] > Orf1a:V2930I (G9053A)S:M177I (G22093A)
Query:
Samples: 1 HK

NY.3 + 478E
S:T478E branch (II) Query: T5278C, A11923G,T3565C
Samples: 3 California, Philippines, NY

NY.6 +S:N237K
Query: C5339T,G22272A,C22986T
Samples: 2 Ohio

LP.8.1.2

DESIGNATED BRANCHES

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: 2008
Places: Including Philippines (GBW)

LP.8.1 + 679R now designated LP.8.1.1

Now proposed in cov-lineages/pango-designation#2834
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.8.1.1: EDITED: A23598G, G22132T, C22120A,-A10323G,-C3261T,-A9328G [old by @xz-keg : A23598G, G22132T, C22120A]
Samples: 669 Singapore, Canada,Australia, New Zealand , Philippines

LP.8.1 + S:N487D now designated LP.8.1.2

LP.8.1>> C23191T > T3814C, S:N487D (A23021G),
Query: A23021G,C25925T,T3565C,-C14235T (NEW) T3814C, A23021G (old query)
Samples: 63 (Australia: NSW, WA), GBW (Japan),California
Tree

LP.8.1.2+S:A1174V Now designated NW.1

LP.8.1.2 >> S:A1174V (C25083T), Orf3a:L101F (C25693T)
Query:C25083T,C25693T,C22120A
Samples: 18
Places: Australia-WA, Canada-BC,Singapore,Japan, Ireland, California,Colorado , HK

LP.8.1 + S:Q677H now Designated LP.8.1.3

proposed in cov-lineages/pango-designation#2876
found first by @cvejris
LP.8.1>> S:Q677H (G23593T)
Query: G23593T,C4999T,G1954A,T3565C
Samples: 24
Places: Netherlands, US (3 states), Japan, France, Denmark,Singapore

LP.8.1 + T22N Designated LP.8.1.6

Now proposed in cov-lineages/pango-designation#2868
found by @HynnSpylor [ Triple N Glycan N22 N30 N188 ]
LP.8.1 > S:T22N (C21627A),A28792T
Query for LP.8.1+ 22N : C4999T,G22132T,C25925T,C21627A,-C4809T (new , added a -s to exclude a recomb)
Samples: 42 Japan, France, Thailand (via Japan), US, Taiwan , Spain,HK

LP.8.1 + S:A475V (II) Now Designated LP.8.1.9

now proposed in cov-lineages/pango-designation#2853
LP.8.1 >> S:A475V (C22986T)
Query: C22120A, G22132T, T22896G, C22986T, A24819G, -A23598G, -G16405A, -A10323G, -C1221T, -C4927T,-T12247C,-C13536T,-C7420T,-T8803C,-C5628T,-A3215G (NEW)
Samples: 36
Places: 7

LP.8.1.1 + S:P85S Now designated NY.1

now proposed in cov-lineages/pango-designation#2861
LP.8.1.1 >> C14235T > S:P85S (C21815T)
Query: C14235T,C21815T,T3565C
Samples:53
Places: Canada, US,Japan,Singapore,Taiwan(GBW),Australia

LP.8.1.1 + S:R765L Designated NY.3

now proposed in cov-lineages/pango-designation#2874
found by @cvejris
LP.8.1.1 >> S:R765L(G23856T)
Query:G23856T,A23598G, G22132T
Samples: 24 HK,Canada,US- 4 States, Philippines (GBW) , Singapore, South Korea, NZL

LP.8.1.1 + 475V (I) Now Designated NY.6

now proposed in cov-lineages/pango-designation#2872
found by @cvejris
LP.8.1.1 >> S:A475V (C22986T)
Query for LP.8.1.1 + 475V: C22986T, A23598G,C22120A,-C21736T,-C8802T,
[ Old queries C22986T,A23598G,G22132T or C22986T,A23598G, 4999T,C22120A ]
Samples: 17
Places:Canada , Philippines (2 GBW), Spain (1 not caught by the query),US, Japan , Denmark

LP.8.1.1 + S:T22N now designated NY.7

[ Originally tracked as second branch of LP.8.1+ 22N + 679R ]
Query: A23598G,C21627A,del21653,-A9328G,
Samples: 10

Designated LP.8.2
LP.8 >> ORF1b:P1452L (C17822T) > S:M153I (G22021C),S:L176F (C22088T)
Query for LP.8.2:C17822T, G22021C ,C22088T
Samples: 4
Countries: US-2 States, Israel, Singapore, Taiwan, Italy, Thailand, Hong Kong, South Korea, Canada, Israel

LP.8.2 + 475V (I). Now designated LP.8.2.1
LP.8.2 >> Orf1a:T1246I (C4002T), S:A475V (C22986T)
Query for LP.8.2 + 475V : C4002T,22986T, G22021C
Samples: 23
Places: Singapore, NY,Minnesota, Taiwan, Hong Kong, Thailand, California, Canada (with 478E by @cvejris ),Israel, Brazil, Norway

Apparent dead sub-branches

Dead

LP.8.2.1 +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 LP.8.2.1 + 190S : A3215G, T10771C
Samples: 1
Places: Taiwan

Dead

LP.8.2 + S:P85Q found by @xz-keg
LP.8.2 >> ORF1b:A373V (T12283C),C14585T, S:P85Q (C21816A), G29260A
Query for LP.8.2 +85Q: T12283C,C14585T, C21816A
Samples: 3
Places: South Korea, NY, Virginia

Dead

LP.8.2 + 475V (II) found by @cvejris
LP.8.2>> A3046G, C8438T > ORF1a:Q2660L (A8244T),S:A475V (C22986T), C27002T
Query: A8244T , C27002T
Samples: 1
Places: Australia

Dead

LP.8.1 + S:A222S found by @cvejris
LP.8.1 >> Orf1aT1093I (C3543T), Orf1b:I2525V (A21040G)> T769C, S:A222S (G22226T), C27247T
Query: T769C, G22226T ,C27247T
Samples: 2 (Italy)

Dead

LP.8.1 + S:L1049I by @cvejris
LP.8.1 >C11200T, T14034C, C14184T, C29077T >> S:L1049I(C24707A)
Query:C11200T, C29077T,C24707A,T3565C
Samples: 2 (Japan,Gbw)

Dead

further sub branch with S:A653V, S:P217L
Query for LP.8.1.1+475V+ ,217L,653V: C22212T, C22986T, C23520T
Samples: 3 British Columbia

DEAD

LP.8.1 +475V (I) found by @HynnSpylor
LP.8.1>> C13536T > T23407C (S:V615V) > S:A475V (C22986T)
Query for LP.8.1+ 475V : C13536T , T23407C,C22986T
Samples: 4 Singapore

Dead

LP.8.1 + S:A475V (III)
LP.8.1 >> C4927T, C19164T, C24442T, C27513T > S:T299I (C22458T) S:A475V (C22986T), S:S680F (C23601T)
Query: C24442T, C27513T ,C23601T
Samples: 1 (Netherlands)

Dead

LP.8.1.8+ S:Q52H
LP.8.1.8 [N:A134V (C28674T)] > S:Q52H( G21718T), T25773G
Query: G21718T, T25773G
Samples: 2 Nevada

DEAD

LP.8.1.1 + 475V + 111N
With a S:D111N sub branch: Query:A6415C ,G21893A, G25455T
samples: 1 (NJ)

Tree updated as of January 3:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_43d01_87d4f0.json?label=id:node_7415160

Screenshot 2025-01-04 alle 02 25 37
@xz-keg
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xz-keg commented Nov 4, 2024

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

@xz-keg xz-keg changed the title LP.8 spike diversity: Branch 1 (44) and Branch 2 (4) plus their new sublineageas with 475V, 679R LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineageas with 475V, 679R Nov 4, 2024
@HynnSpylor
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EPI_ISL_19522303 also gets S:T22N, which is popular recently (seems the first LP.8+S:T22N)

@FedeGueli
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FedeGueli commented Nov 5, 2024

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

@FedeGueli FedeGueli changed the title LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineageas with 475V, 679R LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineages with 475V, 679R Nov 5, 2024
@FedeGueli FedeGueli changed the title LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineages with 475V, 679R LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineages with 475V, 679R , 22N Nov 5, 2024
@FedeGueli FedeGueli changed the title LP.8 spike diversity: Branch 1 (47) and Branch 2 (5) plus their new sublineages with 475V, 679R , 22N LP.8 spike diversity: Branch 1 (57) and Branch 2 (8) plus their new sublineages with 475V, 679R , 22N Nov 6, 2024
@FedeGueli
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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
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Tree updated in the main proposal

@FedeGueli
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BR.1 +2 Rhode Island

@FedeGueli FedeGueli changed the title LP.8 spike diversity: Branch 1 (57) and Branch 2 (8) plus their new sublineages with 475V, 679R , 22N LP.8 spike diversity: Branch 1 (60) and Branch 2 (8) plus their new sublineages with 475V, 679R , 22N Nov 7, 2024
@DailyCovidCases
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DailyCovidCases commented Nov 8, 2024

Branch 1 designated LP.8.1 via cov-lineages/pango-designation@218759a

Branch 2 designated LP.8.2 via cov-lineages/pango-designation@218759a

@xz-keg xz-keg added this to the LP.8.1 LP.8.2 milestone Nov 8, 2024
@xz-keg xz-keg changed the title LP.8 spike diversity: Branch 1 (60) and Branch 2 (8) plus their new sublineages with 475V, 679R , 22N LP.8 spike diversity Nov 8, 2024
@xz-keg xz-keg changed the title LP.8 spike diversity LP.8 spike diversity with S:A475V, T22N, K679R, R190S Nov 8, 2024
@xz-keg xz-keg changed the title LP.8 spike diversity with S:A475V, T22N, K679R, R190S LP.8* spike diversity with S:A475V, T22N, K679R, R190S Nov 8, 2024
@FedeGueli FedeGueli changed the title LP.8* spike diversity with S:A475V, T22N, K679R, R190S LP.8.1 and LP.8.2 spike diversity with S:A475V, T22N, K679R, R190S Nov 9, 2024
@FedeGueli
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Thx @xz-keg for updating the proposal.
Thx @DailyCovidCases for spotting the designations

@cvejris
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cvejris commented Jan 23, 2025

LP.8.1.1 + S:I434V rose from dead: 1xUSA, NY
both also have S:L5F (C21575T)

@FedeGueli
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LP.8.1.1 + S:I434V rose from dead: 1xUSA, NY both also have S:L5F (C21575T)

again among the tracked lineages, thx a lot

@FedeGueli
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GBW from Philippines:LP.8.1.1 + 478E + 765L

@FedeGueli
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FedeGueli commented Jan 26, 2025

Reorganized LP.8.1.1 + 478E in three distinct branches I II III with one being underr 85S branch , another under S:R765L branch, and one other being independent with new query: 22994G,A23598G,C25925T,-A11923G,-C7521T,-C14235T .
There is a fourth sample previously clustering with the first two on Usher but not kept separate in a branch still not clear.

@FedeGueli FedeGueli changed the title Spike diversity: LP.8.1 and LP.8.2 (updated as of Jan 22) Spike diversity: LP.8.1 and LP.8.2 (updated as of Jan 27) Jan 27, 2025
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FedeGueli commented Jan 27, 2025

All updated

S:S680A branch added, i remember someone mentioned it but i cant find who and when

Adding LP.8.1.1 + 185D

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cvejris commented Jan 27, 2025

Big Canada (ON) upload yields:
4x LP.8.1.1 + S:R214H
1x LP.8.1.1 + S:K478E
1x LP.8.1 + S:T500A

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cvejris commented Jan 27, 2025

2nd LP.8.1.1 + S:N477D (on the Orf3a:L106F branch): 1x USA/CT

@FedeGueli
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Big Canada (ON) upload yields: 4x LP.8.1.1 + S:R214H 1x LP.8.1.1 + S:K478E 1x LP.8.1 + S:T500A

also a batch of S.Q677H from Rhode Island

@FedeGueli
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2nd LP.8.1.1 + S:N477D (on the Orf3a:L106F branch): 1x USA/CT

thx added this and updated everything

@FedeGueli
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Lp.8.1.1 + 148T added

@cvejris
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cvejris commented Jan 28, 2025

LP.8.1 + S:A522P (G23126C): 5x Brazil, Para

@HynnSpylor
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LP.8.1 + S:A522P (G23126C): 5x Brazil, Para

I suppose the S:A522P seqs updated in Brazil are all LP.8.1 (12 seqs). The seqs are missing many Spike mutations and all of them get S:F186L and S:R190S.

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cvejris commented Jan 29, 2025

LP.8.1.2+S:A1174V: 2x Hong Kong, 2x Canada (QC), 1x USA (CO)
3rd LP.8.1 + S:Y473F (A22980T) from USA (MA)

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FedeGueli commented Jan 29, 2025

Thx @cvejris @HynnSpylor
edit: wow on e of these 522P samples have S:A522P.

Also rare S:n370D appeared and S:R357K too.
LP.8.1 is showing an unprecedented RBD hypervariability on Jn.1 backbone cc @shay671 i suggest to run your app on Lp.8.1 only to see the difference if this is possible

Adding everything right now.

Added also S:D287E

@FedeGueli
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there is also a 478T reversion branch in Brazil but in a very reversion crowded branch so i don think it is real
cc @xz-keg
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2c5702_9f8c10.json?c=gt-S_478&gmax=25384&gmin=21563&label=id:node_11858402

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FedeGueli commented Jan 29, 2025

LP.8.1.3 (LP.8.1 + 677H) designated via cov-lineages/pango-designation@b00925f

NW.1 ( LP.8.1.2 + 1174V) designated via cov-lineages/pango-designation@d221b9f

FedeGueli referenced this issue in cov-lineages/pango-designation Jan 29, 2025
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FedeGueli commented Jan 29, 2025

@cvejris i checked S:Y473F they are two branches and quite old ones still not added here ( query: A22980T,C22120A)

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FedeGueli commented Jan 29, 2025

NY.1 w 85S
NY.3 w 765L
NY.6 w 475V
all designated via cov-lineages/pango-designation@1f6d884

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FedeGueli commented Jan 29, 2025

FedeGueli referenced this issue in cov-lineages/pango-designation Jan 29, 2025
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LP.8.1.6 + 478E from DK

@cvejris
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cvejris commented Jan 30, 2025

Fyi, LP.8.1 has very high ACE2-binding affinity, which explains our empirical observation that it tolerates many different RBD mutations (which were almost absent in, say, XEC*) - it can "afford" slight decrease in binding affinity to boost up immune evasion
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(25)00015-5/fulltext

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Singapore:
+2 for LP.8.1.1 plus 487D in the N:A173V branch
+1 for LP.8.1.1 plus 478E

@cvejris
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cvejris commented Jan 31, 2025

LP.8.1.1 + S:N487D (II) + S:H146Y (reads as H146del) is 4 seqs now:
2x Singapore (mentioned by @FedeGueli above), 1x Hong Kong (with S:D111N), 1x USA (MN)

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