Spike diversity: LP.8.1 and LP.8.2 (updated as of Feb 24) #2199

FedeGueli · 2024-11-03T19:05:36Z

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: LP.8.1 and LP.8.2, the latter seems dying off

Tracked Branches

LP.8.1

LP.8.1 + S:K478E (I)
LP.8.1 >> Orf1a:H110Y (C593T), C829T, Orf1a:E553K (G1922A), Orf1b:G977S (G16396A), C17733T, S:K478E (A22994G)
Query: C829T, C17733T,G1922A (NEW edited)
Samples: 6 Philippines,US,Japan

LP.8.1 + Orf1a:T999I + S:K679R (I) found by @cvejris
LP.8.1>> Orf1a:T999I (C3261T), S:K679R (A23598G)
Query: C25925T,23598G, C3261T
Samples: 15 but Usher has 47!

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: 12
Places : 8

LP.8.1 + S:N532K by @cvejris proposed in cov-lineages/pango-designation#2903
LP.8.1 > C16308T > T23377C > S:N532K (T23158G)
Query: T23377C,T23158G
Samples 20 Brazil, Scotland,France 2 with further S:K529E, 1 with further S:L822F

LP.8.1 + S:T572I (I)
LP.8.1 >> S:T572I (C23277T), C26735T
Query:C23277T, C26735T,C25925T
Samples: 1 South Korea

LP.8.1 + S:T572I (II)
LP.8.1 >> C13115T > ORF1a:L3644F (C11195T), ORF1b:L1627F (C18508T), C22498T, S:T572I (C23277T),N:G44C(ORf9b:K40N (G28403T), G29779T,
Query: C13115T,C23277T,C22498T,T3565C
Samples:2 Japan Note that the whole branch is likely from South Africa (long branches, great diversity, no local pattern)

LP.8.1 + S:A688V by @cvejris
LP.8.1 >> C13115T > S:A688V (C23625T)
Query: C13115T,C23625T,G1954A
Samples: 10 South Africa , NY

LP.8.1 + S:Y473F by @cvejris
Query:G29706A,A22980T
Samples: 3 MA,US

LP.8.1 + S:G181V + Orf1a:Y2171F by @cvejris
Query: T4150C, A6777T, G22104T
Samples: 4 NSW

LP.8.1 + A258C+ S:K478E (II)
LP.8.1 >> A258C > ORF1a:L2781F (C8606T), ORF1a:I4049V (A12410G), S:k478E A22994G), C25413T, T27484C,A29534G,
Query:C8606T, A12410G, A22994G
Samples: 3 California

LP.8.1 + S:G252S by @cvejris
LP.8.1 > T24364C > S:G252S (G22316A)
Query: T24364C ,G22316A,T3565C
Samples: 7 US

LP.8.1 + G476S by @Over-There-Is
LP.8.1+C2485T,C18457T,ORF1a:I2057V(A6434G), C18457T, S:G476S (G22988A),C25267T,C27276T ORF9b:A57V (C28453T)
Query: G22988A),C25267T,C27276T
Samples: 3 US-NV

LP.8.1.1 + S:N477K
Query: A6601C, C22993A
Samples: 2 Canada

LP.8.1 + S:T22N by @xz-keg
LP.8.1 >> Orf1a:S944L (C3096T) > T3055C > Orf1a:Y1734H (T5465C) > ORF1b:P2633L (C21365T), S:T22N (C21627A)
Query: T5465C, C21365T, C21627A
Samples: 11
Places : US ( 4 Places)

LP.8.1.1

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: 13 US, HK, Philippines ( this has dropout at 487 , very likely having it), Singapore
With a S:H146Y branch that gained further S:D111N (by @xz-keg )

LP.8.1.1 + S:K478E (I) found by @cvejris
LP.8.1.1 > S:K478E (A22994G),
Query: 22994G,A23598G,C25925T,-T11081C,-C5548T,-A11923G,-C7521T,-C14235T (new)
Samples: 18 Singapore,Australia, Canada, Peru', Texas

LP.8.1.1 + S:N477D (II) found by @cvejris
LP.8.1.1. > Orf3a:L106F(C25708T) > Orf1a:E933G (A3063G) > S:N477D (A22991G)
Query:C25708T,A3063G,A22991G
Samples: 7 Canada,Japan, Singapore, South Korea, Spain

LP.8.1.1 + S:A67V
LP.8.1.1 >> S:A67V (C21762T)
Query:C21762T,G22132T, C22120A
Query: 14 England, California,US-CT,NY, Japan, Brazil,Singapore
One sample with 478E

LP.8.1.1 + S:N185D
Lp.8.1.1 >> S:N185D (A22115G)
Query: A22115G,C22120A,G22132T
Samples: 19 Scotland, Nebraska, Ireland ( 2 with S:Q957L),

LP.8.1.1 + S:N148T
LP.8.1.1 > S:N148T (A22005C)
Query: A22005C,23598G,C25925T,C22120A
Samples: 5 Canada-ON, Colorado

LP.8.1.1 + S:T572I (I)
LP.8.1.1 > Orf1a:P1640H (C5184A = PLPRO_P77H) ,C5392T>S:T572I (C23277T) ,G29778A
Query:C5184A ,C5392T,C23277T,T3565C
Samples: 1 Israel

LP.8.1.1 + S:M153V
LP.8.1.1 > Orf1a:A1049V (C3411T), C15540T > Orf1a:S692F (C2340T) > S:M153V (A22019G)
Query:A22019G,C2340T,C15540T
Samples: 3 Spain

Lp.8.1.1 + S:T572I (II)
Query: G20237T,C16111T, C23277T,
Samples: 1 South Korea

LP.8.1.1 + S:K440R
LP.8.1.1> C12253T > C24865T > S:K440R (A22881G)
Query:22881G,C12253T, C24865T
Samples: 2 US

LP.8.1.1 + S:K478T
LP.8.1.1 > S:K478T (A22995C rev) > T658A
Query: T658A,-22995A,, C23039G,C25925T
Samples: 8 US (6 States)

Lp.8.1.1 + S:Y266H
Query: T22358C,C14189T,t3565C
Samples: 25 NY,NJ , 1 Pooled GBW

LP.8.1.1+ S:E154G (I) by @HynnSpylor
LP.8.1.1>> C10834T > S:E154G （A22023G）
Query: A22023G,G1954A, C10834T
Samples: 2 France

LP.8.1.1 + S:L54F + S:E154G (II) by @HynnSpylor
LP.8.1.1 > S:l54F (G21724T) , S:E154G (A22023G)
Query:G21724T ,A22023G
Samples: 2 Scotland France

LP.8.1.1 + S:G257V+ S:T259I
LP.8.1.1 >> Orf1a:T1093I (C3543T), ORF1a:D1742E (T5491G), C21219T, S:G257V (G22332T), S:T259I (C22338T),T22342A, C22624T
Query: 22342A,22338T,T3565C
Samples: 1 HK

LP.8.1.1 + S:T572I (III)
LP.8.1.1 >> C12253T > S:T572I (C23277T)
Query: C12253T, C23277T,T3565C,22896G
Samples: 4 US ( 4 States)

LP.8.1.1 + S:S256L
LP.8.1.1 >> Orf1a:L3644F (C11195T), ORF1b:M1352V (A17521G), G22051T, S:S256L (C22329T)
Query: C11195T, G22051T, C22329T
Samples: 4 UK

NY.1

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

NY.1 + S:S408N + S:D745G
Query: C4668T, C7923T, G22785A
Samples: 2 NZL

NY.2

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

NY.3

NY.3 + 478E 8(I)
Query: T5278C, A11923G,T3565C
Samples: 5 California, Philippines, NY

NY.3 + S:K444R by @cvejris
NY.3 >> T1459C, C22498T, S:K444R (A22893G)
Query: T1459C, C22498T, A22893G
Samples: 1 Taiwan (traveler)

NY.4

NY.4 + S:R765S by @cvejris
NY.4>> C28957T > C22183T > Orf1a:V1750L (G5513C), A5524G > S:R765S (C23855A)
Query: G5513C, A5524G,C23855A
Samples: 8 VA , NY, South Korea

NY.5

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

NY.6

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

NY.7

NY.7+S:A475V
NY.7>> C925T, ORF1b:A788V (C15830T) > C29708T >
C832T, A6739G, ORF1b:R2257S (G20238T), S:A475V(C22986T), T23857C, T26454C, C29200A
Query:C925T, C15830T,C22986T
Samples: 4 UK

NY.8

LP.8.1.2

LP.8.1.2 + S:F565L
LP.8.1.2>> T3814C > T22972C >
ORF1a:I3737T (T11475C), S:F565L (T23255C)
Query: T11475C, T23255C
Samples: 2 MN

NW.1

NW.1 + S:P809S and then S:A67V
NW.1 >>ORF1a:A540V (C1884T), ORF1a:K1202N (G3871T) > S:P809S (C23987T) > T11974C, S:A67V (C21762T)
Query for 809S: C1884T,G3871T,C23987T
Samples: 6 Singapore
Query for 809S + 67V: C23987T,T11974C, C21762T,T3565C
Samples: 5 Singapore

NW.1 + S:T22N found by @HynnSpylor
NW.1 >> T4723C,C5144T, ORF1a:D2136G (A6672G), C11941T, ORF1b:P2256S (C20233T), S:T22N (C21627A), G25401A
Query: T4723C, A6672G
Samples: 1 South Korea

LP.8.1.3

LP.8.1.3 + 475V (I)
Query: G23593T, C22986T,T15417C
Samples: 1 NY

LP.8.1.3 + S:H146Y by @Over-There-Is
Query: T8886C,T15417C,C12924T,
Samples: 6 CO

LP.8.1.4

LP.8.1.4 + S:A522P found by @cvejris and @HynnSpylor now proposed in cov-lineages/pango-designation#2904

LP.8.1.4 [C16308T] > S:A522P (G23126C), C27128T
Query: G23126C, C27128T
Samples: 22 Br,Es,Ny, FR
with a S:L452R singlet (could be artifact) to be checked
with a S:P479L singlet ( with dropout btw 499-507)
Query: G23126C, C27128T, 22997T

LP.8.1.4 +S:K529T
Query: A23148C,C829T, A2986G,T3565C
Samples: 2 Singapore

LP.8.1.4 + S:Q675H
Query: G23587T ,C25710T,T3565C
Samples: 2 French Guyana

LP.8.1.4 + S:A475V by @xz-keg
LP.8.1.4 >> A264G, ORF1a:K3351R (A10317G), S:A475V (C22986T)
Query:A264G, A10317G,C22986T
Samples: 3 Brazil, California

LP.8.1.5

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: 7 Canada QC,Singapore ,Italy
found by @cvejris

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.8.1.5 + S:D111N by @Over-There-Is
LP.8.1.5>> C829T, ORF1a:S1188L(C3828T), Orf1a:K1689R (A5331G),C15951T,C18744T,S:D111N(G21893A), ORF3a:D22Y(G25456T),N:H300Y (C29171T),C29614T
Query: C829T,C3828T,G21893A,T3565C
Samples: 6 Colorado, NY

LP.8.1.5 + S:K478E + Orf9b:D16N/N:G19E
Query: G7925A, A22994G, G28329A
Samples: 1 NSW

LP.8.1.5 + S:R102K
LP.8.1.5 >> C18744T > C15951T > Orf1a:K1689R (A5331G) > ORF1:S216N (G910A, T911A,C912A), S:R102K (G21867A)
Query: T911A, G21867A,A5331G
Samples: 11 NY

LP.8.1.5 + S:V1133I
LP.8.1.5 > S:V1133I (G24959A)
Query: G24959A,T3565C,A10323G,
Samples: 13 US (CA, AZ, CO)

LP.8.1.6

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: 6 Denmark,Canada, Singapore

LP.8.1.6 + S256L + S689N
Query: T8929C, A15945G, G23628A
Samples: 5 US, Germany

LP.8.1.6 + 475V
LP.8.1.6>> C29614T > Orf1a:T319I (C1221T) > S:A475V (C22986T)
Query: C1221T,C22986T,T3565C
Samples: 5 Delaware, Minnesota, Utah

LP.8.1.6 + 679R found by @cvejris
Query for 679R : A9328G,23598G
Samples: 3 ( 2 with this query)Australia, Taiwan, Japan

**LP.8.1.6 + S:L186F (rev) ** by @xz-keg
As @xz-keg described in comments this reversion went through C>A22120T,
LP.8.1.6 >> C29614T > Orf1a:T319I (C1221T) > S:L186F (A22120T )
Query: C22120T, C1221T,t3565C
Samples: 6 US

LP.8.1.7

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

Query: T28582C, C29642T,22986T
Samples:14 (Aus,Us,NZL,Spain, Israel,Philippines)

LP.8.1.7 + S:W64L by @Over-There-Is
LP.8.1.7+ORF1a:P2046S (C6401T), ORF1b:T17I (C13517T), S:W64L(G21753T)
Query:C13517T,G21753T ,T3565C
Samples: 4 MN

LP.8.1.8

LP.8.1.8 + S:A475V(I)
LP.8.1.8 [N:A134V (C28674T)]> T12247C, ORF1b:L80S (T13706C), T19896G,S:A475V (C22986T),N:Q242L(A28998T)
Query:T12247C, T13706C, T19896G
Samples: 25 Ontario (Cluster)

LP.8.1.8 +S:A475V (II) by @xz-keg
LP.8.1.8 >> ORF1a:V2865I (G8858A) > C29119T, C29675T > ORF1a:L1130F (C3653T) > S:A475V (C22986T)
Query: G8858A,C3653T,C22986T,T3565C
Samples:5
Places: Brazil, French Guyana

LP.8.1.8 + S:A1174V
LP.8.1.8 >> ORF1a:V2865I (G8858A) > Orf1a:A498V (C1758T), S:A1174V (C25083T)
Query: G8858A,C1758T,C25083T
Samples: 11 Australia (2 states)

### 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

LP.8.1.1 + S:R214H now designated NY.8

now proposed in cov-lineages/pango-designation#2894
LP.8.1.1 > C4021T, T9352C, ORF1a:A4642V (C14189T) , C26313T > C7834T, T10423C, Orf1a:L3808F (C11687T), S:R214H (G22203A)
Query: C26313T ,C7834T, T10423C
Samples: 22 US, Canada, Japan

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)

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

Dead
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)

Dead
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)

Dead
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

Dead
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

Dead
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

Dead
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)

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

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

Dead
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

Dead
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)

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

Dead
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)

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

Dead
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

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

Dead
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

Dead
LP.8.1 + S:D287E
LP.8.1 >> G4255A > C8320T, Orf1b:T284I (C14318T), S:D287E (T22423A)
Query: G4255A , C8320T, C14318T
Samples: 4 California

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

Dead
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

Dead
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

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

dead
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

dead
LP.8.1.3 + 475V (I)
Query: G23593, C22986,-T15417C,G1954A
Samples: 2 Singapore, CA ( 4 on USher)

TREE

Tree updated as of February 22

xz-keg · 2024-11-04T07:01:33Z

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

HynnSpylor · 2024-11-05T06:41:03Z

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

FedeGueli · 2024-11-05T08:35:20Z

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 · 2024-11-05T08:51:21Z

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

FedeGueli · 2024-11-06T11:52:11Z

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 · 2024-11-06T12:16:21Z

Tree updated in the main proposal

FedeGueli · 2024-11-07T08:10:49Z

BR.1 +2 Rhode Island

DailyCovidCases · 2024-11-08T15:50:35Z

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

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

FedeGueli · 2024-11-09T10:05:39Z

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

FedeGueli · 2025-02-25T22:36:26Z

522P branch new sample from Brazil with 479L and a dropout between 499-507 that could hide something.

FedeGueli · 2025-02-26T09:16:58Z

+2 Illinois, HK for LP.8.1.1 + 487D

FedeGueli · 2025-02-26T09:33:33Z

LP.8.1.1 + S:G257V + S:T259I and a silent nuc at S:A260A

FedeGueli · 2025-02-27T22:27:23Z

cc @cvejris please propose the 532K branch to the main page it is 20 now

xz-keg · 2025-02-28T04:52:24Z

The LP.8.1.1+S:N487D branch gains further S:H146Y and S:D111N in HK

cvejris · 2025-02-28T10:19:50Z

Australian LP.8.1.1 + C1471T+ Orf9b: A11V (C28315T) + S:K478E is 10 seqs now

FedeGueli · 2025-02-28T14:06:17Z

Australian LP.8.1.1 + C1471T+ Orf9b: A11V (C28315T) + S:K478E is 10 seqs now

the entire branch is now 17 i ve added a couple of more exclusions to the query.

FedeGueli · 2025-02-28T15:08:36Z

LP.8.1.1+S:E154G （A22023G）, 3seqs in UK (Scotland) and France

these are two branches now 4 in total 2 on the S:L54F branch (FRA,SCO) and the other only French within a C10834T branch

xz-keg · 2025-02-28T16:30:39Z

LP.8.1.6+S:L186F sub-branch. It is a reversion at spike, but 22120 mutates from C to A to T, so not revesing to original.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_356bc_1d6d30.json?label=id:node_5896596

FedeGueli · 2025-02-28T16:51:48Z

LP.8.1.1 + 477D went to 5 South Korea

FedeGueli · 2025-02-28T16:51:57Z

LP.8.1.6+S:L186F sub-branch. It is a reversion at spike, but 22120 mutates from C to A to T, so not revesing to original.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_356bc_1d6d30.json?label=id:node_5896596

Very interesting thx , i ve added it now

FedeGueli · 2025-02-28T19:26:09Z

I ve added another LP.8.1.1 plus S:T572I : LP.8.1.1 + S:T572I (III)
LP.8.1.1 >> C12253T > S:T572I (C23277T)
Query: C12253T, C23277T,T3565C,22896G
Samples: 4 US ( 4 States)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_112297_1cdfa0.json?c=gt-S_572&gmax=25384&gmin=21563&label=id:node_7454398

FedeGueli · 2025-03-01T08:41:33Z

Pleaase propose this @cvejris and @HynnSpylor

LP.8.1.4 + S:A522P
LP.8.1.4 [C16308T] > S:A522P (G23126C), C27128T
Query: G23126C, C27128T
Samples: 22 Br,Es,Ny, FR
with a S:L452R singlet (could be artifact) to be checked
with a S:P479L singlet ( with dropout btw 499-507)
Query: G23126C, C27128T, 22997T

FedeGueli · 2025-03-01T09:30:08Z

branch w S:R102K in NY

Over-There-Is · 2025-03-01T18:18:48Z

LP.8.1+C2485T,C18457T,C25267T,C27276T,C29311T,A6434G,G22988A,C28453T ORF1b:P1664S;ORF1a:I2057V;S:G476S;ORF9b:A57V US-NV 3

FedeGueli · 2025-03-01T23:21:33Z

LP.8.1+C2485T,C18457T,C25267T,C27276T,C29311T,A6434G,G22988A,C28453T ORF1b:P1664S;ORF1a:I2057V;S:G476S;ORF9b:A57V US-NV 3

added thx!

cvejris · 2025-03-02T11:52:30Z

LP.8.1.3 + T15417C with additional Orf1a:L2874S (T8886C), Orf1a: P4220L (C12924T), Orf1b:P2256S (C20233T), Orf7a:T120I (C27752T) and S:H146Y (T21994C): 6x USA, CO

FedeGueli · 2025-03-03T10:08:20Z

LP.8.1.3 + T15417C with additional Orf1a:L2874S (T8886C), Orf1a: P4220L (C12924T), Orf1b:P2256S (C20233T), Orf7a:T120I (C27752T) and S:H146Y (T21994C): 6x USA, CO

yes it is this one:
LP.8.1.3 + S:H146Y by @Over-There-Is
Query: T8886C,T15417C,C12924T,
Samples: 6 CO

FedeGueli · 2025-03-03T15:44:50Z

LP.8.1.8+ 1174V on the rise in Australia and one more 256L this time on LP.8.1.1

FedeGueli · 2025-03-04T08:25:01Z

Added a californian LP.8.1.5 + S:V1133I branch , not sure if spotted by someone before, please let me know

cvejris · 2025-03-04T09:45:44Z

NW.1 + S:P809S and then S:A67V: 2 new seqs, one has additional A688V
LP.8.1.3 + S:H146Y out of Colorado: 1x CA

FedeGueli · 2025-03-05T01:06:54Z

2 samples from Alberta with S:N477K

FedeGueli · 2025-03-05T08:53:09Z

LP.8.1.8 w 1174V up to 11 QLD again

xz-keg · 2025-03-05T16:21:15Z

There is a separate LP.8.1+S:T22N sub-branch on Orf1a:S944L-ORf1a:Y1734H branch.
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice5_genome_test_22a097_81ae90.json?gt=S.22N&label=id:node_5907316

FedeGueli · 2025-03-05T18:05:44Z

There is a separate LP.8.1+S:T22N sub-branch on Orf1a:S944L-ORf1a:Y1734H branch. https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice5_genome_test_22a097_81ae90.json?gt=S.22N&label=id:node_5907316

thank you great catch! just added it

HynnSpylor · 2025-03-07T12:42:30Z

NW.1(LP.8.1.2.1)+S:T22N (1 seq in South Korea)

FedeGueli · 2025-03-07T15:02:55Z

NW.1(LP.8.1.2.1)+S:T22N (1 seq in South Korea)

Thx! added

cvejris · 2025-03-09T17:25:32Z

LP.8.1.1 + S:N477D (II) +1 Spain

FedeGueli mentioned this issue Nov 3, 2024

KP.1.1.3 + Orf3a:P178L branch with S:F186L,S:V445R and S:Q493E (66 seqs - >10 countries including Philippines) most with further S:R190S (57) cov-lineages/pango-designation#2811

Closed

FedeGueli assigned corneliusroemer Nov 3, 2024

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

FedeGueli added Multiple lineages S:475 S:679 S:190 S:153 S:176 N Glycan S:22 LP.8 labels Nov 5, 2024

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 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 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 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

xz-keg added this to the LP.8.1 LP.8.2 milestone Nov 8, 2024

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 changed the title ~~LP.8 spike diversity~~ LP.8 spike diversity with S:A475V, T22N, K679R, R190S Nov 8, 2024

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 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

cvejris mentioned this issue Feb 28, 2025

LP.8.1 + S:N532K (20seqs, 3 countries) cov-lineages/pango-designation#2903

Open

cvejris mentioned this issue Mar 1, 2025

LP.8.1.4 + S:A522P (49 seqs, 5 countries - March 7th) cov-lineages/pango-designation#2904

Open

Spike diversity: LP.8.1 and LP.8.2 (updated as of Feb 24) #2199

Spike diversity: LP.8.1 and LP.8.2 (updated as of Feb 24) #2199

Comments

FedeGueli commented Nov 3, 2024 • edited Loading

Tracked Branches

LP.8.1

LP.8.1.1

NY.1

NY.2

NY.3

NY.4

NY.5

NY.6

NY.7

NY.8

LP.8.1.2

NW.1

LP.8.1.3

LP.8.1.4

LP.8.1.5

LP.8.1.6

LP.8.1.7

LP.8.1.8

TREE

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