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Spike diversity: LP.8.1 and LP.8.2 (updated as of Jan 27) #2199
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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) |
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 @corneliusroemer i suggest a rapid designation of the two branches. |
Tree updated in the main proposal |
BR.1 +2 Rhode Island |
Branch 1 designated LP.8.1 via cov-lineages/pango-designation@218759a Branch 2 designated LP.8.2 via cov-lineages/pango-designation@218759a |
Thx @xz-keg for updating the proposal. |
LP.8.1.1 + S:I434V rose from dead: 1xUSA, NY |
again among the tracked lineages, thx a lot |
GBW from Philippines:LP.8.1.1 + 478E + 765L |
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 . |
All updated S:S680A branch added, i remember someone mentioned it but i cant find who and when Adding LP.8.1.1 + 185D |
Big Canada (ON) upload yields: |
2nd LP.8.1.1 + S:N477D (on the Orf3a:L106F branch): 1x USA/CT |
also a batch of S.Q677H from Rhode Island |
thx added this and updated everything |
Lp.8.1.1 + 148T added |
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. |
LP.8.1.2+S:A1174V: 2x Hong Kong, 2x Canada (QC), 1x USA (CO) |
Thx @cvejris @HynnSpylor Also rare S:n370D appeared and S:R357K too. Adding everything right now. Added also S:D287E |
there is also a 478T reversion branch in Brazil but in a very reversion crowded branch so i don think it is real |
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 |
@cvejris i checked S:Y473F they are two branches and quite old ones still not added here ( query: A22980T,C22120A) |
NY.1 w 85S |
NY.7 via cov-lineages/pango-designation@841d847 |
LP.8.1.6 + 478E from DK |
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 |
Singapore: |
LP.8.1.1 + S:N487D (II) + S:H146Y (reads as H146del) is 4 seqs now: |
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
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.8.1 + 679R now designated LP.8.1.1
LP.8.1 + S:N487D now designated LP.8.1.2
LP.8.1.2+S:A1174V Now designated NW.1
LP.8.1 + S:Q677H now Designated LP.8.1.3
LP.8.1 + T22N Designated LP.8.1.6
LP.8.1 + S:A475V (II) Now Designated LP.8.1.9
LP.8.1.1 + S:P85S Now designated NY.1
LP.8.1.1 + S:R765L Designated NY.3
LP.8.1.1 + 475V (I) Now Designated NY.6
LP.8.1.1 + S:T22N now designated NY.7
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
Dead
Dead
Dead
Dead
Dead
DEAD
Dead
Dead
DEAD
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
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