Proposal for a Sublineage of BA.2.12.1 with Spike V1264L and N:T282I

[ryhisner]

Description
Sub-lineage of: BA.2.12.1
Earliest sequence: 2022-4-29 (USA, Texas)
Most recent sequence: 2022-6-12 (Denmark)
Countries circulating: mostly the US, a bit in Europe
Number of Sequences: 201 on the USHER tree
Substitutions on top of BA.2.12.1:
Spike: V1264L
N: T282I
Nucleotide: G25352T, C29118T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_2b94d_cbf180.json

Evidence
Relative weekly growth advantage over S:L452Q + S:S704L in the US is, according to CovSpectrum, 83% over the past two months.

https://cov-spectrum.org/explore/United%20States/AllSamples/Past2M/variants?aaMutations=S%3AL452Q%2CS%3AS704L&aaMutations1=S%3AL452Q%2CS%3AS704L%2CS%3AV1264L%2CN%3AT282I&analysisMode=CompareToBaseline&

Genomes:
GISAID_hcov-19_ids_2022_06_17_20_12.csv

[ryhisner]

Using the BA.4 and BA.5 CovSpectrum queries of @shay671, the relative weekly growth advantage/disadvantage of S:L452Q+S:V1264L+N:T282I vs BA.4 and BA.5 in the US over the past two months are pictured below.

https://cov-spectrum.org/explore/United%20States/AllSamples/Past2M/variants?variantQuery=%5B1-of%3A+G27788T%2C+C28724T%2C+%5B1-of%3A+A686-%2CA687-%2CG688-%2CT689-%2CC690-%2CA691-%2CT692-%2CT693-%2CT694-%5D%5D%26%5B3-of%3A+G27788T%2C+C28724T%2C+%5B1-of%3AA686-%2CA687-%2CG688-%2CT689-%2CC690-%2CA691-%2CT692-%2CT693-%2CT694-%5D%2CG12160A%2CT22917G%2CT23018G%5D%26%21%5B2-of%3AC9866T%2CA23040G%5D%26%5B3-of%3AC26858T%2CA27259C%2CG27382C%2CA27383T%2CT27384C%5D%26%5B33-of%3AC241T%2CG4184A%2CA9424G%2CC14408T%2CC23525T%2CA24424T%2CC10198T%2CC17410T%2CA18163G%2CA22786C%2CG27382C%2CC3037T%2CC12880T%2CT22200G%2CA28271T%2CC10449A%2CA27383T%2CA23055G%2CA23063T%2CT22679C%2CC10029T%2CC22674T%2CG22992A%2CT27384C%2CC15714T%2CG22775A%2CC21618T%2CT24469A%2CC26060T%2CC26858T%2CC27807T%2CC28311T%2CA29510C%2CT670G%2CC2790T%2CC9344T%2CA20055G%2CC22686T%2CC22995A%2CA23013C%2CG23948T%2CG28882A%2CC4321T%2CC23604A%2CC25584T%2CG28881A%2CA22688G%2CA23403G%2CT23075C%2CC23854A%2CC26270T%2CG26709A%2CC9534T%2CG22578A%2CT22882G%2CC25000T%2CC26577G%2CG10447A%2CG22813T%2CT23599G%2CG28883C%2CC19955T%2CG21987A%2CA27259C%2C%5B1-of%3AT11288-%2CC11289-%2CT11290-%2CG11291-%2CG11292-%2CT11293-%2CT11294-%2CT11295-%2CT11296-%5D%2C%5B1-of%3AT21633-%2CA21634-%2CC21635-%2CC21636-%2CC21637-%2CC21638-%2CC21639-%2CT21640-%2CG21641-%2CT21765-%2CA21766-%2CC21767-%2CA21768-%2CT21769-%2CG21770-%5D%2C%5B1-of%3AG28362-%2CA28363-%2CG28364-%2CA28365-%2CA28366-%2CC28367-%2CG28368-%2CC28369-%2CA28370-%5D%5D&aaMutations1=S%3AV1264L%2CS%3AL452Q%2CN%3AT282I&analysisMode=CompareToBaseline&
https://cov-spectrum.org/explore/United%20States/AllSamples/Past2M/variants?variantQuery=%5B1-of%3A+G26529A%2CC27889T%5D%26%5B3-of%3A+G12160A%2CT22917G%2CT23018G%2CG26529A%2CC27889T%5D%26%21%5B2-of%3A+C9866T%2CA23040G%2CC26858T%2CA27259C%2CG27382C%2CA27383T%2CT27384C%5D%26%5B30-of%3A+C10449A%2CG21987A%2CT22882G%2CC26270T%2CA28271T%2CG22578A%2CA23403G%2CC25000T%2CC12880T%2CC28311T%2CC15714T%2CC17410T%2CG22775A%2CA22786C%2CG4184A%2CA9424G%2CA20055G%2CC22995A%2CA23063T%2CG23948T%2CC22686T%2CG22992A%2CC23525T%2CG28881A%2CT670G%2CA24424T%2CC2790T%2CA23055G%2CC9534T%2CC19955T%2CT23075C%2CT23599G%2CC26577G%2CG28883C%2CA29510C%2CC23854A%2CT24469A%2CC26060T%2CG26709A%2CG10447A%2CT22200G%2CC3037T%2CC21618T%2CA22688G%2CG22813T%2CC27807T%2CC241T%2CC10198T%2CA18163G%2CC25584T%2CC4321T%2CC9344T%2CT22679C%2CA23013C%2CG28882A%2CC10029T%2CC14408T%2CC22674T%2CC23604A%2C%5B1-of%3A+T11288-%2CC11289-%2CT11290-%2CG11291-%2CG11292-%2CT11293-%2CT11294-%2CT11295-%2CT11296-%5D%2C%5B1-of%3A+T21633-%2CA21634-%2CC21635-%2CC21636-%2CC21637-%2CC21638-%2CC21639-%2CT21640-%2CG21641-%2CT21765-%2CA21766-%2CC21767-%2CA21768-%2CT21769-%2CG21770-%5D%2C%5B1-of%3AG28362-%2CA28363-%2CG28364-%2CA28365-%2CA28366-%2CC28367-%2CG28368-%2CC28369-%2CA28370-%5D%5D&aaMutations1=S%3AV1264L%2CS%3AL452Q%2CN%3AT282I&analysisMode=CompareToBaseline&

[InfrPopGen]

Thanks for submitting. We've added lineage BG.2 with 44 newly designated sequences, and 7 updated designations from BA.2.12.1. Defining mutation(s) G25352C (S:V1264L) and C29118T (N:T282I).

[FedeGueli]

Looking back at BG.2 this issue missed to highlight it belonged to a big BA.2.12.1 branch defined by ORF8:Q18*

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11c4b_46c760.json?label=id:node_6420898

[aviczhl2]

Looking back at BG.2 this issue missed to highlight it belonged to a big BA.2.12.1 branch defined by ORF8:Q18*

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11c4b_46c760.json?label=id:node_6420898

I wonder if usher is able to highlight the difference of the generated main trunk and its related standard variant. It's very easy to miss it.