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Proposal for lineage R.2 as an alias for B.1.1.316.2 #18

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rambaut opened this issue Feb 21, 2021 · 3 comments
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Proposal for lineage R.2 as an alias for B.1.1.316.2 #18

rambaut opened this issue Feb 21, 2021 · 3 comments
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@aineniamh
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designated proposed Proposal for a new lineage
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R.2

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@rambaut
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rambaut commented Feb 21, 2021 •
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Proposal for lineage R.2 as an alias for B.1.1.316.2

Current genomes on 2021-02-20:

USA/NY-NYCPHL-002765/2021|2021-01-25
USA/RI-Broad_RIDOH-00153/2021|2021-01-13
USA/RI-Broad_RIDOH-00166/2021|2021-01-19
USA/MA-Broad_CRSP-00367/2021|2021-01-08
USA/RI-Broad_RIDOH-00171/2021|2021-01-18
USA/RI-Broad_RIDOH-00154/2021|2021-01-13
USA/RI-Broad_RIDOH-00142/2021|2021-01-13
USA/MA-CDC-STM-000002438/2021|2021-01-13

'Defining' SNPs:

ORF1ab:	A1049V
		K1202N
C4999T
		Q1592R
		D4085G	
		A4703S
C15240T

spike:	
C21759T
		E484K
		Q677H
		T732S
A25048G
		E1202Q

Green lineage in tree:
B 1 1 316 ml tree
@rambaut rambaut added designated proposed Proposal for a new lineage labels Feb 21, 2021
@rambaut rambaut added this to the R.2 milestone Feb 21, 2021
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rambaut commented Feb 21, 2021

The pair of genomes:

USA/CA-LACPHL-AF00395/2021|2021-02-01
USA/CA-RD-RA04058/2021|2021-02-04

Has the following defining SNPs:

ORF1ab
		E913D
T8296C
C11824T
		A4774V

spike
		L18F
		V622I
		P681H
		
ORF3a
		G44R
		I63T
		
M		
		A69S

But don't qualify as a sublineage yet.

@rambaut
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rambaut commented Feb 21, 2021

Finally a few SNPs are shared:
R.1 + (2)

C27215T

R.1 + R.2 + (2)

T1164A (reversion? - A in reference)
T19841C

@aineniamh
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R.2 tagged in release 1.0.7

@rambaut rambaut changed the title New lineage for B.1.1.316 with E484K and New lineage for B.1.1.316 with E484K and P681H Feb 21, 2021
@rambaut rambaut changed the title New lineage for B.1.1.316 with E484K and P681H Proposal for lineage R.2 as an alias for B.1.1.316.2 Feb 21, 2021
@peich69 peich69 mentioned this issue Apr 26, 2021
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@peich69 peich69 mentioned this issue May 4, 2021
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