Proposal for new lineage within B.1

[rambaut]

Proposal for new lineage within B.1

Description

Sub-lineage of: B.1
Earliest sequence: 2020-12-15 (England/CAMC-C769B3/2020)
Most recent sequence: 2021-01-28 (England/MILK-119FD0B/2021)
Countries circulating: England (28), Nigeria (7), USA (7), France (5), Canada (4), Ghana (4), Japan (4), Jordan (2), Belgium (1), Italy (1), Spain (1)

Characterised by spike mutations: E484K, Q677H, F888L, 69-70 deletion, 144 deletion and 9 nucleotide mutation in nsp6 (as seen in B.1.1.7, B.1.351, P.1).

Genomes

B.1.525_genomes.txt

List of genomes, collated 2021-02-11, attached.

Evidence

Phylogenetic tree PDF image. Proposed new lineage labels in red:

Phylogenetic tree file:
B.1.525.ml.tree.txt

Proposed lineage name

To be determined as the the next available designation within B.1

defining mutations

gene	amino acid	coordinates
ORF1ab		C1498T
		A1807G
		T8593C
		C9565T
		11288-11296del
	L4715F (L323F)	C14407T
		C18171T
		A20724G
spike	Q52R	A21717G
	69-70del
	144del
	E484K	G23012A
	Q677H	G23593C
	F888L	T24224C
		C24748T
E	L21F	C26305T
M	I82T	T26767C
N	SD2Y deletion	28278-28280del
		A28699G
N/ORF10 intergenic		G29543T

[rambaut]

This will be designated as lineage B.1.525

[aineniamh]

Resolved with pango designation release v1.0.1.

[luederm]

Hey guys,

There are two things that a colleague and I noticed that we would like to bring to your attention.

The first thing is that there looks like there may be a typo for the I82T/T26767C variant. That should be in M not E.

The second has to do with the variant 28278-28280del. We aligned B.1.525 genomes from GISAID to Hu-1 and the deletion looks like it occurs at 28280-28282. This results the deletion of D which does not affect S.

[rambaut]

27278-28280 is a more parsimonious nucleotide deletion but causes an deletion of S and D and replacement with Y

[rambaut]

The resulting (say) VIC18114 sequence is definitely MYNGPQ irrespective of where the deletion is.

[rambaut]

Thanks for pointing out the E/M error.