BA.2 Lineage VCF Request

[m-crown]

BA.2 Lineage VCF Request

This lineage is described at PHE Genomics Variant-Definitions, Pango-Designation and CoVariants

[m-crown]

BA.2

As with the Omicron lineage VCF, BA.2 VCF is primarily built from Andrew Rambaut's list of shared and exclusive mutations between B.1.1.529, BA.1 and BA.2

Compared to Omicron/B.1.1.529, BA.2 contains 20 additional nucleotide mutations resulting in 6 deleted amino acids, 17 missense mutations and one 3AA insertion.

Note: the current table of mutations listed at Pango Designation issue 361 contains A22786T rather than the much more common A22786C. Discussion of this can be seen in Pango Designation issue 410, however at the time of writing the original issue 361 table has not been updated.

This VCF contains the mutation A22786C per 410.

nt	product	AA	source
T670G	NSP1	S135R	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C2790T	NSP3	T24I	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C3037T	NSP3	F106F	Pango-Designation
G4184A	NSP3	G489S	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C4321T	NSP3	A534A	Pango-Designation
C9344T	NSP4	L264F	outbreak.info, Pango-Designation
A9424G	NSP4	V290V	Pango-Designation, PHE Genomics Variant-Definitions
C9534T	NSP4	T327I	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C9866T	NSP4	L438F	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C10029T	NSP4	T492I	outbreak.info, Pango-Designation
C10198T	NSP5	D48D	Pango-Designation, PHE Genomics Variant-Definitions
G10447A	NSP5	R131R	Pango-Designation, PHE Genomics Variant-Definitions
C10449A	NSP5	P132H	outbreak.info, Pango-Designation
11288-11296del	NSP6	S106del, G107del, F108del	outbreak.info, Pango-Designation
C12880T	NSP9	I65I	Pango-Designation
C14408T	NSP12	P323L	outbreak.info, Pango-Designation
C15714T	NSP12	L758L	Pango-Designation
C17410T	NSP13	R392C	outbreak.info, Pango-Designation
A18163G	NSP14	I42V	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C19955T	NSP15	T112I	outbreak.info, Pango-Designation
A20055G	NSP15	E145E	Pango-Designation
C21618T	Surface Glycoprotein	T19I	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
21633_21641del	Surface Glycoprotein	L24S, P25del, P26del, A27del	outbreak.info, Pango-Designation
21987-21995del	Surface Glycoprotein	G142D, V143del, Y144del, Y145del	outbreak.info, Pango-Designation
T22200G	Surface Glycoprotein	V213G	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
G22578A	Surface Glycoprotein	G339D	outbreak.info, Pango-Designation
C22674T	Surface Glycoprotein	S371F	outbreak.info, Pango-Designation
T22679C	Surface Glycoprotein	S373P	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C22686T	Surface Glycoprotein	S375F	outbreak.info, Pango-Designation
A22688G	Surface Glycoprotein	T376A	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
G22775A	Surface Glycoprotein	D405N	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
A22786C	Surface Glycoprotein	R408S	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
G22813T	Surface Glycoprotein	K417N	outbreak.info, Pango-Designation
T22882G	Surface Glycoprotein	N440K	outbreak.info, Pango-Designation
G22992A	Surface Glycoprotein	S477N	outbreak.info, Pango-Designation
C22995A	Surface Glycoprotein	T478K	outbreak.info, Pango-Designation
A23013C	Surface Glycoprotein	E484A	outbreak.info, Pango-Designation
A23040G	Surface Glycoprotein	Q493R	outbreak.info, Pango-Designation
A23055G	Surface Glycoprotein	Q498R	outbreak.info, Pango-Designation
A23063T	Surface Glycoprotein	N501Y	outbreak.info, Pango-Designation
T23075C	Surface Glycoprotein	Y505H	outbreak.info, Pango-Designation
A23403G	Surface Glycoprotein	D614G	outbreak.info, Pango-Designation
C23525T	Surface Glycoprotein	H655Y	outbreak.info, Pango-Designation
T23599G	Surface Glycoprotein	N679K	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C23604A	Surface Glycoprotein	P681H	outbreak.info, Pango-Designation
C23854A	Surface Glycoprotein	N764K	outbreak.info, Pango-Designation
G23948T	Surface Glycoprotein	D796Y	outbreak.info, Pango-Designation
A24424T	Surface Glycoprotein	Q954H	outbreak.info, Pango-Designation
T24469A	Surface Glycoprotein	N969K	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
C25000T	Surface Glycoprotein	D1146D	Pango-Designation
C25584T	ORF3a	T64T	Pango-Designation
C26060T	ORF3a	T223I	outbreak.info, Pango-Designation
C26270T	E	T9I	outbreak.info, Pango-Designation
C26577G	M	Q19E	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions
G26709A	M	A63T	outbreak.info, Pango-Designation
C26858T	M	F112F	Pango-Designation
A27259C	ORF6	R20R	Pango-Designation, PHE Genomics Variant-Definitions
G27382C, A27383T, T27384C	ORF6	D61L	outbreak.info, Pango-Designation
C27807T	ORF7b	L18L	Pango-Designation
A28271T	Intergenic		Pango-Designation
C28311T	N	P13L	outbreak.info, Pango-Designation
28362_28370del	N	E31del, R32del, S33del	outbreak.info, Pango-Designation
G28881A, G28882A, G28883C	N	R203K, G204R	outbreak.info, Pango-Designation
A29510C	N	S413R	outbreak.info, Pango-Designation, PHE Genomics Variant-Definitions

[m-crown]

BA.2 VCF was added in 95be8bf. The VCF file is available here