Table 2.

Relationships between mutations in spike protein and lineages/variants assigned in workflow version 2.

Version 2	Wild-type	Omicron BA.1	Omicron BA.2/3	Omicron BA.2/3 with R346X	Omicron BA.2/3 with K444X	Omicron BA.2/3 with V445X	Omicron BA.2/3 with R346X + K444X or V445X	Omicron BA.2.3.20	Omicron BQ.1	Omicron BQ.1.1	Omicron XBB	Omicron XBB.1.5	Omicron BA.2.12.1	Omicron BA.2.75	Omicron BA.4/5	Omicron BA.4/5 with V445X	Omicron BA.4/5 with K444X	Omicron BA.4/5 with R346S	Omicron BA.4/5 with R346X + K444X or V445X	Omicron BA.4.6/BF7	Omicron BA.5.9	Delta	Alpha	Beta	Gamma
G339	a	D	N,D,H	N,D,H	N,D,H	N,D,H	N,D,H	D	D	D	H	H	D	H	D	D	D	D	D	D	D
R346		R,K		T,S,I			T,S,I			T	T	T		R,T,I				S	S,T,I	T	I
K356														T,K
L368			L,I	L,I	L,I	L,I	L,I				I	I
D405			N	N	N	N	N	N	N	N	N	N	N,D	N	N,D	N,D	N,D	N,D	N,D	N,D	N,D
R408			Xb	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X
K417		X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X	X			N	T
N440		K	N,K	N,K	N,K	N,K	N,K	N,K	K	K	K	K	N,K	K	N,K	N,K	N,K	N,K	N,K	N,K	N,K
K444					R,T,M,N,R,Q,A		R,T,M,N,R,Q,A	R	T	T				K,M,T			R,T,M,N,R,Q,A		R,T,M,N,R,Q,A
V445						A,P,F	V,A,P,F				P	P				A,P,F			V,A,P,F
G446		S	G,S	G,S	G,S	G,S	G,S	G,S			S	S		S	G,S	G,S	G,S	G,S	G,S	G,S	G,S
N450								D						N,D	N,D	N,D	N,D	N,D	N,D	N,D	N,D
L452			L,M,R	L,M,R	L,M,R	L,M,R	L,M,R	M	R	R			Q	L,R	X	X	X	X	X	X	X	R
N460			N,K	N,K	N,K	N,K	N,K	K	K	K	K	K		K							N,K
S477		N	N	N	N	N	N	N	N	N	N	N	N	N	N	N	N	N	N	N	N
T478		K	K	K	K	K	K	K,E	K	K	K	K	K	K	K	K	K	K	K	K	K	K
E484		A	A	A	A	A	A	R	A	A	A	A	A	A	A	A	A	A	A	A	A			K	K
F486									V	V	S	P		F,S	V,A	V,A	V,A	V,A	V,A	V,A	V,A
F490											S	S		F,S
Q493		R	R	R	R	R	R						R
G496		S
Q498		R	R	R	R	R	R	R,Q	R	R	R	R	R	R	R	R	R	R	R	R	R
N501		Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y		Y	Y	Y

This variant definition was used to obtain the data shown Fig. 5.

^aThe same as Wild-type (null).

^bAny residues.