Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron

Table 1

Polymorphic amino acids residues of spike protein of SARS-CoV-2 Wuhan Hu-1 and all variants with possible biological function.

Amino acid position	SARS-CoV-2 variant									Known Function/probable biological impact
	Wuhan Hu-1	Alpha	Beta	Gamma	Delta	Lambda	Mu	Omicron	GH/490R
9	P								L	SP
18	L		F	F						NTD
19	T				R					NTD; GML
20	T			N						NTD; AGM
26	P			S						NTD; IdA; PCE
67	A							V		NTD
69	H	Del						Del		NTD
70	V	Del						Del		NTD; PCE
75	G					V				NTD
76	T					I				NTD; GML
80	D		A							NTD
95	T				I		I	I		NTD
136	C								Del	NTD; CRL
137	N								Del	NTD
138	D			Y					Del	NTD
139	P								Del	NTD
140	F								Del	NTD
141	L								Del	NTD
142	G				D			D	Del	NTD
143	V	Del						Del	Del	NTD
144	Del	Del	Del	Del	Del	Del	T	Del	Del	NTD
145	Y	V					S	Del	Del	NTD
146	Y						N	Del		NTD
154	M				T					NTD
157	E				G					NTD
158	F				Del					NTD
159	R				Del					NTD
191	R			S						NTD; AGM
212	N							I		NTD; PCE
213	L							V		NTD; PCE
214	V							R		NTD; PCE
215	R							E		NTD
216	Del	Del	Del	Del	Del	Del	Del	P	Del	NTD
217	Del	Del	Del	Del	Del	Del	Del	E	Del	NTD
218	D		G						G	NTD
244	L		Del							NTD; IdB
245	L		Del							NTD; IdB
246	A		Del							NTD; IdB
248	H								P	NTD; IdB
249	R					N				NTD; AGM
250	S					Del				NTD; PCE
251	Y					Del				NTD; PCE
252	L					Del				NTD; PCE
253	T					Del				NTD; PCE
254	P					Del				NTD; PCE
255	G					Del				NTD; PCE
256	D					Del				NTD; PCE
342	G							D		RBD; IdD
349	R						K			RBD; IdD
374	S							L		RBD
376	S							P		RBD
378	S							F		RBD; IdE/He4
420	K		N	T				N		RBD; He5
443	N							K		RBD; RBS
449	G							S		RBD; RBS
455	L				R	Q				RBD; RBS; IdF
480	S							N		RBD; RBS
481	T				K			K		RBD; RBS
487	E		K	K			K	A	K	RBD; RBS; IdG
493	F					S				RBD; RBS; IdG
496	Q							R		RBD; RBS; IdG
499	G							S		RBD; RBS; IdG
501	Q							R		RBD; RBS; IdG
504	N	Y	Y	Y			Y	Y		RBD; RBS
508	Y							H		RBD
550	T							K		IdH/He6-7
573	A	D								IdH/He6-7
617	D	G	G	G	G	G	G	G	G	IdH/He6-7
658	H			Y				Y
678	Q					H				S1/S2-CS
682	N							K		S1/S2-CS; PCE
684	P	H			R		H	H	R	S1/S2-CS; PCE
693	Q		H							S1/S2-CS; PCE
704	A		V
719	T	I								GML
767	N							K		He9-11
799	D							Y		FP
858	N							K
862	T					N
953	D				N		N			HR1
957	Q							H		HR1
972	N							K		HR1
984	L							F		HR1; PCE
985	S	A								HR1; PCE
1023	A						S
1030	T			I
1121	D	H
1179	V			F						HR2; TM

The positions were determined after alignment of all variants as available at supplementary material. Numbering 1–143 is equal to residues no. 1–143 of Wuhan-Hu-1. Number 144–215 is Wuhan-Hu-1 plus 1. Number >215 become Wuhan-Hu-1 plus 3; SP: signal peptide; NTD: N-terminal domain of S1; S1/S2 CS: S1/S2 cleavage site; RBD: receptor binding domain; RBS: receptor binding site; FP: fusion peptide; HR1 or HR2: heptad repeat 1 or 2; TM: transmembrane; IdA, IdB, IdC, IdD, IdE/He4, IdF, IdG, IdH/He6-7, IdI/He12-13, He1, He2-3, He5, He8, He9-11, He14, He15, and He16: corresponding linear epitopes as described in Supplementary Material 1; PCE: probable conformational epitopes; GML: glycosylation motive loss; AGM: additional glycosylation motive; CRL: cysteine residue loss.