Table 1.

Frequencies in non-Omicron SARS-CoV-2 genomes of non-synonymous mutations seen in the S-gene of BA.1.

Mutation	Percentage of genomes in Oct 2021	Frequency rank out of 7202 mutations	Selection Regime	Relative frequency changes in VOC lineages (alternative amino acid state)				Seen in other human beta CoV
				α	β	γ	δ
S/67V	0.435	85	Positive*	↑	↑
S/95I	16.047	21	Positive*		↑	↑
S/142D	0.002	5417	Positive*
S/212I	0.006	2814	Negative
S/339D	0.006	2883	Negative					HKU1*
S/371L	<0.005	>7202	Negative
S/373P	0.007	2719	Negative*
S/375F	0.003	4778	Negative
S/417N	0.529	73	Positive*			(T)		OC43
S/440K	0.156	216	Positive*	↑↑ (S)
S/446S	0.007	2666	Positive*
S/477N	2.038	35	Positive		↑↑ (I)	↑ (I)		HKU1*
S/478K	32.32	13	Positive*		↑			SARS-1*
S/484A	0.004	3498	Positive*	↑ (K)	(K)	(K)
S/493R	0.007	2737	Neutral					OC43
S/496S	0.013	1691	Neutral					HKU1/OC43
S/498R	<0.005	>7202	Negative
S/501Y	37.036	2	Positive*
S/505H	0.003	4099	Neutral
S/547K	0.013	1740	Positive
S/614G	98.97	1	Positive*
S/655Y	2.513	30	Positive	↑	↑
S/679K	0.041	534	Positive			↑		OC43*
S/681H	35.613	3	Positive*				(R)
S/764K	0.005	3291	Negative
S/796Y	0.083	322	Positive					SARS-1*
S/856K	<0.005	>7202	Negative*					OC43
S/954H	<0.005	>7202	Negative
S/969K	<0.005	>7202	Negative*					HKU1*
S/981F	<0.005	>7202	Neutral

Rows in bold indicate mutations at previously negatively selected or neutrally evolving sites. VOC columns track fold changes in mutation frequencies at corresponding sites in other VOCs (before and after boundaries are defined to create somewhat balanced sizes of sequence sets; the boundary is 2021/04/15 for α,β,γ and 2021/06/01 for δ). If another amino-acid residue is included in parentheses, then this residue has increased in frequency at the same site. ↑ - 2–10x fold increase ↑↑ - >10x fold increase. - lineage defining/majority mutation. (*) in other human beta-CoV - consensus residue in species matches the BA.1 residue; based on the sequence alignment from¹¹