Table 1. The mutation sites on SARS-CoV-2 Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N) proteins on Delta and Omicrons^a.

VoCb	Spike (S1-RBD residues at 319–541)	E	M	N
Delta	T19R, G142D, Δ156–157, R158G, $\underset{\_}{\mathrm{L}452\mathrm{R}}$, T478K, D614G, P681R, & D950N	T9I	I82T	D63G, R203M, & D377Y
Omicron (BA.1)	A67V, Δ69–70, T95I, G142D, Δ143, Y144del, Δ145, Δ211, L212I, +214EPE, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, N764K, D796Y, N856K, and Q954H, L969K, & $\underset{\_}{\mathrm{L}981\mathrm{F}}$	T9I	D3G, Q19E, & A63T	P13L, Δ31–33, R203K, & G204R
Omicron (BA.2)	T19I, L24S, Δ25–27, G142D, V213G, G339D, S371F, S373P, S375F, T,376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, $\underset{\_}{\mathrm{Q}493\mathrm{R}}$, Q498R, N501Y, Y505H, D614G, H655Y, N679K, N764K, D796Y, N856K, Q954H, & L969K	T9I	Q19E & A63T	P13L, Δ31–33, R203K, G204R, & $\mathrm{S}413\mathrm{R}$
Omicron (BA.4)	T19I, L24S, Δ25–27, $\mathrm{\Delta }69–70$, G142D, V213G, G339D, S371F, S373P, S375F, T,376A, D405N, R408S, K417N, N440K, $\mathrm{L}452\mathrm{R}$, S477N, T478K, E484A, $\mathrm{L}486\mathrm{V}$, $\mathrm{Q}493$, Q498R, N501Y, Y505H, D614G, H655Y, N679K, N764K, D796Y, N856K, and Q954H, & L969K	T9I	Q19E & A63T	P13L, Δ31–33, $\mathrm{P}151\mathrm{S}$, R203K, G204R, & $\mathrm{S}413\mathrm{R}$
Omicron (BA.5)	T19I, L24S, Δ25–27, $\mathrm{\Delta }69–70$, G142D, V213G, G339D, S371F, S373P, S375F, T,376A, D405N, R408S, K417N, N440K, $\mathrm{L}452\mathrm{R}$, S477N, T478K, E484A, $\mathrm{L}486\mathrm{V}$, $\mathrm{Q}493$, Q498R, N501Y, Y505H, D614G, H655Y, N679K, N764K, D796Y, N856K, and Q954H, & L969K	T9I	$\mathrm{D}3\mathrm{N}$, Q19E, & A63T	P13L, Δ31–33, R203K, G204R, & $\mathrm{S}413\mathrm{R}$

^a Reported mutation sites on Spike, E, M, and N proteins [Refs: 15–18 and 44–47].

^b Omicron BA.4 and BA.5 have identical mutation site profile on Spike protein, which are more related to BA.2 than BA.1. Among BA.2, BA.4 and BA.5, the between-variant differences in mutation sites on S, E, M, and N proteins are marked in red.

^c Except for N969K (on BA.1 through BA.5) and L981F (on BA.1) within S_957-984 peptide on the S2 spike protein, none of the other four designer epitope peptides (Table 2) for UB-612 vaccine has an aa-residue that overlaps with the reported mutation sites on Spike, M, and N proteins.