Table 2. Rationally-designed sequence-conserved Th/CTL epitope peptides on M, N, and S2 proteins across all SARS-CoV-2 Variants of Concern (VoCs)a.
| Wild type & VoCs | M protein SARS-CoV-2 M101-156 (CTL epitopes) |
N protein SARS-CoV-2 N305-331 (Th/CTL epitopes) |
S2 proteinb,c SARS-CoV-2 S957-984 (Th/CTL epitopes) |
S2 Protein SARS-CoV-2 S891-917 (Th epitope) |
S2 Protein SARS-CoV-2 S996-1028 (Th/CTL epitope) |
|---|---|---|---|---|---|
|
Wuhan
(Original) |
GLMWLSYFIASFRLFARTRSMWS | AQFAPSASAFFGMSRIGMEVTPSGTWL | QALNTLVKQLSSNFGAISSVLNDILSRL | GAALQIPFAMQMAYRFNGIGVTQNVLY | LITGRLQSLQTVVTQLIRAAEIRASANLAATK |
| Alpha, Beta, & Gamma | GLMWLSYFIASFRLFARTRSMWS | AQFAPSASAFFGMSRIGMEVTPSGTWL | QALNTLVKQLSSNFGAISSVLNDILSRL | GAALQIPFAMQMAYRFNGIGVTQNVLY | LITGRLQSLQTVVTQLIRAAEIRASANLAATK |
| Delta | GLMWLSYFIASFRLFARTRSMWS | AQFAPSASAFFGMSRIGMEVTPSGTWL | QALNTLVKQLSSNFGAISSVLNDILSRL | GAALQIPFAMQMAYRFNGIGVTQNVLY | LITGRLQSLQTVVTQLIRAAEIRASANLAATK |
|
Omicron
c
(BA.1) |
GLMWLSYFIASFRLFARTRSMWS | AQFAPSASAFFGMSRIGMEVTPSGTWL | QALNTLVKQLSSKFGAISSVLNDIFSRL | GAALQIPFAMQMAYRFN GIGVTQNVLY |
LITGRLQSLQTVVTQLIRAAEIRASANLAATK |
|
Omicron
c
(BA.2/BA.4/ BA.5) |
GLMWLSYFIASFRLFARTRSMWS | AQFAPSASAFFGMSRIGMEVTPSGTWL | QALNTLVKQLSSKFGAISSVLNDILSRL | GAALQIPFAMQMAYRFN GIGVTQNVLY |
LITGRLQSLQTVVTQLIRAAEIRASANLAATK |
a The presence of T cell epitopes is critical for the induction of B and T cell memory responses against viral antigens. SARS-CoV-2 CTL and Th epitopes, validated by HLA binding and T cell functional assays, are highly conserved between SARS-CoV-2 and SARS-CoV-1 viruses, with minor between-variant differences seen only at S957-984. The Wuhan wild-type peptides (M, N and S2x3) are employed for precision-design of UB-612 vaccine against COVID-19 [Ref. 90]. Identification of T cell epitopes on SARS-CoV-1 (2003), determined using HLA-binding assays, were used to determine corresponding T cell epitopes in SARS-CoV-2 (2019) by sequence alignment.
b Except for N969K (on BA.1 through BA.5) and L981F (on BA.1) within S957-984 peptide on the S2 spike protein, none of the other four designer epitope peptides for UB-612 vaccine has an aa-residue that overlaps with the reported mutation sites on Spike, M, and N proteins (Table 1).
c At S957-984, there are minor sequence differences between Omicron BA.1 and BA.2/BA.4/BA.5, marked in red.