Table 1.
Identified ‘overlapping-epitope-clusters-to-patches’ method-based CTL Ag-Patches from the entire proteome of the SARS-CoV-2 virus. The identified highly immunogenic Ag-Patches were utilized to design three CTLs (CTL-MPV-1, CTL-MPV-2 and CTL-MPV-3) Multi-Patch Vaccines. The identified Ag-Patches were highly conserved in nature and were identified on the basis of significant number of overlapping epitope-forming clusters (Figures 2, 3 and 4).
| S.No. | CTL-MPVs | CTL epitope cluster-based Ag-Patches | Number of epitopes in cluster | Conservancy | Source SARS-CoV-2 protein |
|---|---|---|---|---|---|
| 1 | CTL-MPV-1 | GTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLI FLWLLWPVTLACFVLAAV | 36 | 96.64%(461/477) | M-Protein/6-70 |
| 2 | CTL-MPV-1 | RINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFN | 28 | 96.01%(458/477) | M-Protein/72-113 |
| 3 | CTL-MPV-1 | KEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKL | 21 | 97.69%(466/477) | M-Protein/166-206 |
| 4 | CTL-MPV-1 | TTRTQLPPAYTNSFTRGVYYPDKVFRSSV | 6 | 93.02%(467/502) | S-Protein/19-47 |
| 5 | CTL-MPV-1 | STQDLFLPFFSNVTWF | 4 | 91.43%(459/502) | S-Protein/50-65 |
| 6 | CTL-MPV-1 | VLPFNDGVYFASTEKSNIIRGWIF | 6 | 93.62%(470/502) | S-Protein/83-106 |
| 7 | CTL-MPV-1 | GVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFL | 7 | 91.23%(458/502) | S-Protein/142-176 |
| 8 | CTL-MPV-1 | KQGNFKNLREFVFKNIDGYFKIYSKHTPI | 4 | 91.83%(461/502) | S-Protein/182-210 |
| 9 | CTL-MPV-1 | EPLVDLPIGINITRFQTLLA | 3 | 93.22%(468/502) | S-Protein/224-243 |
| 10 | CTL-MPV-1 | TPGDSSSGWTAGAAAYYVGYLQPRTFLLK | 6 | 93.42%(469/502) | S-Protein/250-278 |
| 11 | CTL-MPV-1 | SETKCTLKSFTVEKGIYQTSNFR | 4 | 93.22%(468/502) | S-Protein/297-319 |
| 12 | CTL-MPV-1 | FPNITNLCPFGEVFNATRFASV | 3 | 93.42%(469/502) | S-Protein/329-350 |
| 13 | CTL-MPV-1 | RISNCVADYSVLYNSASFSTFKCY | 7 | 93.82%(471/502) | S-Protein/357-380 |
| 14 | CTL-MPV-1 | NVYADSFVIRGDEVR | 2 | 93.62%(470/502) | S-Protein/394-408 |
| 15 | CTL-MPV-1 | SKVGGNYNYLYRLFRKSNLKPFER | 10 | 92.62%(465/502) | S-Protein/443-466 |
| 16 | CTL-MPV-1 | NTSNQVAVLYQDVNCTEV | 3 | 67.33%(338/502) | S-Protein/603-620 |
| 17 | CTL-MPV-1 | RVYSTGSNVF | 2 | 93.82%(471/502) | S-Protein/634-643 |
| 18 | CTL-MPV-1 | SPRRARSVASQSIIAY | 5 | 93.82%(471/502) | S-Protein/680-695 |
| 19 | CTL-MPV-1 | FTISVTTEILPVSMTKTSVDCTMY | 4 | 93.82%(471/502) | S-Protein/718-741 |
| 20 | CTL-MPV-1 | NTQEVFAQVKQIYKTPPIK | 3 | 91.83%(461/502) | S-Protein/777-795 |
| 21 | CTL-MPV-1 | KRSFIEDLLFNKVTLA | 3 | 93.02%(467/502) | S-Protein/814-829 |
| 22 | CTL-MPV-1 | PLLTDEMIAQY | 3 | 93.42%(469/502) | S-Protein/863-873 |
| 23 | CTL-MPV-1 | LQIPFAMQMAYRFNGI | 5 | 93.82%(471/502) | S-Protein/894-909 |
| 24 | CTL-MPV-1 | FPQSAPHGVVF | 2 | 93.42%(469/502) | S-Protein/1052-1062 |
| 25 | CTL-MPV-1 | FVSNGTHWFVTQR | 2 | 93.22%(468/502) | S-Protein/1095-1107 |
| 26 | CTL-MPV-1 | YEQYIKWPWYIWLGFIAGLIAIV | 8 | 93.42%(469/502) | S-Protein/1206-1228 |
| 27 | CTL-MPV-2 | NQRNAPRITFGGPS | 2 | 96.78%(482/498) | N-Protein/8-21 |
| 28 | CTL-MPV-2 | RSKQRRPQGLPNNTASWFTALTQHGK | 6 | 99.19%(494/498) | N-Protein/36-61 |
| 29 | CTL-MPV-2 | NSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYL | 14 | 97.38%(485/498) | N-Protein/77-113 |
| 30 | CTL-MPV-2 | LPYGANKDGIIW | 2 | 98.99%(493/498) | N-Protein/121-132 |
| 31 | CTL-MPV-2 | KSAAEASKKPRQKRTATKAYNVTQAF | 5 | 97.38%(485/498) | N-Protein/249-274 |
| 32 | CTL-MPV-2 | QELIRQGTDY | 2 | 97.18%(484/498) | N-Protein/289-298 |
| 33 | CTL-MPV-2 | IAQFAPSASAFFGMSRIGMEVTPSGTWLTY | 12 | 97.18%(484/498) | N-Protein/304-333 |
| 34 | CTL-MPV-2 | LLNKHIDAYKTFPPTEPKK | 4 | 96.98%(483/498) | N-Protein/352-370 |
| 35 | CTL-MPV-2 | DEWSMATYYLF | 2 | 99.55%(451/453) | ORF1ab/898-908/nsp3 |
| 36 | CTL-MPV-2 | ETISLAGSYK | 2 | 100%(453/453) | ORF1ab/1503-1512/nsp3 |
| 37 | CTL-MPV-2 | TQVVDMSMTY | 2 | 99.77%(452/453) | ORF1ab/1581-1590/nsp3 |
| 38 | CTL-MPV-2 | AVMYMGTLSYEQF | 3 | 97.79%(443/453) | ORF1ab/1767-1779/nsp3 |
| 39 | CTL-MPV-2 | LVAEWFLAYILFTRFFYV | 3 | 100%(453/453) | ORF1ab/2323-2340/nsp3 |
| 40 | CTL-MPV-2 | RMYIFFASFYYVWKSY | 3 | 99.11%(449/453) | ORF1ab/2382-2397/nsp3 |
| 41 | CTL-MPV-2 | AYVNTFSSTFNVPMEK | 3 | 98.89%(448/453) | ORF1ab/2593-2608/nsp3 |
| 42 | CTL-MPV-2 | CLAYYFMRFRRAF | 3 | 96.02%(435/453) | ORF1ab/3059-3071/nsp4 |
| 43 | CTL-MPV-2 | MVMFTPLVPFWITIAY | 4 | 100%(453/453) | ORF1ab/3129-3144/nsp4 |
| 44 | CTL-MPV-2 | FYWFFSNYLKRRVVF | 2 | 98.67%(447/453) | ORF1ab/3153-3167/nsp4 |
| 45 | CTL-MPV-2 | LPSLATVAYFNMVY | 2 | 98.01%(444/453) | ORF1ab/3641-3654/nsp6 |
| 46 | CTL-MPV-2 | LILMTARTVY | 2 | 100%(453/453) | ORF1ab/3692-3701/nsp6 |
| 47 | CTL-MPV-2 | TACTDDNALAYY | 5 | 99.77%(452/453) | ORF1ab/4161-4172/nsp9 |
| 48 | CTL-MPV-2 | YTMADLVYAL | 2 | 100%(453/453) | ORF1ab/4514-4523/nsp12 |
| 49 | CTL-MPV-2 | KLFDRYFKYWDQTY | 2 | 100%(453/453) | ORF1ab/4673-4686/nsp12 |
| 50 | CTL-MPV-2 | ARLYYDSMSY | 2 | 99.11%(449/453) | ORF1ab/4904-4913/nsp12 |
| 51 | CTL-MPV-2 | VDTDFVNEFYAYLRKHFSM | 3 | 100%(453/453) | ORF1ab/5129-5147/nsp12 |
| 52 | CTL-MPV-2 | FPLCANGQVFGLY | 2 | 99.55%(451/453) | ORF1ab/5405-5417/nsp13 |
| 53 | CTL-MPV-2 | IPLMYKGLPWNVVR | 2 | 100%(453/453) | ORF1ab/6075-6088/nsp14 |
| 54 | CTL-MPV-2 | YVMHANYIFW | 2 | 98.89%(448/453) | ORF1ab/7020-7029/nsp16 |
| 55 | CTL-MPV-3 | SEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAY | 20 | 99.17%(478/482) | E-Protein/6-42 |
| 56 | CTL-MPV-3 | VSLVKPSFYVYSRVKNLNSSR | 5 | 99.58%(480/482) | E-Protein/49-69 |
| 57 | CTL-MPV-3 | FMRIFTIGTVTLK | 5 | 99.37%(478/481) | ORF3a/4-16 |
| 58 | CTL-MPV-3 | TIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRW | 14 | 77.33%(372/481) | ORF3a/34-69 |
| 59 | CTL-MPV-3 | HFVCNLLLLFVTV | 5 | 97.50%(469/481) | ORF3a/78-90 |
| 60 | CTL-MPV-3 | LLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKCR | 27 | 95.42%(459/481) | ORF3a/95-134 |
| 61 | CTL-MPV-3 | YFLCWHTNCYDY | 3 | 97.08%(467/481) | ORF3a/145-156 |
| 62 | CTL-MPV-3 | TTSPISEHDYQIGGY | 2 | 97.92%(471/481) | ORF3a/175-189 |
| 63 | CTL-MPV-3 | YYQLYSTQLSTDTGVEHVTFFIYNKI | 6 | 99.16%(477/481) | ORF3a/211-236 |
| 64 | CTL-MPV-3 | FHLVDFQVTIAEILLIIMRTFKVSIWNLDYII | 12 | 98.33%(473/481) | ORF6/2-33 |
| 65 | CTL-MPV-3 | MKIILFLALITLATCELYHY | 7 | 99.58%(478/480) | ORF7a/1-20 |
| 66 | CTL-MPV-3 | LLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDG VKHVYQLRARSVSPKLFIR | 18 | 98.75%(474/480) | ORF7a/30-89 |
| 67 | CTL-MPV-3 | EVQELYSPIFLIVAAIVFITLCFTLKRK | 11 | 97.70%(469/480) | ORF7a/92-119 |
| 68 | CTL-MPV-3 | MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLEL | 24 | 97.88%(231/236) | ORF7b/1-34 |
| 69 | CTL-MPV-3 | MKFLVFLGIITTVAAF | 9 | 98.95%(475/480) | ORF8/1-16 |
| 70 | CTL-MPV-3 | YVVDDPCPIHFYSKWYIRVGARKSAPLIELC | 12 | 98.95%(475/480) | ORF8/31-61 |
| 71 | CTL-MPV-3 | IQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVL | 19 | 51.25%(246/480) | ORF8/71-118 |
| 72 | CTL-MPV-3 | IQYIDIGNYTVSCSPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVL | 19 | 47.50%(228/480) | ORF8/71-118 |
| 73 | CTL-MPV-3 | MGYINVFAFPFTIYSLLLCR | 15 | 99.37%(476/479) | ORF10/1-20 |