Table 2.
Identified ‘overlapping-epitope-clusters-to-patches’ method-based HTL Ag-Patches from the entire proteome of the SARS-CoV-2 virus. The identified highly immunogenic Ag-Patches were utilized to design two HTL (HTL-MPV-1 and HTL-MPV-2) 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. | HTL-MPVs | CTL epitope cluster based Ag-Patches | Number of epitopes in cluster | Conservancy | Source SARS-CoV-2 protein |
|---|---|---|---|---|---|
| 1 | HTL-MPV-1 | VNSVLLFLAFVVFLLVTLAILT | 8 | 99.58%(480/482) | E-Protein/14-35 |
| 2 | HTL-MPV-1 | IKLIFLWLLWPVTLAC | 2 | 98.11%(468/477) | m-protein/49-64 |
| 3 | HTL-MPV-1 | VGLMWLSYFIASFRLFAR | 4 | 97.27%(464/477) | m-protein/88-105 |
| 4 | HTL-MPV-1 | SRTLSYYKLGASQRVAGDS | 5 | 98.53%(470/477) | m-protein/173-191 |
| 5 | HTL-MPV-1 | SKTQSLLIVNNATNVVIKVCE | 7 | 93.22%(468/502) | S-protein/112-132 |
| 6 | HTL-MPV-1 | REFVFKNIDGYFKIYSK | 3 | 91.83%(461/502) | S-protein/190-206 |
| 7 | HTL-MPV-1 | GINITRFQTLLALHRSYLTPGDSSSGWTAG AAAYYVGY | 9 | 92.82%(466/502) | S-protein/232-269 |
| 8 | HTL-MPV-1 | QPTESIVRFPNITNLCPFG | 5 | 93.42%(469/502) | S-protein/321-339 |
| 9 | HTL-MPV-1 | ADYSVLYNSASFSTFKC | 3 | 93.82%(471/502) | S-protein/363-379 |
| 10 | HTL-MPV-1 | YADSFVIRGDEVRQIAPGQ | 5 | 93.62%(470/502) | S-protein/396-414 |
| 11 | HTL-MPV-1 | VVVLSFELLHAPATVCGPK | 5 | 92.23%(463/502) | S-protein/510-528 |
| 12 | HTL-MPV-1 | IAIPTNFTISVTTEILPVS | 5 | 93.82%(471/502) | S-protein/712-730 |
| 13 | HTL-MPV-1 | ECSNLLLQYGSFCTQLNR | 4 | 93.82%(471/502) | S-protein/748-765 |
| 14 | HTL-MPV-1 | QQLIRAAEIRASANLA | 2 | 93.22%(468/502) | S-protein/1010-1025 |
| 15 | HTL-MPV-1 | REGVFVSNGTHWFVTQ | 2 | 93.22%(468/502) | S-protein/1091-1106 |
| 16 | HTL-MPV-1 | PWYIWLGFIAGLIAIVMVTIMLCC | 9 | 93.42%(469/502) | S-protein/1213-1236 |
| 17 | HTL-MPV-1 | DDQIGYYRRATRRIRGGDG | 5 | 98.79%(492/498) | N-Protein/81-99 |
| 18 | HTL-MPV-1 | GTRNPANNAAIVLQLPQGTTL | 7 | 97.38%(485/498) | N-Protein/147-167 |
| 19 | HTL-MPV-1 | WPQIAQFAPSASAFFGMSR | 5 | 97.38%(485/498) | N-Protein/301-319 |
| 20 | HTL-MPV-1 | TPSGTWLTYTGAIKLDDKD | 5 | 97.18%(484/498) | N-Protein/325-343 |
| 21 | HTL-MPV-1 | SDFVRATATIPIQASLP | 3 | 99.37%(478/481) | 3a/26-42 |
| 22 | HTL-MPV-1 | APFLYLYALVYFLQSINFV | 5 | 96.46%(464/481) | 3a/103-121 |
| 23 | HTL-MPV-1 | DTGVEHVTFFIYNKIVDEPEEHV | 7 | 99.37%(478/481) | 3a/222-244 |
| S.No. | HTL-MPVs | CTL epitope cluster- based Ag-Patches | Number of epitopes in cluster | Conservancy | Source SARS-CoV-2 protein |
| 24 | HTL-MPV-2 | AIILASFSASTSAFVET | 3 | 100%(453/453) | 1ab/474-490/nsp2 |
| 25 | HTL-MPV-2 | YAFASEAARVVRSIFS | 2 | 99.55%(451/453) | 1ab/534-549/nsp2 |
| 26 | HTL-MPV-2 | TLEETKFLTENLLLYIDIN | 5 | 99.77%(452/453) | 1ab/1242-1260/nsp3 |
| 27 | HTL-MPV-2 | VQQESPFVMMSAPPAQYEL | 5 | 99.77%(452/453) | 1ab/1798-1816/nsp3 |
| 28 | HTL-MPV-2 | LLQLCTFTRSTNSRIKASM | 5 | 98.23%(445/453) | 1ab/2176-2194/nsp3 |
| 29 | HTL-MPV-2 | SKLINIIIWFLLLSVCL | 3 | 97.79%(443/453) | 1ab/2224-2240/nsp3 |
| 30 | HTL-MPV-2 | EWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFI SNSWLMWLIINLVQMA | 17 | 100%(453/453) | 1ab/2326-2375/nsp3 |
| 31 | HTL-MPV-2 | VRMYIFFASFYYVWKSYV | 4 | 98.45%(446/453) | 1ab/2381-2398/nsp3 |
| 32 | HTL-MPV-2 | WLKQLIKVTLVFLFVAAIFYLITPVH | 9 | 99.77%(452/453) | 1ab/2769-2794/nsp4 |
| 33 | HTL-MPV-2 | FSAVGNICYTPSKLIEYT | 4 | 99.55%(451/453) | 1ab/2889-2906/nsp4 |
| 34 | HTL-MPV-2 | DISASIVAGGIVAIVVTCL | 5 | 100%(453/453) | 1ab/3042-3060/nsp4 |
| 35 | HTL-MPV-2 | FTPLVPFWITIAYIICIST | 5 | 100%(453/453) | 1ab/3132-3150/nsp4 |
| 36 | HTL-MPV-2 | VQSTQWSLFFFLYENAFLP | 5 | 92.27%(418/453) | 1ab/3595-3613/nsp6 |
| 37 | HTL-MPV-2 | QAIASEFSSLPSYAAFAT | 4 | 99.33%(450/453) | 1ab/3942-3959/nsp8 |
| 38 | HTL-MPV-2 | TQMNLKYAISAKNRART | 3 | 99.77%(452/453) | 1ab/4932-4948/nsp12 |
| 39 | HTL-MPV-2 | RAMPNMLRIMASLVLARKH | 5 | 100%(453/453) | 1ab/5016-5034/nsp12 |
| 40 | HTL-MPV-2 | FVNEFYAYLRKHFSMMIL | 4 | 100%(453/453) | 1ab/5133-5150/nsp12 |
| 41 | HTL-MPV-2 | PEVKILNNLGVDIAAN | 2 | 99.77%(452/453) | 1ab/6519-6534/nsp15 |
| 42 | HTL-MPV-2 | SQMEIDFLELAMDEFIERY | 5 | 99.11%(449/453) | 1ab/6659-6677/nsp15 |
| 43 | HTL-MPV-2 | FAWWTAFVTNVNASSS | 2 | 98.89%(448/453) | 1ab/6985-7000/nsp16 |
| 44 | HTL-MPV-2 | HANYIFWRNTNPIQLSSY | 4 | 98.89%(448/453) | 1ab/7023-7040/nsp16 |
| 45 | HTL-MPV-2 | EILLIIMRTFKVSIWNLDYIINLIIK | 6 | 99.16%(477/481) | orf6/13-38 |
| 46 | HTL-MPV-2 | MKIILFLALITLATCELY | 4 | 99.37%(478/481) | orf7a/1-18 |
| 47 | HTL-MPV-2 | LSLIDFYLCFLAFLLFLVLIMLIIFWFSLEL | 14 | 97.88%(231/236) | 7b/4-34 |
| 48 | HTL-MPV-2 | CTQHQPYVVDDPCPIHFYS | 5 | 99.16%(476/480) | orf8/25-43 |
| 49 | HTL-MPV-2 | YINVFAFPFTIYSLLLCRM | 5 | 99.37%(476/479) | orf10/3-21 |