Table 1.
Comparison of Baselines, S-protein Peptides, and OptiVax Designed Peptide Vaccines (Using All SARS-CoV-2 Proteins or SMN Proteins Only) on Various Population Coverage Evaluation Metrics and Vaccine Quality Metrics (Percentage of Peptides with Mutation rate > 0.001 or with Non-zero Probability of being Glycosylated)
| Peptide Set | Vaccine Size | EvalVax-Unlinked | EvalVax-Robust p(n≥1) | EvalVax-Robust p(n≥5) | EvalVax-Robust p(n≥8) | Exp. # Peptide-HLA Hits/Vaccine Size | Exp. # Peptide-HLA Hits (White) | Exp. # Peptide-HLA Hits (Black) | Exp. # Peptide-HLA Hits (Asian) | Peptides Glycosylated | Peptides Mutation Rate > 0.001 | On Cleavage Site | Protein Origins | In SARS-CoV |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MHC Class I Peptide Vaccine Evaluation | ||||||||||||||
| OptiVax Augmented Nonredundant S-Protein | 126 + 16 | 100.00% | 100.00% | 99.97% | 99.27% | 20.50% | 27.20 | 27.68 | 32.44 | 0.00% | 0.00% | 0.00% | M, N, ORF1a, ORF1b, ORF3a, S1, S2 | 30.28% |
| S-Protein | 3795 | 99.96% | 100.00% | 99.17% | 98.29% | 0.91% | 30.84 | 32.14 | 41.13 | 15.57% | 29.99% | 0.63% | S1, S2 | 29.30% |
| OptiVax-Unlinked | 19 | 99.79% | 99.99% | 89.15% | 49.59% | 40.72% | 7.34 | 6.90 | 8.97 | 0.00% | 0.00% | 0.00% | ORF1a, ORF1b, ORF3a, S1 | 42.11% |
| Nonredundant S-protein | 126 | 99.84% | 99.93% | 97.37% | 91.69% | 16.82% | 19.20 | 19.99 | 24.38 | 0.00% | 0.00% | 0.00% | S1, S2 | 27.78% |
| OptiVax-Robust | 19 | 99.39% | 99.91% | 93.21% | 67.75% | 49.26% | 9.36 | 8.52 | 10.21 | 0.00% | 0.00% | 0.00% | ORF1a, ORF1b, ORF3a, ORF9b, S1 | 52.63% |
| OptiVax-Robust – size 15 | 15 | 99.07% | 99.89% | 86.69% | 54.36% | 54.47% | 8.17 | 7.20 | 9.14 | 0.00% | 0.00% | 0.00% | ORF1a, ORF1b, ORF9b, S1 | 53.33% |
| Nonredundant S1-subunit | 68 | 99.18% | 99.76% | 86.53% | 56.36% | 12.23% | 8.31 | 8.84 | 7.80 | 0.00% | 0.00% | 0.00% | S1 | 8.82% |
| (Srivastava et al., 2020) | 37 | 95.86% | 99.75% | 52.94% | 16.00% | 13.51% | 5.37 | 4.99 | 4.64 | 8.11% | 37.84% | 0.00% | E, M, N, ORF10, ORF1a, ORF1b, ORF3a, ORF6, ORF7a, ORF7b, ORF8, S1 | 45.95% |
| OptiVax-Robust – S/M/N only | 26 | 97.49% | 98.15% | 67.37% | 26.24% | 22.31% | 5.31 | 5.64 | 6.45 | 0.00% | 0.00% | 0.00% | M, N, S1, S2 | 57.69% |
| (Herst et al., 2020) | 52 | 90.89% | 95.82% | 56.52% | 19.99% | 9.88% | 5.20 | 4.44 | 5.77 | 7.69% | 34.62% | 0.00% | N | 55.77% |
| (Herst et al., 2020) – top 16 | 16 | 80.41% | 93.46% | 9.47% | 0.03% | 15.73% | 2.75 | 2.60 | 2.20 | 12.50% | 12.50% | 0.00% | N | 68.75% |
| Random subset of binders | 19 | 81.04% | 90.33% | 25.02% | 4.58% | 16.74% | 3.01 | 2.83 | 3.70 | 0.00% | 29.89% | 0.00% | N/A | 40.37% |
| (Baruah and Bose, 2020) | 5 | 71.91% | 90.10% | 0.55% | 0.00% | 33.60% | 1.93 | 1.44 | 1.67 | 0.00% | 40.00% | 0.00% | S1, S2 | 40.00% |
| (Fast et al., 2020) | 13 | 78.66% | 85.29% | 58.51% | 30.56% | 44.25% | 5.59 | 4.98 | 6.69 | 7.69% | 30.77% | 0.00% | E, M, N, ORF1a, S1, S2 | 23.08% |
| (Poran et al., 2020) | 10 | 69.12% | 85.13% | 3.21% | 0.01% | 19.23% | 1.68 | 1.72 | 2.37 | 0.00% | 30.00% | 0.00% | ORF1a, ORF1b, ORF3a, ORF8, S1 | 20.00% |
| (Vashi et al., 2020) | 51 | 68.63% | 80.80% | 1.52% | 0.00% | 3.12% | 1.90 | 1.70 | 1.17 | 11.76% | 43.14% | 5.88% | S1, S2 | 5.88% |
| (Abdelmageed et al., 2020) | 10 | 66.91% | 78.49% | 23.49% | 2.72% | 28.34% | 2.93 | 2.50 | 3.07 | 10.00% | 10.00% | 0.00% | E | 80.00% |
| (Lee and Koohy, 2020) | 13 | 64.96% | 75.75% | 39.82% | 37.09% | 34.15% | 4.77 | 3.69 | 4.86 | 0.00% | 7.69% | 0.00% | E, N, ORF1a, ORF1b, S2 | 53.85% |
| (Akhand et al., 2020) | 31 | 49.46% | 71.24% | 0.08% | 0.00% | 3.47% | 1.09 | 1.11 | 1.02 | 3.23% | 35.48% | 0.00% | E, M, N, S1 | 41.94% |
| (Singh et al., 2020) | 7 | 53.91% | 66.59% | 1.38% | 0.00% | 19.87% | 1.34 | 1.30 | 1.53 | 0.00% | 28.57% | 0.00% | E, M, N, S1, S2 | 71.43% |
| (Bhattacharya et al., 2020) | 13 | 44.56% | 61.09% | 0.00% | 0.00% | 5.67% | 0.79 | 0.69 | 0.73 | 23.08% | 46.15% | 7.69% | S1, S2 | 23.08% |
| (Ahmed et al., 2020) | 16 | 45.25% | 52.30% | 35.61% | 4.15% | 15.57% | 2.56 | 2.18 | 2.73 | 12.50% | 25.00% | 0.00% | N, S2 | 100.00% |
| (Saha and Prasad, 2020) | 5 | 29.90% | 41.77% | 0.00% | 0.00% | 8.86% | 0.56 | 0.36 | 0.41 | 0.00% | 20.00% | 0.00% | S1 | 20.00% |
| (Gupta et al., 2020) | 7 | 30.23% | 38.91% | 21.08% | 1.41% | 23.92% | 1.32 | 0.55 | 3.15 | 0.00% | 42.86% | 0.00% | S1, S2 | 14.29% |
| (Khan et al., 2020) | 3 | 27.14% | 34.98% | 0.00% | 0.00% | 17.33% | 0.76 | 0.56 | 0.24 | 0.00% | 66.67% | 0.00% | S1, S2 | 0.00% |
| (Mitra et al., 2020) | 9 | 13.97% | 23.86% | 0.00% | 0.00% | 2.83% | 0.15 | 0.08 | 0.54 | 22.22% | 11.11% | 0.00% | S1, S2 | 11.11% |
| MHC Class II Peptide Vaccine Evaluation | ||||||||||||||
| OptiVax-Unlinked | 19 | 91.67% | 99.67% | 95.94% | 83.30% | 64.45% | 14.37 | 12.71 | 9.66 | 0.00% | 0.00% | 0.00% | M, ORF1a, ORF1b, S2 | 52.63% |
| OptiVax-Robust | 19 | 90.76% | 99.67% | 97.21% | 88.48% | 76.04% | 16.64 | 15.71 | 11.00 | 0.00% | 0.00% | 0.00% | M, ORF1a, ORF1b, S1, S2 | 42.11% |
| OptiVax Augmented Nonredundant S-protein | 102 + 26 | 91.65% | 99.67% | 98.73% | 97.27% | 26.81% | 43.79 | 36.06 | 23.12 | 0.00% | 0.00% | 0.00% | M, ORF1a, ORF1b, S1, S2 | 29.69% |
| (Ramaiah and Arumugaswami, 2020) | 134 | 87.28% | 98.88% | 90.20% | 83.97% | 25.18% | 45.04 | 38.25 | 17.93 | 20.15% | 44.78% | 0.00% | E, M, N, S1, S2 | 30.60% |
| S-protein | 16315 | 89.80% | 98.76% | 95.99% | 95.73% | 2.22% | 492.82 | 385.60 | 208.34 | 30.01% | 57.50% | 1.43% | S1, S2 | 16.06% |
| OptiVax-Robust – S/M/N only | 22 | 86.34% | 98.57% | 85.37% | 62.49% | 42.51% | 11.31 | 9.69 | 7.05 | 0.00% | 0.00% | 0.00% | M, N, S1, S2 | 36.36% |
| Nonredundant S-protein | 102 | 84.91% | 98.56% | 82.72% | 77.19% | 16.61% | 23.54 | 17.04 | 10.23 | 0.00% | 0.00% | 0.00% | S1, S2 | 28.43% |
| Nonredundant S1-subunit | 53 | 77.14% | 95.81% | 63.43% | 41.82% | 16.33% | 13.07 | 8.74 | 4.16 | 0.00% | 0.00% | 0.00% | S1 | 3.77% |
| Random subset of binders | 19 | 72.41% | 93.61% | 58.67% | 32.40% | 31.59% | 7.72 | 6.49 | 3.79 | 0.00% | 63.79% | 0.00% | N/A | 23.55% |
| (Fast et al., 2020) | 13 | 67.29% | 86.99% | 15.24% | 3.69% | 19.69% | 3.65 | 2.26 | 1.77 | 30.77% | 38.46% | 0.00% | E, M, N, ORF1a, S1, S2 | 0.00% |
| (Banerjee et al., 2020) | 9 | 56.73% | 83.51% | 12.49% | 0.66% | 26.65% | 3.16 | 2.35 | 1.68 | 22.22% | 44.44% | 0.00% | S1, S2 | 55.56% |
| (Tahir ul Qamar et al., 2020) | 11 | 39.44% | 72.75% | 0.27% | 0.00% | 11.62% | 1.84 | 1.46 | 0.53 | 0.00% | 72.73% | 0.00% | E, M, N, ORF10, ORF6, ORF7a, ORF8 | 36.36% |
| (Poran et al., 2020) | 10 | 42.30% | 69.37% | 0.00% | 0.00% | 9.83% | 1.47 | 0.91 | 0.57 | 20.00% | 90.00% | 0.00% | ORF1a, ORF1b, ORF3a, S2 | 20.00% |
| (Akhand et al., 2020) | 31 | 43.90% | 60.45% | 9.22% | 1.01% | 6.08% | 2.53 | 2.54 | 0.59 | 3.23% | 48.39% | 0.00% | E, M, N, S1 | 29.03% |
| (Singh et al., 2020) | 7 | 41.48% | 56.29% | 0.96% | 0.00% | 14.02% | 1.44 | 1.11 | 0.39 | 0.00% | 28.57% | 0.00% | E, M, N, S1, S2 | 71.43% |
| (Ahmed et al., 2020) | 5 | 27.69% | 54.96% | 0.00% | 0.00% | 13.08% | 0.74 | 0.72 | 0.51 | 0.00% | 20.00% | 0.00% | N, S2 | 100.00% |
| (Mitra et al., 2020) | 5 | 25.46% | 47.92% | 0.04% | 0.00% | 13.14% | 0.90 | 0.58 | 0.49 | 60.00% | 20.00% | 0.00% | S1, S2 | 0.00% |
| (Vashi et al., 2020) | 20 | 20.78% | 35.12% | 0.04% | 0.00% | 3.36% | 0.96 | 0.62 | 0.44 | 15.00% | 35.00% | 5.00% | S1, S2 | 0.00% |
| (Abdelmageed et al., 2020) | 10 | 19.15% | 28.40% | 0.96% | 0.00% | 4.79% | 0.92 | 0.27 | 0.24 | 60.00% | 70.00% | 0.00% | E | 30.00% |
| (Baruah and Bose, 2020) | 3 | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00 | 0.00 | 0.00 | 66.67% | 100.00% | 0.00% | S1 | 0.00% |
S-protein includes all possible S-protein peptides of lengths 8–10 (MHC class I) and 13–25 (MHC class II). Nonredundant peptide sets are a result of OptiVax analysis of nonredundant displayed peptides. The table is sorted by EvalVax-Robust p(n ≥ 1). Random subsets are generated 200 times. The binders used for generating random subsets are defined as peptides that are predicted to bind with affinity ≤ 50 nM to more than 5 of the alleles.