Table 3. List of top-scoring SARS-CoV-2-derived helper T-cell epitopes, their average adjusted ranks, and population coverage results in the most-affected countries with COVID-19 .
| Sequence | Position | APR * | Coverage of MHC class I allele | Coverage a (%) | Average hit b | Pc90 c |
| TLDSKTQSLLIVNNATNVVIKVCEFQF# | 109–135 | 0.19 | DRB1*04:01, DRB1*13:02, DRB3*02:02 | 14.24±9.16 | 0.15±0.1 | 0.12±0.01 |
| YRVVVLSFELLHAPATVCGPKKS# | 508–530 | 0.25 | DRB1*01:01 | 10.74±6.4 | 0.11±0.07 | 0.11±0.01 |
| FKNLREFVFKNIDGYFKIYSKHTPI# | 186–210 | 0.39 | DRB5*01:01 | NA | NA | NA |
| IGINITRFQTLLALHRSYLTP# | 231–251 | 0.50 | DRB1*01:01, DRB1*15:01, DRB5*01:01 | 23.81±12.87 | 0.25±0.14 | 0.14±0.02 |
| MFVFLVLLPLVSSQCVNLT | 1–19 | 0.52 | DRB1*01:01, DRB1*11:01 | 20.44±10.42 | 0.21±0.11 | 0.13±0.02 |
| KVGGNYNYLYRLFRKSNLKPFER# | 444–466 | 0.57 | DRB1*11:01 | 11.09±4.95 | 0.11±0.05 | 0.11±0.01 |
| IAIPTNFTISVTTEILPVSMT# | 712–732 | 0.58 | DRB1*07:01 | 17.35±7.49 | 0.17±0.07 | 0.12±0.01 |
| TITSGWTFGAGAALQIPFAMQ# | 881–901 | 0.58 | DRB1*01:01, DRB1*09:01 | 15.2±9.3 | 0.15±0.1 | 0.12±0.02 |
| HFPREGVFVSNGTHWFVTQRNF# | 1088–1109 | 0.59 | DRB1*13:02, DRB3*01:01, DRB3*02:02 | 6.98±4.07 | 0.07±0.04 | 0.11±0.01 |
| VYADSFVIRGDEVRQIAPGQTGK | 395–417 | 0.64 | DRB3*01:01 | NA | NA | NA |
| SKHTPINLVRDLPQGFSALEP# | 205–225 | 0.64 | DRB1*03:01, DRB3*01:01 | 19.12±12.55 | 0.19±0.13 | 0.13±0.03 |
| KCVNFNFNGLTGTGVLTES | 537–555 | 0.69 | DRB1*09:01 | 6.21±7.34 | 0.06±0.07 | 0.11±0.01 |
| ADYSVLYNSASFSTFKC | 363–379 | 0.70 | DRB3*02:02 | NA | NA | NA |
| NATRFASVYAWNRKRISN | 343–360 | 0.71 | DRB5*01:01 | NA | NA | NA |
| ECSNLLLQYGSFCTQLNR | 748–765 | 0.71 | DRB1*15:01 | 15.01±8.07 | 0.15±0.08 | 0.12±0.01 |
| ENQKLIANQFNSAIGKI | 918–934 | 0.72 | DRB3*02:02 | NA | NA | NA |
| GNCDVVIGIVNNTVYDPL | 1124–1141 | 0.72 | DRB1*13:02 | 6.98±4.07 | 0.07±0.04 | 0.11±0.01 |
| AALQIPFAMQMAYRFNGI | 892–909 | 0.74 | DRB4*01:01 | NA | NA | NA |
| VQPTESIVRFPNITNLCPFG | 320–339 | 0.78 | DRB1*04:05, DRB1*15:01 | 18.42±8.21 | 0.19±0.08 | 0.12±0.01 |
| FGGFNFSQILPDPSK | 797–811 | 0.81 | DRB1*04:05 | 4.81±6.13 | 0.05±0.06 | 0.1±0.01 |
| ALNTLVKQLSSNFGAIS | 958–974 | 0.81 | DRB1*04:01 | 8.0±7.17 | 0.08±0.07 | 0.11±0.01 |
| DLFLPFFSNVTWFHAI | 53–68 | 0.91 | DRB1*04:01, DRB3*02:02 | 8.0±7.17 | 0.08±0.07 | 0.11±0.01 |
| RAAEIRASANLAATKM | 1014–1029 | 0.93 | DRB3*02:02 | NA | NA | NA |
| LTDEMIAQYTSALLAGT | 865–881 | 0.94 | DRB1*15:01 | 15.01±8.07 | 0.15±0.08 | 0.12±0.01 |
Abbreviation: APR,Average percentile rank.
a Average (±SD) projected population coverage. b Average number of epitope hits/HLA combinations recognized by the population. c Minimum number of epitope hits/HLA combinations recognized by 90% of the population. Four HLA-II alleles (DRB5*01:01, DRB3*01:01, DRB4*01:01, and DRB3*02:02) were not available in population coverage calculation. NA: not available. Final selected CD4+ T-cell epitopes are indicated by #.