S protein is the largest structural protein of SARS-CoV-2 [26]. Previous studies have reported that SARS-CoV-2 S protein can induce the immune system to produce neutralizing antibodies [27]. S protein is the most antigenic protein of SARS-CoV-2, and it is also the main target protein for the development of vaccines and clinical diagnosis.
DNA has a double-helix structure that is relatively stable and does not often make mistakes during replication and propagation. RNA, however, has a single-stranded structure, which lacks this stability, making it more likely than DNA to mutate during replication and propagation. SARS-CoV-2, an RNA virus, is likely to mutate during transmission. In order to understand if the sequence, structure, and epitopes of SARS-CoV-2 have changed, we performed this bioinformatics analysis to compare these properties of SARS-CoV-2 in the sequences published by China, USA, Czech, Korea, Greece, Australia, Thailand, Turkey, Sweden, and India.
According to the results, the 5th, 115th, 197th, 221st, 247th, 261st, 271st, 323rd, 367th, 453rd, 501st, 614th, 631st, 771st, 797th, 829th, 930th, 939th, 1181st, 1248th, and 1250th amino acids have changed in the sequences published by USA, Czech, Korea, Greece, Australia, Thailand, Turkey, Sweden, and India. However, the similarity of the sequence was still more than 99%, indicating that the sequence did not change greatly as the virus spread. After analyzing the secondary structures of SARS-CoV-2 S protein, we found that the secondary structures had changed as the amino acid mutated, creating an additional turn region in the mutation area of the sequence in Korea, while a coil region and a turn region disappeared in the mutation amino acids of Sweden and India, respectively. The turn and coil are mostly located on the surface of the protein, and structures are prominent. There are possible epitope regions in the turn and coil. Therefore, the antigenicity of SARS-CoV-2 in Korea may be enhanced, while it may be weakened in Sweden and India. We constructed a 3D model of SARS-CoV-2 S protein to show the location of mutated amino acids and found that almost all of the mutated amino acids were on the outside of the SARS-CoV-2 S protein. This suggests that the exterior of the protein structure is exposed to the external environment and seems to be prone to mutation. In terms of epitope analysis, B cell epitopes analysis suggested that antigenicity of SARS-CoV-2 from Greece, Australia, Sweden and India (MT050493.1) were weakened while the antigenicity of SARS-CoV-2 in Korea, USA (MT370991.1, MT457401.1, MT457395.1, MT444634.1), India (MT396242.1) may be enhanced. Australia, Sweden, and India (MT050493.1) may be weakened. These results of B cell epitope analysis were almost consistent with the results of T cell epitope analysis. Interestingly, the antigenicity of SARS-CoV-2 from USA were enhanced after mutation. Previous research indicated that USA may be the birthplace of SARS-CoV-2 (Forster et al., 2020) (Appendix figure 1), suggesting SARS-CoV-2 of China may come from the United States. Therefore, the mutations may lead to a decrease in the antigenicity of the virus in the process of spreading. The antigen mutations bring difficulties to herd immunity, and there may be double virus infections, which may bring opportunities for resistance to mutant viruses.