A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity?

Abstract

The S glycoprotein of coronaviruses is important for viral entry and pathogenesis with most variable sequences. Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this study. In phylogenetic analysis, two subtypes (SARS-CoV-2a and -b) were confirmed within SARS-CoV-2 strains. These two subtypes were divided by a novel synonymous mutation of D614G. This may play a crucial role in the evolution of SARS-CoV-2 to evade the host immune system. The region containing this mutation point was confirmed as a B-cell epitope located in the S1 domain, and SARS-CoV-2b strains exhibited severe reduced antigenic indexes compared to SARS-CoV-2a in this area. This may allow these two subtypes to have different antigenicity. If the two subtypes have different serological characteristics, a vaccine for both subtypes will be more effective to prevent COVID-19. Thus, further study is urgently required to confirm the antigenicity of these two subtypes.

Keywords: COVID-19; SARS-CoV-2; antigenicity; spike protein.

Figure 1

Characterization of the complete S gene in SARS-CoV-2. (A) Phylogenetic analysis of SARS-CoV-2 strains based on the S gene. The phylogenetic trees were reconstructed from 144 sequences of SARS-CoV-2 collected globally. Thus, the two subtypes (SARS-CoV-2a and -2b) were completely divided. (B) Alignment of SARS-CoV sequences including the aa 614 position are highlighted in gray. A novel reliable synonymous mutation was identified to distinguish the A and B subtypes. SARS-Cov-2a and -2b strains consistently exhibited Ala (D) and Gly (G) at the amino acid sequence position 614, respectively. (C) Identification of B-cell epitopes in the adjacent area with aa 614. The B-cell epitope was predicted by BepiPred-2.0 [24], the Chou & Fasman method [25], the Kolaskar and Tongaonkar method [26], and Parker’s Hydrophilicity [27]. The 614–621 region was predicted to consist of epitopes. (D) The 3D-structure of SARS-CoV-2 spike protein by Mol soft Mol Browser 3.8–5 according to the original publication from the National Center for Biotechnology Information (NCBI): PDB;6VXX. The predicted B-cell epitope (aa 613–620) highlighted in black color was located at a relatively well-exposed part. (E) Sequence alignment of SARS-CoV-1 and -2. The S1 subunit is responsible for receptor binding and the S2 subunit mediates membrane fusion. The S1 subunit consists of two major domains capable of binding to host receptors: an amino (N)-terminal domain (NTD) and a carboxy (C)-terminal domain (CTD) and two sub-domains that may allow receptor-induced conformational changes: SD-1 and SD-2. (F) The antigenic index of each amino acid constituting this region (amino acids 613–621) by the Jameson–Wolf method [28].

Figure 1

Characterization of the complete S gene in SARS-CoV-2. (A) Phylogenetic analysis of SARS-CoV-2 strains based on the S gene. The phylogenetic trees were reconstructed from 144 sequences of SARS-CoV-2 collected globally. Thus, the two subtypes (SARS-CoV-2a and -2b) were completely divided. (B) Alignment of SARS-CoV sequences including the aa 614 position are highlighted in gray. A novel reliable synonymous mutation was identified to distinguish the A and B subtypes. SARS-Cov-2a and -2b strains consistently exhibited Ala (D) and Gly (G) at the amino acid sequence position 614, respectively. (C) Identification of B-cell epitopes in the adjacent area with aa 614. The B-cell epitope was predicted by BepiPred-2.0 [24], the Chou & Fasman method [25], the Kolaskar and Tongaonkar method [26], and Parker’s Hydrophilicity [27]. The 614–621 region was predicted to consist of epitopes. (D) The 3D-structure of SARS-CoV-2 spike protein by Mol soft Mol Browser 3.8–5 according to the original publication from the National Center for Biotechnology Information (NCBI): PDB;6VXX. The predicted B-cell epitope (aa 613–620) highlighted in black color was located at a relatively well-exposed part. (E) Sequence alignment of SARS-CoV-1 and -2. The S1 subunit is responsible for receptor binding and the S2 subunit mediates membrane fusion. The S1 subunit consists of two major domains capable of binding to host receptors: an amino (N)-terminal domain (NTD) and a carboxy (C)-terminal domain (CTD) and two sub-domains that may allow receptor-induced conformational changes: SD-1 and SD-2. (F) The antigenic index of each amino acid constituting this region (amino acids 613–621) by the Jameson–Wolf method [28].

Figure 1

Characterization of the complete S gene in SARS-CoV-2. (A) Phylogenetic analysis of SARS-CoV-2 strains based on the S gene. The phylogenetic trees were reconstructed from 144 sequences of SARS-CoV-2 collected globally. Thus, the two subtypes (SARS-CoV-2a and -2b) were completely divided. (B) Alignment of SARS-CoV sequences including the aa 614 position are highlighted in gray. A novel reliable synonymous mutation was identified to distinguish the A and B subtypes. SARS-Cov-2a and -2b strains consistently exhibited Ala (D) and Gly (G) at the amino acid sequence position 614, respectively. (C) Identification of B-cell epitopes in the adjacent area with aa 614. The B-cell epitope was predicted by BepiPred-2.0 [24], the Chou & Fasman method [25], the Kolaskar and Tongaonkar method [26], and Parker’s Hydrophilicity [27]. The 614–621 region was predicted to consist of epitopes. (D) The 3D-structure of SARS-CoV-2 spike protein by Mol soft Mol Browser 3.8–5 according to the original publication from the National Center for Biotechnology Information (NCBI): PDB;6VXX. The predicted B-cell epitope (aa 613–620) highlighted in black color was located at a relatively well-exposed part. (E) Sequence alignment of SARS-CoV-1 and -2. The S1 subunit is responsible for receptor binding and the S2 subunit mediates membrane fusion. The S1 subunit consists of two major domains capable of binding to host receptors: an amino (N)-terminal domain (NTD) and a carboxy (C)-terminal domain (CTD) and two sub-domains that may allow receptor-induced conformational changes: SD-1 and SD-2. (F) The antigenic index of each amino acid constituting this region (amino acids 613–621) by the Jameson–Wolf method [28].