The antigenicity of SARS-CoV-2 Delta variants aggregated 10 high-frequency mutations in RBD has not changed sufficiently to replace the current vaccine strain

Abstract

Emerging SARS-CoV-2 variants are the most serious problem for COVID-19 prophylaxis and treatment. To determine whether the SARS-CoV-2 vaccine strain should be updated following variant emergence like seasonal flu vaccine, the changed degree on antigenicity of SARS-CoV-2 variants and H3N2 flu vaccine strains was compared. The neutralization activities of Alpha, Beta and Gamma variants' spike protein-immunized sera were analysed against the eight current epidemic variants and 20 possible variants combining the top 10 prevalent RBD mutations based on the Delta variant, which were constructed using pseudotyped viruses. Meanwhile, the neutralization activities of convalescent sera and current inactivated and recombinant protein vaccine-elicited sera were also examined against all possible Delta variants. Eight HA protein-expressing DNAs elicited-animal sera were also tested against eight pseudotyped viruses of H3N2 flu vaccine strains from 2011-2019. Our results indicate that the antigenicity changes of possible Delta variants were mostly within four folds, whereas the antigenicity changes among different H3N2 vaccine strains were approximately 10-100-fold. Structural analysis of the antigenic characterization of the SARS-CoV-2 and H3N2 mutations supports the neutralization results. This study indicates that the antigenicity changes of the current SARS-CoV-2 may not be sufficient to require replacement of the current vaccine strain.

Fig. 1. Circulating variants and most common amino acid changes in SARS-CoV-2 S protein.

a VOC and VOI count. The VOC and VOI count data were obtained from outbreak.org (https://outbreak.info/situation-reports?name) up to July 19th, 2021. VOCs and VOIs were classified by the WHO. b The percentage of the top 12 amino acid changes in S protein. These data were sourced from COVIDCG.org (https://covidcg.org/?tab=home&undefined=All&selectedGene=S&residueCoordinates=319,541&startDate=2019-12-15&undefined=All) up to July 19th, 2021. c The amino acid changes introduced in this study. The most common amino acid changes except for L452R and T478K are indicated. (d) The illustration of the VOCs and VOIs. Delta was used as the template on which to add mutations. L452R and T478K located in the RBD of B.1.617.2 were not included in the additional mutagenesis. S spike, SARS-CoV-2 severe acute respiratory syndrome coronavirus 2, VOC variant of concern, VOI variant of interest, WHO World Health Organization, COVID coronavirus disease

Fig. 2. Neutralization activity of Alpha, Beta, and Gamma S protein-immunized sera against VOCs and VOIs.

The SARS-CoV-2 S protein from D614G, Alpha, Beta, or Gamma variants were used to immunize mice. The sera were collected for neutralization activity testing against the indicated VOCs and VOIs. The mean results of neutralization ED₅₀ from three repeated experiments are shown as a dot plot. a–d The red arrow indicates neutralization against homologous pseudotyped virus. The dashed lines represent the geometric mean and fourfold reduction for serum response of the homologous virus, respectively. e ED₅₀ heat map of homologous and heterologous sera and virus. f ED₅₀ of one serum against homologous and heterologous variants are summarized into one column. S spike, VOC variant of concern, VOI variant of interest, ED₅₀, 50% effective dilution

Fig. 3. Neutralization activity of Alpha, Beta, and Gamma S protein- immunized sera against possible Delta variants with multiple amino acid changes in RBD.

The S protein trimer from D614G and three VOCs (Alpha, Beta, Gamma) were used individually to immunize mice. Sera were collected and tested for neutralization activity against B.1.617.2 (Delta) variant-based possible variants with multiple amino acid changes in RBD. Mean ED₅₀ from three repeated experiments are shown as dot plots. The dashed lines represent the geometric mean and fourfold reduction for serum response of the reference Delta variant, respectively. Dashed lines indicate a fourfold difference of ED₅₀ compared with the Delta reference strain. S spike, RBD receptor binding domain, SARS-CoV-2 severe acute respiratory syndrome coronavirus 2, VOC variant of concern, ED₅₀ 50% effective dilution

Fig. 4. Neutralization activity of convalescent and vaccine-elicited sera against possible Delta variants with multiple amino acid changes in RBD.

The neutralization activity of convalescent serum (a), recombinant S protein vaccine-immunized sera (b and c), and inactive vaccine-immunized sera (d) against different potential SARS-CoV-2 variants were tested. Mean ED₅₀ from three repeated experiments are shown as dot plots. The dashed lines represent the geometric mean and fourfold reduction for serum response of the reference Delta variant, respectively. RBD receptor binding domain, SARS-CoV-2 severe acute respiratory syndrome coronavirus 2, ED₅₀ 50% effective dilution

Fig. 5. Neutralization activity of influenza HA plasmid-immunized sera against H3N2 vaccine strains.

Guinea pigs were immunized with influenza HA plasmids of the vaccine strains of 2011–2019. Sera were collected for neutralization activity testing against pseudotyped viruses of the H3N2 vaccine strains from 2011–2019. Mean ED₅₀ from three repeated experiments are shown as dot plots. Dashed lines indicate 4-, 10-, and 100-fold differences compared with the corresponding vaccine strain. The homologous neutralization activity is compared in the last graph. HA haemagglutinin, H3N2 haemagglutinin 3 neuraminidase 2, ED₅₀ 50% effective dilution

Fig. 6. Antigenic variation analyses of H3N2 HA and SARS-CoV-2 S proteins.

a The percent identities of amino acid sequences of representative H3N2 HA and SARS-CoV-2 S protein are shown respectively. b The surface view of an H3N2 HA trimer (A/Victoria/361/2011; PDB code: 4O5N) is shown. One monomer of the HA surface is colored using the ConSurf server according to sequence conservation from the most conserved (dark purple) to the most divergent (dark green) based on the alignment of H3N2 sequences from different vaccine strains. The five antigenic sites A (yellow), B (cyan), C (green), D (blue) and E (pink) are highlighted in dotted circles. c The surface view of the SARS-CoV-2 D614G S protein trimer (PDB code: 7KE9) is shown. One monomer of the S surface is colored using the ConSurf server according to sequence conservation from the most conserved (dark purple) to the most divergent (dark green) based on the alignment of S sequences from different VOC strains. The receptor-binding sites are highlighted in dotted circles. HA haemagglutinin, H3N2 haemagglutinin 3 neuraminidase 2, SARS-CoV-2 severe acute respiratory syndrome coronavirus 2, S spike, PDB protein data bank, VOC variant of concern