SARS-CoV-2 spike subunit conformation determines plasma-neutralizing activity triggered by COVID-19 vaccines and natural infection

By Neha MathurNov 14 2022Reviewed by Aimee Molineux

In a recent study published in Science Immunology, researchers evaluated the effect of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein conformation on S-directed neutralizing antibodies (nAbs).

Background

Serum-neutralizing activity is the most widely used correlate of protection against coronavirus disease 2019 (COVID-19). Thus, it is crucial to understand the molecular basis of the elicitation of nAbs by a wide range of COVID-19 vaccines and SARS-CoV-2 infections in humans. It is also noteworthy that all regions of SARS-CoV-2 S, namely, the S1 and S2 subunit, the N-terminal domain (NTD), the receptor-binding domain (RBD), and the S2 subunit have a role to play in eliciting cross-neutralizing activity against SARS-CoV-2 variants.

About the study

In the present study, researchers evaluated plasma immunoglobulin G (IgG) titers against prefusion-stabilized SARS-CoV-2 S trimer, the S1 subunit, the NTD, the RBD, and the S2 subunit in the pre-fusion (S2_(Pre)) and post-fusion (S2_(Post)) states.

The team retrieved serum samples from individuals not previously exposed to SARS-CoV-2 but recipients of a primary vaccination series of any of the following vaccines: mRNA-1273, BNT162b2, NVX-CoV2373, and Ad26.COV2.S, AZD1222, Sputnik V, or BBIBP-CorV. They benchmarked these samples against COVID-19 convalescent plasma obtained from people infected with the Wuhan-Hu1 strain before or in January 2021.

Further, the team compared perfusion S, S1, and S2_(Pre)-directed antibody titers to post-fusion S2-directed antibodies across all seven vaccines and infections. Finally, they investigated the relationship between antibody-binding titers and neutralization potency.

Study findings

Enzyme-linked immunosorbent assays (ELISA) results showed that the recipients of two doses of mRNA-1273 or BNT162b2 had the highest prefusion S binding titers, with geometric mean titers (GMTs) of 8.1 and 7.5, respectively. Conversely, Wuhan-Hu 1-infected individuals had the lowest and most heterogeneous prefusion S binding titers, with a GMT value of 3.8.

The recipients of a two-dose regimen of NVX-CoV2373, Ad26.COV2.S, AZD1222, Sputnik V, and BBIBP-CorV displayed intermediate prefusion S binding with GMTs of 4.8, 5.3, 6.3, 5.0, and 5.2, respectively. Intriguingly, the trend did not change when the researchers computed S binding titers using the S1 subunit, the NTD, or the RBD as ELISA antigens.

The researchers noted preferential targeting of prefusion S by antibodies elicited by most vaccines, particularly those containing the ‘2P’ prefusion-stabilizing S mutations. The S1/S2(Post) binding ratio followed the same trend following infection and two-dose vaccination. Vaccines containing prefusion-stabilizing mutations, thus, elicited a higher proportion of S- and S1 relative to S2(Post)-directed polyclonal plasma antibodies compared to infection and vaccines lacking such mutations.

Vaccination markedly enhanced the magnitude of antibody binding responses against all antigens tested; however, vaccine type was the primary determinant of the magnitude of boosting. For instance, post- to pre-vaccination prefusion S binding titers increased 2.6, 1.8, and 2.1 times after a two-dose regimen of BNT162b2, AZD1222, and a single dose of Ad26.COV2.S, respectively.

The explanation for such observations lies hidden in the metastable nature of the S trimer. The S trimer is inherently prone to shedding the S1 subunit and refolding to form post-fusion trimers; thus, the absence of prefusion-stabilizing S mutations in the AZD1222 vaccine explains why it elicited slightly lower S/S2(Post) binding ratios relative to BNT162b2 and Ad26.COV2.S. The study data showed that immunization with any of these three vaccines after an infection turned nAb responses preferentially toward prefusion S relative to post-fusion S2, unlike infection. Consistent with prior reports, vaccinating previously infected individuals elicited higher nAb titers than the two doses of mRNA-1273 or BNT162b2 in naive individuals. The authors noted a strong positive correlation between in vitro plasma inhibitory activity and the magnitude of antibody responses against the prefusion-stabilized S trimer for all vaccines and infection-elicited polyclonal antibodies.

Furthermore, the authors noted a positive correlation between NTD- and RBD-specific binding nAb titers, two domains nested in the S1 subunit. A comparable positive correlation between neutralizing activity and S1 binding antibody responses suggested the significant role of S1-directed antibodies for SARS-CoV-2 neutralization.

Conclusions

The study demonstrated that prefusion SARS-CoV-2 S binding titers correlated with plasma neutralizing activity primarily due to targeting of the S1 subunit, which comprises antigenic sites recognized by most nAbs, which are subsequently shed upon refolding.

Targeting the S2 subunit did not contribute much to vaccine-elicited polyclonal neutralizing activity due to the low frequency and weak potency of fusion machinery-directed nAbs.However, screening larger cohorts might help identify subjects with a higher proportion of S2-targeting neutralizing antibodies. So, the rapid accumulation of amino acid residue mutations in the SARS-CoV-2 S1 subunit throughout the COVID-19 pandemic might reflect, at least partially, the selective pressure exerted by host-neutralizing antibodies.

The study results reinstated the benefits of eliciting the higher quality of humoral immune responses elicited by vaccination compared to natural infection. Besides direct nAb-mediated viral neutralization, Fc-mediated effector functions (examples include antibody-dependent phagocytosis and complement activation) play a key role in vivo protection. Nevertheless, these findings should direct the clinical development of RBD-based vaccines against SARS-CoV-2 and sarbecoviruses for future pandemic preparedness.