Towards developing a variant-proof SARS-CoV-2 vaccine

New targets for broad-spectrum vaccines are urgently needed to defend the variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In a recent study in Cell Research, Pang et al. reported a novel variant-proof SARS-CoV-2 vaccine targeting a transient intermediate conformational status of the HR domains in the S2 subunit.

The S2 subunit of spike protein is known to be highly conserved compared to the S1 subunit among different coronaviruses. Thus, a pan-coronavirus fusion inhibitor against the S2 subunit of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) would be appreciated for dealing with the future potential variants and sublineages.¹ During cell infection by the SARS-CoV-2 virus, the heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of spike protein S2 region assemble into a six-helix bundle to fuse virus envelope to the host cell membrane, and release viral RNA into the host cell.² An S2 subunit structural analysis has shown that mutations do not alter the global architecture of the post-fusion HR1–HR2 bundle in the variants, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors against most variants of SARS-CoV-2.³ Synthetic peptides or other inhibitory molecules for blocking the HR transformation are logical approaches to inhibit viral entry to the host cells.^4,5 However, the short half-life of peptides limits their clinical application. Moreover, the S2 conformation is highly dynamic during membrane fusion, presenting a significant challenge in discovering blocking peptides or antibodies against this protein subunit.⁶ In this aspect, viral proteins mimicking the intermediate conformation are valuable for designing vaccines targeting the coronavirus S2 protein. Several S2 vaccines have been reported, providing beneficial information.^7,8

In a study published in Cell Research, the authors have designed and developed a novel SARS-CoV-2 vaccine (HR1–HR2–HR1, HR121 recombinant protein) targeting the HR1 domain present in the fusion intermediate conformation of the S2 subunit of SARS-CoV-2 spike protein.⁹ Interestingly, two molecules of this HR121 protein were assembled into a dimer to mimic the HR1 helices at the fusion intermediate conformation of the S2 subunit, resulting in the exposure of the antigen epitopes that elicit antibodies to block the interaction between viral HR1 and HR2 domains, and inhibition of fusion between cellular and viral membranes. The authors observed that HR121 could evoke prolonged potent cross-neutralizing antibodies to SARS-CoV-2 and all the variants, including Omicron and its current sublineages. Notably, the HR121 vaccine showed complete protection of hACE2 mice, hamsters, and monkeys against the SARS-CoV-2 challenge. These data confirm that the conserved HR1 domain in the S2 subunit of the SARS-COV-2 spike protein can serve as a novel target for developing variant-proof SARS-CoV-2 vaccines or pan-sarbecovirus vaccines.

Most recent COVID-19 vaccines under investigation are still based on the spike or RBD proteins, chasing the emerged variants or containing RBDs from divergent sarbecovirus.¹⁰ S2-targeted vaccines are additional choices for broader protection. The combination of multiple SARS-CoV-2 key immunogenic domains is another potential vaccine strategy. A ferritin nanoparticle vaccine containing RBD and HR subunits was reported to elicit high-titer S-specific neutralizing antibodies (NAbs), protecting hACE2 mice from SARS-CoV-2 virus infection.¹¹ Remarkably, only the RBD–HR but not RBD nanoparticles could induce NAbs to other coronaviruses. Recently, a study of a simplified version of the RBD–HR trimer was published, which also induced protective immunity against variants and Omicron sublineages.¹² These studies demonstrate the potential of vaccines of S2 in conjunction with RBD in pan-coronavirus prophylactics and therapeutics.

Several potential obstacles may be addressed in the future. First, it still needs a long-term investigation to determine whether the broad-spectrum S2-based vaccines result in much less immune escape for coronaviruses than the S1-based vaccines. Second, for HR-based vaccine development, it is elaborate and time-consuming to choose successful intermediate fusion conformation on one hand and, on the other hand, to avoid post-fusion conformations that distract the host immunity by non-neutralizing epitope exposure. Moreover, the study by Pang et al. reveals that antigen-stabilizing strategies may require further exploration to design stable coronavirus S2-associated vaccines.

In summary, Pang et al. developed an HR121 vaccine based on the fusion domain of S2. The HR121 vaccine can induce robust NAbs to protect animal models from SARS-CoV-2 infection. Moreover, the NAbs induced by HR121 demonstrated similar activities against Omicron and its sublineages. Their study opens a new avenue for inventing a series of pan-sarbecovirus vaccine candidates.