Challenges and developments in universal vaccine design against SARS-CoV-2 variants

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had become a global concern because of its unexpectedly high pathogenicity and transmissibility. SARS-CoV-2 variants that reduce the immune protection elicited from previous vaccination or natural infection raise challenges in controlling the spread of the pandemic. The development of universal vaccines against these variants seems to be a practical solution to alleviate the physical and economic effects caused by this disease, but it is hard to achieve. In this review, we describe the high mutation rate of RNA viruses and dynamic molecular structures of SARS-CoV-2 variants in several major neutralizing epitopes, trying to answer the question of why universal vaccines are difficult to design. Understanding the biological basis of immune evasion is crucial for combating these obstacles. We then summarize several advancements worthy of further study, including heterologous prime-boost regimens, construction of chimeric immunogens, design of protein nanoparticle antigens, and utilization of conserved neutralizing epitopes. The fact that some immunogens can induce cross-reactive immune responses against heterologous coronaviruses provides hints for universal vaccine development. We hope this review can provide inspiration to current universal vaccine studies.

Fig. 1. Circulating strains of SARS-CoV-2 are fast-changing.

a Genetic relationships of global SARS-CoV-2 strains. The unrooted phylogenic tree is constructed by Nextstrain according to the sequences of 3050 SARS-CoV-2 spike glycoproteins from GISAID collected between December 2019 and October 2022 (https://nextstrain.org/ncov/gisaid/global/6m?l=unrooted&m=div). The tree is colored by clade and branch length represents the divergence of each clade. The Omicron variants show the highest antigenic distinction to the ancestral strain. b Time course of prevalent SARS-CoV-2 variants substitutions worldwide. The x-axis represents the date and the y-axis shows the frequencies of viral strains in percentage. Omicron subvariants have rapidly outcompeted previously prevalent Delta variants and become dominant.

Fig. 2. Composition of SARS-CoV-2 S and alignment of S mutation points of SARS-CoV-2 variants.

a S can be proteolytically cleaved into S1 and S2 subunit. The S1 subunit contains the immunodominant N-terminal domain (NTD) and receptor-binding domain (RBD) as well as other subdomains. Fusion peptide (FP), heptad repeat 1 (HR1), heptad repeat 2 (HR2), transmembrane domain (TM), C-terminal peptide (CP) together with other unnamed parts comprise the S2 subunit. Names of the variants are labeled on both sides of the table. Mutation points are distinguished by different colors. Changes in Omicron-related strains are labeled with darker colors. Amino acid sequence of the index virus is included as a reference. At each given point, a hyphen means the amino acid is identical to that of the reference, Δ stands for deletion, ins stands for insertion, and various capital letters indicate substitutions. b Spatial positions of mutations in Alpha, Beta, Gamma, Delta, and Omicron variants are highlighted in structure models (PDB 6XR8).

Fig. 3. Schematic demonstration of chimeric antigen design.

a Combinations of chimeric RBDs. Prototype-Beta chimeric RBD-dimer is a tandem repeat single chain dimer built with one prototype RBD and one Beta RBD. Similarly, Delta-Omicron RBD-dimer is built with one Delta and one Omicron RBD. For NVSI-06-08 or chimeric RBD trimer, three RBDs were truncated from prototype, Beta and Kappa variants and connected end-to-end. Structural arrangements of chimeric RBD dimers or trimer are shown in lower panel. Each monomer is marked by the same color as that shown in the upper panel. b Antigenic S ectodomain formed by building blocks from different SARS-CoV-2 strains. The recombinant monomeric spike variant (STFK1628x, annotated as chimeric S) contains the NTD from Mu variant, RBD-S2 from Gamma variant and RBD region is additionally patched by mutations from Delta variant. For the Delta RBD-Omicron chimera design, the Omicron spike is used as a backbone and the Delta RBD is inserted directly upstream of the Omicron RBD. c There are four spike chimera constructs from different Beta-CoVs in total. Spike chimera 1 contains an HKU3-1-derived NTD, SARS-CoV-derived RBD, and SARS-CoV-2-derived S2. Spike chimera 2 contains a SARS-CoV-2-derived RBD, and the NTD and S2 are of SARS-CoV origin. The origins of the building blocks in spike chimera 3 are opposite to that of spike chimera 2. Spike chimera 4 includes an RBD from RsSHC014 and the rest are from SARS-CoV-2. A model of chimera 1 is generated by PyMOL based on a previously solved cryo-EM structure (PDB 6XR8).

Fig. 4. Overview of antigens presented by nanoparticles.

Plug-and-play platform increases the efficiency of protein subunit vaccine production. Aquifex aeolicus lumazine synthase (LuS) is chosen as a scaffold to induce significantly higher neutralizing responses. The RBDs fused with an Fc tag forms an antigen dimer automatically, enabling rapid generation of vaccines targeting to variants. Sortase-A (Srt-A) is chosen for accurately ligating antigens onto nanoparticles. More than one antigen can be assembled onto the same ferritin nanoparticle using SpyTag, SpyTag003 or I53-50A, which can induce cross-reactive immunity against other coronaviruses or Sarbecoviruses. SARS SARS-CoV, SARS-2 SARS-CoV-2.

Fig. 5. S2 is more conserved and has distinct neutralizing epitopes.

a Heatmap diagram showing the S1 and S2 sequence identity of SARS-CoV-2 variants and other representative Beta-CoVs compared with the ancestral SARS-CoV-2 strain. Sequence information of each strain was obtained from the NCBI database and identity was generated automatically while blasting against the corresponding sequence from the reference. Pink, low identity; Green, high identity. b 3D structural model diagram presents the neutralizing epitopes of SARS-CoV-2 S2. The entire SARS-CoV-2 spike trimer is shown with the transparent molecular surface and S2 trimer is shown in a cartoon. Peptides that interact with isolated monoclonal antibodies are highlighted with different colors, with corresponding sequences and positions listed below. A zoomed-in view of the interaction between the CC40.8 antibody and the S2 stem-helix is shown in the cyan rectangle. The main chain of the S2 stem peptide is colored in green, while the heavy chain (HC) and light chain (LC) of the antibody are shown in orange and yellow, respectively. The S trimer model is generated by PyMOL based on a previously solved cryo-EM structure (PDB 6XR8). Zoomed-in view of the interaction between CC40.8 and stem helix is reconstructed by PyMOL (PDB 7SJS).

Fig. 6. Four strategies in SARS-CoV-2 universal vaccine design.

They are heterologous prime-boost vaccination regimens, construction of protein nanoparticle antigens, design of chimeric immunogens, and utilization of conserved neutralizing epitopes.