Distinguishing features of current COVID-19 vaccines: knowns and unknowns of antigen presentation and modes of action

Abstract

COVID-19 vaccines were developed with an unprecedented pace since the beginning of the pandemic. Several of them have reached market authorization and mass production, leading to their global application on a large scale. This enormous progress was achieved with fundamentally different vaccine technologies used in parallel. mRNA, adenoviral vector as well as inactivated whole-virus vaccines are now in widespread use, and a subunit vaccine is in a final stage of authorization. They all rely on the native viral spike protein (S) of SARS-CoV-2 for inducing potently neutralizing antibodies, but the presentation of this key antigen to the immune system differs substantially between the different categories of vaccines. In this article, we review the relevance of structural modifications of S in different vaccines and the different modes of antigen expression after vaccination with genetic adenovirus-vector and mRNA vaccines. Distinguishing characteristics and unknown features are highlighted in the context of protective antibody responses and reactogenicity of vaccines.

Fig. 1. Biosynthesis and intracellular transport of S.

a Infected cells: Subgenomic mRNAs for viral structural proteins are translated in association with the ER (S, M, and E) or in the cytoplasm (N), and virus assembly takes place in the ERGIC. Virus particles are transported through the TGN and released from the cells probably via lysosomes. During transport, S is cleaved into S1 and S2 by the cellular protease furin in the TGN. Some spike molecules, not assembled into virions, are also transported to the plasma membrane despite the presence of an ER retention signal. b Transfected cells: Biosynthesis of S occurs in the absence of interactions with other viral proteins. Proteolytic cleavage into S1 and S2 occurs in the TGN similar to that in infected cells, but some shedding of cleaved S1 and conversion of S2 into its post-fusion structure (S2*) may occur in the absence of stabilizing mutations. ER—endoplasmic reticulum; ERGIC—endoplasmic reticulum Golgi intermediate compartment; TGN—Trans Golgi Network; RNP—Ribonucleoprotein; Viral proteins: S—spike, M—membrane; E—envelope; N—nucleoprotein.

Fig. 2. Structures of the spike protein in pre- and post-fusion conformations.

a Trimeric pre-fusion spike with all RBDs in ‘down’ position. b Trimeric pre-fusion spike with one RBD in ‘up’ position. c Monomeric S protein of the pre-fusion spike with the RBD in red and NTD in gold, as well as the following structural details: The two stabilizing prolines (2 P) are shown in pink, the FP in orange. The two protease cleavage sites are indicated by arrows. d Trimeric post-fusion structure of S2, with the three dissociated S1 subunits, shaded in light colors. RBD—receptor binding domain; NTD—N-terminal domain; FP—fusion peptide. The structures were generated with PyMol, using protein data bank (PDB) files 7KRR and 7KRS for the pre-fusion forms, 6XRA for the post-fusion form. The domains were colored according to reference..

Fig. 3. Configuration of mRNA vaccines.

a Schematic of the vaccine mRNA in BionTech-Pfizer and Moderna vaccines. UTR—untranslated region. b Schematic of a lipidnanoparticle (LNP) used for delivery of mRNA vaccines. PEG—polyethyleneglycol.

Fig. 4. Principle of adenovirus vector vaccines.

a Schematic of replication-incompetent adenoviral vector particle and its DNA. E1 and E3: Early adenovirus genes 1 and 3, respectively. b Formation of vaccine particles in production cell line complementing E1 from chromosomally integrated E1 gene. Release of newly produced vector particles through cell lysis. c Expression of spike in cells of vaccinated individuals. More or less shedding of S1 and conversion of S2 into its post-fusion structure (S2*) may occur in the absence of stabilizing mutations.

Fig. 5. Signal sequence-mediated transport of S into the lumen of the ER.

a Schematic of the process using the authentic viral signal peptide only (as in the vaccines of BionTech-Pfizer, Moderna, Janssen-Johnson&Johnson and Gamaleya Institute). In the CanSino vaccine, the signal peptide of S is replaced by that of human tPA (https://patents.google.com/patent/CN111218459B/en). b Schematic of the process using an additional N-terminal leader sequence (signal peptide and propeptide of tPA), as used in the vaccine of Oxford-Astra Zeneca, based on reference. ). SP—signal peptide; SRP—signal recognition particle; tPA—tissue plasminogen activator; ER—endoplasmic reticulum; C-ter—C terminus; N-ter—N terminus.