Increasing intrinsic protein disorder improves CD8+ immunogenicity for a SARS CoV2 vaccine candidate antigen

CD8+ T cell targeting of the conserved SARS CoV2 RNA-dependent RNA polymerase (RdRp, nsp12) may offer a means for cross-protection against diverse coronavirus strains. Native RdRp, however, displays primary sequence immunoevasion (PSI) that inhibits in cis RdRp-derived peptide presentation on major histocompatibility complex class I. We show that this is related to the highly ordered nature of RdRp, which can be reversed by dividing RdRp into two intrinsically disordered, complementary sub-fragments (RdRp^Frag). RdRp^Frag possesses nearly all of the native peptide epitopes found in the full-length protein. Using a syngeneic MC38 cancer cell mouse model, cellular RdRp^Frag expression suppressed tumor growth and markedly increased specific tumor-infiltrating effector T lymphocytes as measured by tetramer assays. mRNA vaccination with WA-1 strain RdRp^Frag elicited more potent CD8+ T cell responses than native WA-1 strain RdRp mRNA but did not significantly prevent acute Omicron SARS CoV2 early infection in transgenic hamster challenge studies. These findings suggest highly ordered protein evolution may be an unrecognized PSI mechanism used by viruses to evade T cell recognition. Increasing antigen intrinsic disorder by protein subfragmentation may improve antigenicity for antiviral or antitumor vaccine candidates.