SARS-CoV-2 ORF8 limits expression levels of Spike antigen

Abstract

Survival from COVID-19 depends on the ability of the host to effectively neutralize virions and infected cells, a process largely driven by antibody-mediated immunity. However, with the newly emerging variants that evade Spike-targeting antibodies, re-infections and breakthrough infections are increasingly common. A full characterization of SARS-CoV-2 mechanisms counteracting antibody-mediated immunity is needed. Here, we report that ORF8 is a SARS-CoV-2 factor that controls cellular Spike antigen levels. ORF8 limits the availability of mature Spike by inhibiting host protein synthesis and retaining Spike at the endoplasmic reticulum, reducing cell-surface Spike levels and recognition by anti-SARS-CoV-2 antibodies. With limited Spike availability, ORF8 restricts Spike incorporation during viral assembly, reducing Spike levels in virions. Cell entry of these virions leaves fewer Spike molecules at the cell surface, limiting antibody recognition of infected cells. Our studies propose an ORF8-dependent SARS-CoV-2 strategy that allows immune evasion of infected cells for extended viral production.

Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves

“…Given that the Spike protein is the best protective antigen for both infection and vaccines, mutations in other genes are more likely to provide fitness advantages if they affect Spike expression. E.g., ORF8 limits the amount of Spike proteins that reaches the cell surface and is incorporated into virions, reducing recognition by anti-SARS-CoV-2 antibodies [30]. ORF8 has accordingly been target of convergent evolution in Omicron (e.g., ORF8:S667F in BR.2.1, ORF8:G8x in XBB.1) and in SARS-related coronaviruses [31].…”

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

“…A dispensable ORF8 and increased viral replication speed due to a shortened genome cannot explain positive fitness effects associated with premature stop codons. Recent work by Kim et al identifies an intriguing biological mechanism underlying positive selection for ORF8 knockout and the timeline for knockout to sweep 55 . Their study finds that ORF8 covalently interacts with spike at the endoplasmic reticulum, reducing onward transport of spike to the cell membrane and incorporation into virus particles.…”