In a recent article published within the journal PNAS, researchers investigate whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants of concern (VOCs), especially Omicron, have evolved to evade CD8+ T cell-mediated immunity just like how these VOCs have acquired mutations inside the spike (S) protein to withstand neutralizing antibodies (nAbs). To this end, they pursued evidence of the in vitro and in vivo inhibition of major histocompatibility complex class I (MHC-I) upregulation in SARS-CoV-2-infected cells.

Study: Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Image Credit: Starshaker / Shutterstock.com

Background

MHC-I presents viral antigens for CD8+ cytotoxic T lymphocyte (CTL) activation. Upon activation, these cells kill and eliminate virus-infected cells throughout the human body.

Several viruses have developed the flexibility to inhibit MHC-I processing. SARS-CoV-2, for instance, uses its open reading frame 8 (ORF8) protein to autophagic-ally degrade MHC-I molecules and escape CTL surveillance.

Several studies conducted inside the first three months of the coronavirus disease 2019 (COVID-19) pandemic reported that SARS-CoV-2 rapidly evolved its ORF8 gene. So far, it stays unclear whether this evolution enhanced the flexibility of SARS-CoV-2 to shut down MHC-I and subsequently evade antigen-specific memory CD8+ T-cell immunity conferred by prior infection or COVID-19 vaccination.

In regards to the study

In the current study, researchers analyze the potential of SARS-CoV-2 Alpha, Beta, Gamma, and Delta VOCs, in addition to three variants of interest (VOIs), including Epsilon B.1.427/B.1.429, and Iota/B.1.526, to downregulate the MHC-I pathway.

As much as 965 sequences of pre-Omicron and other SARS-CoV-2 lineages were downloaded from various sources, resembling the Global Initiative on Sharing All Influenza Data (GISAID) database. ORF8 amino acid sequence alignment was performed to discover any nonsynonymous mutations in SARS-CoV-2 variants that resulted in differential MHC-I regulation.

Seven SARS-CoV-2 envelope (E), membrane (M), and ORF8-expressing mutants were generated using the usual polymerase chain response (PCR)-based mutagenesis method. These mutants were used to find out whether variant-specific mutations altered MHC-I downregulating capability of the SARS-CoV-2 ORF8 protein.

Calu-3 and HEK293T cells were used to evaluate the impact of SARS-CoV-2 infection on MHC-I expression two days after infection. For the in vivo studies, male C57BL6 mice were intranasally infected with 1 × 105 plaque-forming units (PFU) of SARS-CoV-2 or influenza virus A/Puerto Rico/8/34.

Study findings

The ancestral SARS-CoV-2 strain vigorously suppressed MHC-I surface expression, whereas pre-Omicron VOCs evolved only to some extent for modulating the MHC-I pathway. While all SARS-CoV-2 variants possess the potential to suppress MHC-I expression, the Omicron subvariants were related to the best ability to suppress surface MHC-I expression on account of the T9I mutation of their E protein.

Eight nonsynonymous mutations and two deletions from 16 SARS-CoV-2 variants were implicated in MHC-I regulation of ORF8. Further, a premature stop codon on the Q27 position of the Omicron B.1.1.7 subvariant was found to truncate the length of ORF8 and sure alter its functionality. None of those mutations or deletions were conserved among the many viral lineages, thus suggesting that these variant-specific mutations were acquired independently during SARS-CoV-2 evolution.

In SARS-CoV-2-infected cells, MHC-I upregulation was completely shut down, thus indicating that SARS-CoV-2 viral proteins robustly inhibited MHC-I upregulation inside the cell. Contrastingly, influenza virus infection markedly up-regulated MHC-I expression in vitro.

Conclusions

SARS-CoV-2 uses multiple strategies to suppress MHC-I expression. Moreover, MHC-I downregulation by SARS-CoV-2 was found to impair CTL recognition of infected cells for killing and the priming of CD8+ T-cells.

Interestingly, the SARS-CoV-2 ancestral strain was entirely equipped to flee from CD8+ T cell-mediated immunity. Thus, this strain was under no evolutionary pressure to optimize the downregulation of MHC-I expression, whereas it was under greater pressure to evolve and evade nAb-induced or type I interferon-induced immunity.

MHC-I evasion by SARS-CoV-2 stays a vital viral technique to combat host immunity and provides essential insights into SARS-CoV-2 pathogenesis and evolution. These findings could help predict challenges in discovering CD8 T-cell-based therapies for COVID-19.

Along with evading nAbs and possessing increased transmissibility, which is probably going on account of their heavily mutated S proteins, all Omicron subvariants optimized evasion from T-cell recognition. Although partially, this characteristic allows these mutant strains to cause breakthrough infections and reinfections, even in a largely vaccinated population. Nevertheless, the implications of enhanced MHC-I inhibition by Omicron variants remain unclear.

Journal reference:

• Moriyama, M., Lucas, C., Monteiro, V. S., et al. (2023). Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. PNAS. doi:10.1073/pnas.2221652120