How SARS-CoV-2 Omicron subvariants have evolved to evade host T-cell immunity

In a recent article published in 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 similar to how these VOCs have acquired mutations within the spike (S) protein to resist 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 ability to inhibit MHC-I processing. SARS-CoV-2, for example, uses its open reading frame 8 (ORF8) protein to autophagic-ally degrade MHC-I molecules and escape CTL surveillance.

Several studies conducted within the first three months of the coronavirus disease 2019 (COVID-19) pandemic reported that SARS-CoV-2 rapidly evolved its ORF8 gene. To date, it remains unclear whether this evolution enhanced the ability 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.

About the study

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

Up to 965 sequences of pre-Omicron and other SARS-CoV-2 lineages were downloaded from various sources, such as the Global Initiative on Sharing All Influenza Data (GISAID) database. ORF8 amino acid sequence alignment was performed to identify 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 standard polymerase chain reaction (PCR)-based mutagenesis method. These mutants were used to determine whether variant-specific mutations altered MHC-I downregulating capability of the SARS-CoV-2 ORF8 protein.

Calu-3 and HEK293T cells were used to assess 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 associated with the highest ability to suppress surface MHC-I expression due to the T9I mutation in 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 at the Q27 position of the Omicron B.1.1.7 subvariant was found to truncate the length of ORF8 and likely alter its functionality. None of these mutations or deletions were conserved among the 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 within 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. Furthermore, 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 escape 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 remains an important viral strategy to combat host immunity and provides important insights into SARS-CoV-2 pathogenesis and evolution. These findings could help predict challenges in discovering CD8 T-cell-based therapies for COVID-19.

In addition to evading nAbs and possessing increased transmissibility, which is likely due to 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 consequences of enhanced MHC-I inhibition by Omicron variants remain unclear.