The SARS-CoV-2 accessory factor ORF7a downregulates MHC class I surface expression

Abstract

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 500 million infections and more than six million deaths worldwide. Although the viral genomes of SARS-CoV-1 and SARS-CoV-2 share high sequence homology, the clinical and pathological features of COVID-19 differ profoundly from those of SARS. It is apparent that changes in viral genes contribute to the increased transmissibility of SARS-CoV-2 and pathology of COVID-19. Cytotoxic T lymphocytes play a key role in the elimination of virus-infected cells, mediated by recognition of virus-derived peptides that are presented on MHC class I molecules. Here, we show that SARS-CoV-2 can interfere with antigen presentation thereby evading immune surveillance. SARS-CoV-2 infection of monkey and human cell lines resulted in reduced cell-surface expression of MHC class I molecules. We identified a single viral gene product, the accessory factor open reading frame 7a (ORF7a), that mediates this effect. ORF7a interacts with HLA class I molecules in the ER, resulting in ER retention or impaired HLA heavy chain (HC) trafficking to the Golgi. Ultimately, these actions result in reduced HLA class I surface expression on infected cells. Whereas ORF7a from SARS-CoV-2 reduces surface HLA class I levels, the homologous ORF7a from the 2002 pandemic SARS-CoV-1 did not, suggesting that SARS-CoV-2 ORF7a acquired the ability to downregulate HLA-I during evolution of the virus. We identified a single amino acid in the SARS-CoV-1 ORF7a luminal domain that, upon mutating to the corresponding SARS-CoV-2 ORF7a sequence, induced a gain-of-function in HLA surface downregulation. By abrogating HLA class I antigen presentation via ORF7a, SARS-CoV-2 may evade host immune responses by inhibiting anti-viral cytotoxic T cell activity, thereby contributing to the pathology of COVID-19.

SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression

“…Given the functional consequence of localization of ORF7a we have observed, we suggest that studies employing C-terminally tagged ORF7a need to be interpreted with caution. However, a recent report that has not been peer-reviewed found that C-terminally tagged ORF7a was capable of down-regulating MHC-I in HEK293T cells ( 41 ) and that the C-terminal tail was not necessary for this function ( 42 ). While we expressed ORF7a-ARA in an inducible manner, the ORF7a in these two studies was transiently expressed, and we are investigating whether this or other mechanisms account for this difference.…”

SARS-CoV-2 ORF8: One protein, seemingly one structure, and many functions

“…O R F 6 w a s i d e n t i fi e d a s a p o t e n t i a l immunomodulatory protein based on its role in targeting NLRC5, a critical transcriptional regulator of the gene coding for MHC I heavy chain (17). More recently, in bioRxiv-deposited articles, ORF3a and ORF7a were shown to reduce MHC I cell-surface expression via distinct mechanisms (13,14). ORF3a exerted a more general effect on suppressing the trafficking of proteins, including MHC I molecules, through the secretory pathway (13).…”

“…ORF3a exerted a more general effect on suppressing the trafficking of proteins, including MHC I molecules, through the secretory pathway ( 13 ). On the other hand, ORF7a acted more specifically by associating with the MHC I heavy chain, possibly as a molecular mimic of β 2 m, thereby slowing the export of correctly assembled MHC I molecules out of the ER ( 13 , 14 ).…”

“…For example, ORF3b, ORF6, ORF7a, and ORF8 act as a type I interferon (IFN) antagonist (9)(10)(11)(12). ORF3a, ORF6, ORF7a, and ORF8 interfere with the major histocompatibility complex class I (MHC I) pathway at the transcriptional or post-translational levels (13)(14)(15)(16)(17). ORF9b interacts with cellular organelles suppressing antiviral responses, while the functions of ORF7b and ORF10 remain to be further elucidated (8,18).…”

SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition

“…To successfully establish infection and replicate in the host, many viruses have acquired the ability to inhibit MHC-I processing and presentation of viral antigens (14). Likewise, SARS-CoV-2 utilizes its viral proteins to interfere with the MHC-I pathway (15)(16)(17)(18)(19). SARS-CoV-2 ORF8 protein induces autophagic degradation of MHC-I and confers resistance to CTL surveillance (15).…”