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

Abstract

Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β 2 -microglobulin (β 2 m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8 + T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that down-regulate MHC-I expression to avoid CD8 + T cell recognition. Here, we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, down-regulate MHC-I expression using distinct mechanisms. First, ORF3a, a viroporin, reduces the global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β 2 m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a specific mechanism that allows immune evasion by SARS-CoV-2.

Genomic surveillance of SARS-CoV-2 positive passengers on flights from China to Italy, December 2022

“…It includes three separate domains: an N-terminal signal sequence (15 residues), an ectodomain with Ig-like fold (beta sandwich), a short transmembrane domain, and a C-terminal cytoplasmic tail containing a di-lysine motif ( 117 KRKTE 121 ) for endoplasmic reticulum (ER) localisation. Among the various interactions with host proteins, ORF7a interacts specifically with the major histocompatibility complex (MHC)-I heavy chain, acting as a molecular mimic of β 2 -microglobulin (β 2 m) to inhibit MHC-I heavy chain association with β 2 m; this slows the exit of properly assembled MHC-I molecules from the ER [12], potentially limiting cell-mediated immune responses. Zheng et al found that F59, absent in SARS-CoV, is associated with such function [13].…”

“…The BF.7 variant has been circulating in United States and Europe since August 2022 [12][13][14], and in Inner Mongolia since September 2022. The apparently high prevalence of BF.7.14 in China is presumably due to a founder effect: selection pressure from immune escape is much lower in China, where the contribution of previous infection-elicited immunity is less relevant than elsewhere, so it makes sense not to expect a rapid takeover by BQ.1* and XBB*.…”

Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies

“…These observations, along with the emergence of de novo responses to non-Spike antigens during the second week, indicate that vaccine-induced humoral immunity does not sufficiently control SARS-CoV-2 replication to prevent T cell engagement or the generation of new immune responses to non-Spike antigens. Moreover, although SARS-CoV-2 has been reported to downregulate MHC class I 42,43 , this effect did not prevent CD8 T cell priming during breakthrough infection, though it is possible that some aspects of immune evasion delayed the kinetics of these responses. Nonetheless, despite rapid induction of activation markers and Ki67, a marker of proliferation, in Spike-specific memory CD8 T cells, numerical expansion of these cells in the blood was inconsistent.…”

“…Alternatively, if pre-existing antibody titers are low and new production of antibody lags, memory T cells could play a key role in controlling viral replication during the early phase of infection, thus limiting viral spread and disease progression. It is also possible that SARS-CoV-2 possesses strategies to evade initial host immune responses enabling temporary escape from early activation of immune memory 42, 43, 44, 45 . In any of these scenarios, even a low level of pre-existing neutralizing antibodies could be an important correlate of protection from severe disease 46 .…”

Pathways to altered virulence of SARS-CoV-2

“…Enhanced innate immune suppression has already been observed for SARS-CoV-2, as variants of SARS-CoV-2 (alpha, delta, and omicron) all demonstrate robust overexpression of the N protein, as well as the protein products of the Orf 9b and Orf 6 genes (101). SARS-CoV-2 also suppresses the T cell response through these gene products by downregulating MHC I expression (102)(103)(104). Gain-of-function immune suppression is not linked to the spike protein and is consequently free to evolve independently of ACE2 affinity.…”