The untimely descent of Omicron upon the United States over the holidays has reignited fears that Covid-19 is here to stay. But as new variants continue to come out of the woodwork and wreak havoc across the world, scientists continue to unveil the exact mechanisms by which SARS-CoV-2 evades immune protection. The hope is that even if the virus evolves to further suppress immunity, novel antiviral Covid-19 therapies can counteract its program of evasion before it begins, minimizing adverse health outcomes for high-risk groups or preventing them altogether.

I’ve discussed at length in previous pieces how SARS-CoV-2 is remarkably adept at targeting and inhibiting the natural (innate) immune response, the body’s first line of defense against invading pathogens. By coding for viral proteins that block immune detection of microbial threats, SARS-CoV-2 is able to establish infection and proliferate to high titers before the immune system can react. One of these proteins is open reading frame 6, or Orf6. Thanks to a recent study we now know much more about how it acts.

The point of interference that is the primary focus of this study, authored by Yoo, is major histocompatibility complex class I (MHC-I). MHC molecules have one primary function: to present antigens, or fragments of a foreign substance, to the immune system so it can generate antibodies specific to that substance. MHC-I molecules present antigens to cytotoxic T cells in particular, which play a critical role in the adaptive immune response. Activation of the MHC-I pathway in turn relies on the production of type II interferons, a subtype of the signaling proteins that induce much of our innate immune activity. For SARS-CoV-2, interferons are enemy number one; MHC-I represents one angle of many from which the virus attempts to delay interferon production.

MHC class I pathway

Activation of IFNGR by IFNγ triggers immediate phosphorylation of STAT1. Subsequently, … [+]“SARS-COV-2 INHIBITS INDUCTION OF THE MHC CLASS I PATHWAY BY TARGETING THE STAT1-IRF1-NLRC5 AXIS” HTTPS://WWW.NATURE.COM/ARTICLES/S41467-021-26910-8.PDF

Orf6 suppresses MHC-I RNA synthesis

Yoo found that SARS-CoV-2 Orf6 suppresses MHC-I via two major routes. The first is preventing transcription. Orf6 has previously been shown to inhibit type I interferons by inhibiting nuclear localization of STAT1, which is required for interferon type I and III messenger RNA synthesis. Induction of gamma interferons is known to stimulate MHC-I production. Yoo show that in a similar fashion, by inhibiting STAT1 nuclear import, Orf6 also inhibits gamma interferon production, thereby limiting the expression of MHC-I.

Orf6 suppresses NLRC5

The second route Orf6 takes to suppress MHC-I is by preventing nuclear localization of NLRC5. IRF1 (interferon responsive factor 1) and NLRC5 (NOD-like receptor family CARD domain containing five) are two key transcription regulators for MHC-I. Orf6 inhibits them by binding to proteins along the karyopherin pathway, preventing their import and further attenuating MHC-I production.  In SARS-CoV-2 genes they tested in the laboratory, Yoo observed, in the presence of Orf6, an 87 percent reduction in IRF1 activity and an 83 percent reduction in NLRC5 activity.

Orf6 binds to another component of nuclear import called Nup98. Another recent paper found that Orf6 blocks entry of NLRC5 by interfering with Nup98, which is required to import a broad array of nuclear proteins. The carboxy terminus is key to the ability of Orf6 to perform this function.

In summary, SARS-CoV-2 tamps down MHC-I, rendering it invisible to some aspects of the immune system. This study shows that SARS-CoV-2 targets a key regulatory protein at two different levels. One, to prevent its synthesis, and two, to prevent it from entering the nucleus, where it must act to induce MHC-I.

Orf6 seems to be one of the most central players because not only does it suppress MHC-I, which is important for clearance, but it also suppresses interferons type I and III, meaning it suppresses a whole host of interferon-stimulated genes. Recent studies show the activity of Orf6 is increased in some of the variants, as compared to the original Wuhan strain. In particular, Nevan Krogan’s research group has shown, in their study “Evolution of enhanced innate immune evasion by SARS-CoV-2,” that three genes, N, Orf6, and Orf9b, are overexpressed in the Alpha variant. This increased propensity for immune suppression can account in part for the increased replicative abilities and even pathogenesis of new variants.

Immune suppression mediated by viral proteins is not a disarmament tactic specific to SARS-CoV-2 alone. Notably, other studies show that cancer cells downregulate NLRC5 for the same purpose, to evade immune detection. But SARS-CoV-2 does appear to be more proficient at inhibiting natural immunity than other potentially lethal respiratory viruses, like influenza. In SARS-CoV-2-infected patients, Yoo observed an average 66 percent reduction in MHC-I expression. In cells infected with influenza, no such reduction occurred—in fact, it was the opposite, with a 20-fold increase in MHC-I indicative of a robust innate immune response.

We need Covid-19 drug development efforts that account for the ways in which this disease differs immunologically from the flu. If we can’t gain the upper hand over SARS-CoV-2, it will continue to outmaneuver the best of our pandemic control measures.