Immune evasion by SARS-CoV-2: the role of HLA class I

ABSTRACT Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic of coronavirus-induced disease 2019 (COVID-19). Since December 2019, coordinated research efforts have provided a wealth of critical data that have enhanced our ability to diagnose and treat COVID-19. To date, however, much of the molecular and cellular mechanisms underlying the pathogenesis of COVID-19 remain elusive. The genome of SARS-CoV-2 contains nine independent open reading frames (ORFs) coding for proteins that are not essential for viral replication but seem to exert important functions in modulating host antiviral immunity. Of these accessory proteins, the ORF8 protein stands out for its unique characteristics. ORF8 is a highly variable protein among SARS-related CoVs. ORF8 also appears to be involved in a network of host-pathogen interactions inside infected cells: ORF8 impairs immune pathways such as antigen presentation, interferon type I, and nuclear factor-kB, as well as possibly activate growth pathways. A central question is how ORF8 mediates interactions with multiple host protein targets. Towards this goal, we are investigating ORF8 interaction with major histocompatibility class I (MHC I) molecules. It was shown recently that SARS-CoV-2 ORF8 suppresses CD8+ T cell responses by downregulating MHC I molecules, both in vitro and in vivo. We hypothesize that ORF8 suppresses surface expression of HLA-A and HLA-B molecules to protect infected cells from recognition by CD8+ T cells, but spares HLA-C and HLA-E to avoid activation of natural killer (NK) cells. The possibility that ORF8 displays a locus specificity toward MHC I would provide a mechanism for SARS-CoV-2 to walk a fine line between adaptive and innate immunity. Specifically, we will undertake an analysis of interactions between ORF8 and MHC I by using a panel of HLA- A, -B, -C, and -E molecules, and also determine if ORF8 selectively downregulates MHC I in relevant cell systems (Aim 1). We will extend these studies to ORF8 variants that have been positively selected during the course of the pandemic and evaluate if and how these mutations affect MHC I binding and downregulation (Aim 2). The successful completion of these Aims is expected to uncover unknown features of ORF8 and elucidate its role in suppressing antigen presentation, as well as inform us on the selective pressure that MHC I exerts on SARS-CoV-2. The immediate and long-term impact of our proposed research is high. This is the first study that: (1) characterizes molecular interaction of ORF8 with a host protein; and (2) evaluates clinically relevant ORF8 variants. By studying the immune interactions underlying ORF8-mediated downregulation of MHC I, we will increase our understanding of how SARS-CoV-2 derails cellular immunity. Importantly, our study will stimulate similar investigations of other ORF8-interactors, providing novel opportunities for the development of therapeutics directed against ORF8 or its host targets.