key: cord-0872591-sedk5rnj
authors: Setaro, Alessandra C.; Gaglia, Marta M.
title: All hands on deck: SARS-CoV-2 proteins that block early anti-viral interferon responses()
date: 2021-11-12
journal: Curr Res Virol Sci
DOI: 10.1016/j.crviro.2021.100015
sha: f38e459cbb0fab94ba0ea7cf0b6720739176b347
doc_id: 872591
cord_uid: sedk5rnj

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is responsible for the current pandemic coronavirus disease 2019 (COVID-19). Like other pathogens, SARS-CoV-2 infection can elicit production of the type I interferon (IFN) cytokines by the innate immune response. A rapid and robust type I and III IFN response can curb viral replication and improve clinical outcomes of SARS-CoV-2 infection. To effectively replicate in the host, SARS-CoV-2 has evolved mechanisms for evasion of this innate immune response, which could also modulate COVID-19 pathogenesis. In this review, we discuss studies that have reported the identification and characterization of SARS-CoV-2 proteins that inhibit type I IFNs. We focus especially on the mechanisms of nsp1 and ORF6, which are the two most potent and best studied SARS-CoV-2 type I IFN inhibitors. We also discuss naturally occurring mutations in these SARS-CoV-2 IFN antagonists and the impact of these mutations in vitro and on clinical presentation. As SARS-CoV-2 continues to spread and evolve, researchers will have the opportunity to study natural mutations in IFN antagonists and assess their role in disease. Additional studies that look more closely at previously identified antagonists and newly arising mutants may inform future therapeutic interventions for COVID-19.

As of November 2nd, 2021, SARS coronavirus 2 (SARS-CoV-2) has infected at least 247 million people 30 and killed more than 5 million worldwide. The scientific community is making a continuous effort to 31 understand this virus and to better combat the disease it causes, COVID-19. Like all successful pathogens, 32 SARS-CoV-2 needs to evade host responses to replicate. Indeed, SARS-CoV-2 suppresses the ability of 33 the infected host to turn on the expression and secretion of the type I and possibly type III interferons 34 (IFNs) [1] . Type I and III IFNs are the first line of defense against viral infections and are crucial early 35

anti-viral factors. SARS-CoV-2 may also reduce cellular responses to IFNs, which normally drive the 36 expression of anti-viral interferon stimulated genes (ISGs) [2], although not all studies agree on this point 37 [3, 4] . Here we will review efforts to identify and characterize proteins from SARS-CoV-2 that can inhibit 38 IFN induction and signaling, as well as evidence that this early response has a crucial role in COVID-19 39 infection ( Figure 1 ). 40 41

severity 43 44 Evidence that the type I IFNs are crucial for COVID-19 pathogenesis comes from studies in COVID-19 45 patients that had disease of varying severity. Patients with mild and moderate COVID-19 have higher 46 IFN-α levels in the blood compared with patients with more severe disease and their type I IFN response 47 is more sustained [5] . This reduction may be due to a failure of innate immune cells to mount a type I IFN 48 response to infection, as evidenced by the reduced frequency and activity of plasmacytoid dendritic cells, 49 the main producers of IFN-α during viral infection [6] . There may also be a transient IFN response in the 50 lungs that is stronger in patients with moderate disease compared to those with severe COVID-19 [6] . 51

These results suggest that the failure to mount a strong type I IFN response contributes to severe COVID-52 19, presumably because an effective type I IFN response is needed to rapidly clear SARS-CoV-2 ( Figure  53 1). 54

Genetic studies of patients with severe disease also support the idea that an efficient type I IFN response 55 is crucial for COVID-19 recovery ( Figure 1 ). Zhang et al. found that at least 3.5% of patients with life-56 threatening COVID-19 had polymorphisms in one of eight genes involved in type I IFN responses and 57 previously associated with severe influenza or other viral infections, including the pathogen sensor TLR3 58 and the type I IFN receptor subunits IFNAR1 and IFNAR2 [7] . At least some of the polymorphisms 59 analyzed were loss-of-function or hypomorphic mutations, although they had had no noticeable effect on 60 J o u r n a l P r e -p r o o f likely bona fide and strong type I IFN antagonists: nsp1, nsp13, and ORF6 as inhibitors of IFN induction, 124 and nsp1, nsp13, nsp14, ORF6, and ORF7b as inhibitors of ISG induction [4, [23] [24] [25] [26] [27] [28] [29] [30] . Also, while most of 125 the screening studies did not test the protease nsp3/PLpro, individual studies revealed that PLpro cleaves 126 the IFN transcription factor IRF3 and interferon-stimulated protein ISG15 ( Figure 2) [31, 32] . Most of the 127 screening studies did not find an effect for the protease nsp5/3CLpro on IFN induction, but 3CLpro does 128 inhibit the pro-inflammatory NFkB pathway by cleaving TAB1, a regulator of the TAK1 protease ( Figure  129 2) [32]. 130

Follow-up studies reveal that SARS-CoV-2 proteins antagonize the type I IFN response at many different 131 points to evade host detection and antiviral response (Figure 2 ), although thorough follow up studies are 132 limited for most proteins. We will discuss results for nsp1 and ORF6 in more detail in subsequent 133 sections, as these proteins have been studied more in-depth and are likely more potent IFN antagonists, as 134 they have been identified in most of the screening studies ( Figure 3 ). Strikingly, collectively these studies 135 indicate that the majority of SARS-CoV-2 proteins may play some role in the disruption of type I IFN 136 signaling (Figure 2-3) . Given that SARS-CoV-2 viral replication can be suppressed by IFN-β treatment 137 [3, 19] , this redundancy in IFN antagonism may be important to viral replication and survival. While none 138 of the studies specifically looked at type III IFN, the same or similar signaling pathways are thought to 139 induce type III IFNs as well. Therefore, the SARS-CoV-2 proteins are generally expected to also impact 140 type III IFNs. 141

To note, all of the screening studies ( Figure 3) [41] Chen Z, Chen J. Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors 389 Charts of studies that have tested the role of SARS-CoV-2 proteins on type I IFN (A) or interferon-stimulated gene (ISG) induction (B). Proteins that showed an effect in each study are in red, proteins that did not have an effect in grey and proteins that were not tested in white.

J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f

Imbalanced 270 Host Response to SARS-CoV-2 Drives Development of COVID-19

CoV-2 triggers an MDA-5-dependent interferon response which is unable to control replication in 274 lung epithelial cells

Type I Interferon Susceptibility Distinguishes SARS-CoV-2 from SARS-CoV

SARS-CoV-2 279 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress 280 the effects of added interferon

Impaired type I interferon 283 activity and inflammatory responses in severe COVID-19 patients

Systems 286 biological assessment of immunity to mild versus severe COVID-19 infection in humans

Inborn errors of type I IFN 289 potentially affecting pathogenesis

Dynamic competition 392 between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation

SARS-CoV-2 infection triggers widespread host mRNA 395 decay leading to an mRNA export block

SARS-CoV-2 uses a 398 multipronged strategy to impede host protein synthesis

The N-terminal 401 domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and 402 preservation of viral gene expression

The viral protein NSP1 405 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 406 translation

Structural Basis and Function of the N Terminus of 408 SARS-CoV-2 Nonstructural Protein 1. Microbiol Spectr 2021:e0016921

Structure of nonstructural protein 1 from SARS-CoV-2

SARS-CoV-2 Nonstructural Proteins 1 and 13 Suppress Caspase-1 413 and the NLRP3 Inflammasome Activation

Protein 1 Inhibits the Interferon Response by Causing Depletion of Key Host Signaling Factors

Emerging of a 419 SARS-CoV-2 viral strain with a deletion in nsp1

Genome-wide 422 analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

Genomic monitoring of SARS-CoV-2 425 uncovers an Nsp1 deletion variant that modulates type I interferon response

Sarbecovirus ORF6 428 proteins hamper induction of interferon signaling

Severe acute 431 respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear 432 import factors on the rough endoplasmic reticulum/Golgi membrane

SARS-CoV-2 435 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and 436 Nup98

Overexpression of 438 SARS-CoV-2 protein ORF6 dislocates RAE1 and NUP98 from the nuclear pore complex

SARS-CoV-2 Orf6 442 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling

A SARS-CoV-2 protein 445 interaction map reveals targets for drug repurposing

Characterization of SARS-CoV-2 448 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance

The type I interferon response in COVID-19: implications for treatment

Crystal structure of SARS-CoV-2 Orf9b in 454 complex with human TOM70 suggests unusual virus-host interactions

SARS-CoV-2 Orf9b suppresses type I 457 interferon responses by targeting TOM70

SARS-CoV-2 N Protein Targets TRIM25-460 Mediated RIG-I Activation to Suppress Innate Immunity

SARS-CoV-2 ORF9b inhibits RIG-I-MAVS 463 antiviral signaling by interrupting K63-linked ubiquitination of NEMO

Protease cleavage of RNF20 facilitates coronavirus replication via 466 stabilization of SREBP1