SARS-CoV-2 emerged in November 2019 in Wuhan, China, from multiple zoonotic cross-species transmission events in humans. The subsequent COVID-19 pandemic - declared by the WHO on March 11, 2020 - is ongoing, and has seen substantial viral evolution and new variants (1–9). Between November 2019 and November 2022, over 632 million cases of COVID-19 were confirmed globally, with more than 6.6 million confirmed deaths and models predicting nearly 20 million deaths (10, 11).

Our understanding of the host immune response to SARS-CoV-2 is constantly growing, as are the discoveries related to immune modulatory effects related to the virus and viral proteins. This review will cover the SARS-CoV-2 genome, virion structure, viral entry and replication, the host immune response, and SARS-CoV-2 immune antagonism. Understanding the host immune response and viral immune antagonism is crucial - as the current state of research - as this knowledge can guide novel treatment strategies and inform public health measures.

SARS-CoV-2 is an enveloped, positive-sense RNA virus of the family coronaviridae ( 12 ). Within the coronaviridae family, SARS-CoV-2 is part of the betacoronavirus genera, also known as genus sarbecoviruses (13). The 29.903 kilobase SARS-CoV-2 genome was published in January 2020 (3, 5, 14). The ancestral lineage A and B genomes are ~80% similar to SARS-CoV and 96.2% similar to the Bat RaTG13 virus (4, 14, 15). From 5’ to 3’, the genome is organized as 5’-cap structure, 5’ UTR, ORF1ab, S, ORF3a-d, E, M, ORF6, ORF7a-b, ORF8, ORF9b-c, N, ORF10, and 3’ UTR ( Figure 1A ) (13, 16–19). The genome contains coding for four structural proteins, 11 accessory proteins, and 16 nsps (12). The four structural genes are S, E, M, and N. The structural proteins and the genome form an enveloped virion able to infect cells (15). The 11 accessory genes and proteins are ORF3a-d, ORF6, ORF7a and b, ORF8, ORF9b and c, and ORF10, and serve various functions from host interaction to immune modulation (18–20). The 16 nsps are identified numerically as nsp1-16 (12). All the nsps are synthesized from ORF1a and ORF1ab (12, 15–17). The change from ORF1a to ORF1ab is facilitated by the ribosomal frameshift of a stop codon at the end of ORF1a (16, 17).

The structural proteins form the virus’s envelope and hold the RNA genome. The N protein coats the genome, whereas S, M, and E are embedded in the lipid bilayer membrane (16). The N protein is composed of positively charged amino acids and binds the negatively charged backbone of genomic RNA (12). The S protein is a 1273 amino acid protein divided into S1 and S2 portions (21), and domains (17, 22). S1 contains the NTD and the RBD (22). Juxtaposed is the S1/S2 furin cleavage site. S2 includes the S2’ cleavage site, FP, HR1, CH, HR2, TM, and the cytoplasmic tail (22, 23). Spike proteins complex into trimers that protrude from the viral envelope surface. On the viral envelope is an average of 15-30 of these S protein trimers (12, 24). Cellular entry by SARS-CoV-2 relies on S protein binding to ACE2 and S protein priming by TMPRSS2 (25). Cathepsin B and L can also serve the same function as TMPRSS2 but within the endosome (15, 21, 26). The E protein, a single-span transmembrane protein, facilitates viral assembly and release, and is an important component in pathogenesis (27). In addition to being transmembrane, the E protein contains channel activity, forming pores and allowing ion transport (28). The M protein is the most abundant structural protein, and spans the membrane three times and interacts with both the E and the S proteins to facilitate the structure of the lipid envelope (12, 27).

The replication cycle ( Figure 1B ) begins after SARS-CoV-2 binding to ACE2 via the S1 subunit of the S protein (16, 25). The spike protein S1 ectodomain changes conformation from open to closed, and in the open conformation, the RBD interacts with ACE2 in humans (12, 14, 29). The S2 subunit of the S protein then facilitates membrane fusion (16). Two cleavage sites in the S protein are responsible for the pre-fusion to post-fusion conformational change (30, 31). The S1/S2 site, consisting of the polybasic furin motif, separates the S1 and S2 domains (4, 26, 32, 33). The S2’ cleavage site drives the fusion of the virus with the cell membrane (16, 34). The S1/S2 site is cleaved by TMPRSS2 and results in the removal of the S1 subunit (16, 35). The S2’ site is cleaved by TMPRSS2, furin, and cathepsins, inducing an irreversible conformational change in the S protein (16, 36). Removing the S1 subunit and activating S2 allows S2 to form a pre-hairpin that embeds into the target cellular membrane. The pre-hairpin folds back and creates a six-hairpin bundle that pulls the viral and cellular membranes together.

The genomic vRNA will release into the cytosol and uncoat (21). Immediately, the polyproteins pp1a and pp1ab will be translated from ORF1ab (21). These proteins are required for replication and viral survival. The majority of the replication machinery is in the ORF1b portion of the genome and are produced with the ORF1a to ORF1ab -1 frameshift, which occurs at a ~20-50% rate (16). These polyproteins are co- and post-translationally processed into the RTC by nsp3 (PLPro) and nsp5 (3CLpro) (13, 16, 21, 37). The RTC is responsible for replication, transcription, RNA processing, and formation of within the ER to serve as replication factories (15, 16). The viral RTC will replicate the viral genome and subgenomic mRNA for the assembly of new viruses (21).

The RTC will synthesize negative-strand full-length genomes from the positive-strand RNA genome for the subsequent generation of positive-strand progeny genomes (16). Additionally, the RTC will generate subgenomic mRNA via discontinuous transcription utilizing transcription regulatory sequences located at the 5’ end of each ORF (16). The negative-strand subgenomic mRNAs then facilitate the generation of positive-strand subgenomic mRNA. These positive-strand subgenomic mRNA then serve as translation templates for viral protein production. Replication occurs in specialized ER structures known as DMV (16, 38). Structural proteins are processed through the endoplasmic reticulum to the Golgi apparatus. Here the S, E, and M structural proteins are retained at the budding ERGIC, where interaction with N-encapsidated genomic vRNA results in the formation of secretory vesicles (21). The M protein incorporates viral components into the virions. The N protein interacts with both the genome and the E protein to enable packaging into the virion. The E protein participates in viral assembly by functioning as an ion channel and participating in membrane curvature (16). Virions are released from the cell via exocytosis.

We are now delving into the role of SARS-CoV-2 modulation or antagonism of the immune system, which SARS-CoV-2 is very effective at (55). Firstly, we will cover the structural proteins. Inside the cell, the Spike protein will antagonize the immune response by interacting with IRF3 (70). In the case of the M protein, it antagonizes innate immunity by inhibiting the TRAF complex, which is involved in the promoter activation of NF-κB and subsequent IFN transcription (16, 71). Additionally, the M protein interacts with MAVS, impairing the IFN downstream response, and further, blocks phosphorylation of STAT1, an element responsible for inducing ISG (72, 73). Lastly, the M protein triggers cell apoptosis with the N protein as a cofactor (74). Switching to the N protein, it targets the initiation of RIG-1 pathway via blocking TRIM25, and additionally prevents phosphorylation of STAT1, STAT2, and IRF3, blocking the entry of all three into the nucleus and inhibiting the IFN and ISG responses (16, 51). The N protein is also shown to prevent the aggregation of MAVS, as well as promote the activation and assembly of the inflammasome (75, 76).

Now moving on to the non-structural proteins. Nsp1 blocks the phosphorylation of IRF3, IRF7, STAT1, and cJun. Nsp1 additionally directly inhibits the IFN and NF-κB promoters and interacts with host 40S ribosomal subunits via 18S rRNA to inhibit host protein translation. Further, nsp1 degrades transcripts lacking a 5’ viral leader sequence (16, 38, 52, 77–80). Regarding nsp3, it blocks cytokine production (81). Nsp3, like N protein, also block the phosphorylation of IRF3, preventing nuclear translocation, and antagonize type I IFN activity (16, 81, 82). Transitioning to nsp5, it proteolytically cleaves RIG-I and induces the degradation of MAVS, thus preventing detection of viral dsRNA and inhibiting the IFN pathway (83). In the case of nsp8 and nsp9, they bind to the SRP and disrupt protein trafficking, suppressing the type I IFN response (52). As for nsp10, it impairs the activity of IRF3 and NF-κB binding sites (81). Exploring nsp6 and nsp13, they bind to an intermediary between MAVS and IRF3 signaling; thus limiting IRF3 activation (63, 73, 77, 84). Nsp6 and nsp13 also inhibit phosphorylation of STAT1 and STAT2 (73). Additionally, nsp13 limits nuclear translocation of NF-κB (77). Nsp13, nsp14, nsp15, and ORF6 prevent nuclear translocation of IRF3 (85). Turning to nsp14, nsp15, and nsp16, they modify the viral RNA and prevent recognition by RIG-1 and MDA-5 (38). Nsp14 additionally targets the IFNAR receptor for lysosomal degradation (81). Lastly, nsp16 additionally binds to the spliceosome and interrupts mRNA splicing, further suppressing the IFN response (52).

Now we move on to the ORFs. ORF3a blocks the phosphorylation of STAT1, activates the NLRP3 inflammasome, prevents phagosome and lysosome fusion, and induces cell death via the extrinsic apoptosis pathway (18, 20, 73, 81). ORF3b antagonizes type I IFN activity (86). Regarding ORF6, it blocks the translocation of IRF3 and the STAT1 complex into the nucleus and inhibits the MHC class I pathway (16, 73, 87). ORF6 also binds to the interferon-inducible nuclear export complex of Nup98 and Rae1, preventing the nuclear release of mRNA (63, 84). Moreover, ORF6, ORF3b and ORF8 inhibit the ISRE to type I IFN production (38, 88). Focusing on ORF7a, it inhibits the translocation of STAT2 to the nucleus, reduces phagolysosome acidity, and binds to monocytes, decreasing their ability to present antigens (18, 73, 81, 89). In the case of ORF7b, it suppresses STAT1 and STAT2 phosphorylation (73). Turning to ORF8, it directly interacts with MHC class I proteins on the ER membrane and facilitates their degradation via autophagosome degradation (90). Additionally, ORF8 is a secreted protein that mimics IL17A and interacts with IL17 receptors on monocytes. This interaction of monocytes upregulates gene expression in fibrosis signaling, coagulation dysregulation, and inflammation (91). Examining ORF9b, it interacts with Tom70, thereby interfering with MAVS and type I IFN expression (84, 92). As for ORF9c, it upregulates IL-6 signaling while impairing IFN signaling (93). Lastly, ORF10 induces mitophagy and thereby causes the degradation of MAVS (94).

The rapid emergence and spread of SARS-CoV-2 worldwide has vastly changed research over the past years. This dynamic has included more than 10,000 new SARS-CoV-2 articles released per month (95). This review aims to summarize some of the most relevant and referenced immune response resources into a comprehensive summary of the current state of the host immune response to SARS-CoV-2. This amalgamation of information represents the background and current state of understanding in an ever-evolving and dynamic field. Understanding the virus-host immune interactions can provide valuable insights for developing targeted therapeutics, such as antivirals and immunomodulatory drugs, which can mitigate the severity of the infection and limit viral spread. Furthermore, this knowledge can inform pandemic preparedness by helping to identify potential therapeutic targets and designing effective pre-emptive interventions.

The topics covered herein require constant reevaluation as more evidence is published worldwide. Such reflection will allow for refining the selection of drug targets and elucidating and understanding the molecular basis of pathogenesis. Understanding the molecular pathway of SARS-CoV-2 viral inhibition of IFN production and signaling for drug targets and pathogenesis can point to other prospective treatments, such as IFN mimicry, small molecules, solubilizable ACE2 in place of monoclonal antibodies (96), prophylactic RIG-I agonists (97), or nanobody-fusions targeting specific ORFs. There are many currently available and approved IFN receptor agonists that clinical trials could further explore (ropeginterferon alfa-2b, peginterferon alfa-2b, etc). These points of continuous assessment allow for the most effective management of SARS-CoV-2, COVID-19, and future pandemics.

DM prepared the initial manuscript. DM, YD, and MG collectively produced the final version. All authors contributed to the article and approved the submitted version.