Coronaviruses are enveloped viruses with a positive-sense RNA genome and with a nucleocapsid of helical symmetry. Coronavirus nucleoproteins localize to the cytoplasm and the nucleolus, a subnuclear structure, in both virus-infected primary cells and in cells transfected with plasmids that express N protein. Coronavirus N protein is required for coronavirus RNA synthesis, and has RNA chaperone activity that may be involved in template switch. Nucleocapsid protein is a most abundant protein of coronavirus. During virion assembly, N protein binds to viral RNA and leads to formation of the helical nucleocapsid. Nucleocapsid protein is a highly immunogenic phosphoprotein also implicated in viral genome replication and in modulating cell signaling pathways. Because of the conservation of N protein sequence and its strong immunogenicity, the N protein of coronavirus is chosen as a diagnostic tool.
SARS-CoV-2 ORF3b is homologous to SARS-CoV ORF3b, although the proposed protein is much shorter due to the presence of premature stop codons (Probable). Elicits strong specific antibody response (PubMed:32807944).
Replication of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) requires proteolytic processing of the replicase polyprotein by two viral cysteine proteases, a chymotrypsin-like protease (3CLpro) and a papain-like protease (PLpro). These proteases are important targets for development of antiviral drugs that would inhibit viral replication and reduce mortality associated with outbreaks of SARS-CoV. PLpro is a cysteine protease located within the non-structural protein 3 (NS3) section of the viral polypeptide. PLPro activity is required to process the viral polyprotein into functional, mature subunits; specifically, PLPro cleaves a site at the amino-terminus of the viral replicase region. In addition to its role in viral protein maturation, PLPro possesses a deubiquitinating and deISGylating activity. In vivo, this protease antagonizes innate immunity by inhibiting IRF3-induced production of type I interferons.
The coronaviral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro), are attractive antiviral drug targets because they are essential for coronaviral replication. PLpro has the additional function of stripping ubiquitin and ISG15 from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Targeting PLpro with antiviral drugs may have an advantage in not only inhibiting viral replication but also inhibiting the dysregulation of signaling cascades in infected cells that may lead to cell death in surrounding, uninfected cells.
The spike (S) glycoprotein of coronaviruses contains protrusions that will only bind to certain receptors on the host cell. Known receptors bind S1 are ACE2, angiotensin-converting enzyme 2; DPP4, dipeptidyl peptidase-4; APN, aminopeptidase N; CEACAM, carcinoembryonic antigen-related cell adhesion molecule 1; Sia, sialic acid; O-ac Sia, O-acetylated sialic acid. The spike is essential for both host specificity and viral infectivity. The spike (S) glycoprotein of coronaviruses is known to be essential in the binding of the virus to the host cell at the advent of the infection process. It's been reported that SARS-CoV-2 (COVID-19 coronavirus, 2019-nCoV) can infect the human respiratory epithelial cells through interaction with the human ACE2 receptor. The spike protein is a large type I transmembrane protein containing two subunits, S1 and S2. S1 mainly contains a receptor binding domain (RBD), which is responsible for recognizing the cell surface receptor. S2 contains basic elements needed for the membrane fusion. The S protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity. The main functions for the Spike protein are summarized as: Mediate receptor binding and membrane fusion; Defines the range of the hosts and specificity of the virus; Main component to bind with the neutralizing antibody; Key target for vaccine design; Can be transmitted between different hosts through gene recombination or mutation of the receptor binding domain (RBD), leading to a higher mortality rate.
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