Virus Biology

Updated by Rohin Gawdi on 5/03/2020.

Summary: Virus Biology

• SARS-CoV-2 spike (S) protein contains two subunits: S1 and S2.

• The S1 subunit on SARS-CoV-2 tightly binds Angiotensin Converting Enzyme 2 (ACE2), similarly to SARS-CoV

  • SARS-CoV-2 binds more tightly to isolated ACE2 of N28 variant than to cell-bound ACE2

  • This indicates the possible role of recombinant ACE2 in treatment for COVID-19 infection.

• The S2 subunit mediates viral membrane fusion via cleavage at S1/S2 junction, which requires a unique protease function on host cell.

  • The cell-surface protease TMPRSS-2 is most suspected of cleaving SARS-CoV-2 S protein at the cell surface, allwowing fusion.

  • TMPRSS-2 is ubiquitously expressed yet is dispensible to cellular function, making it an attractive therapeutic target for anti-viral therapy.

• SARS-CoV-2 contains a newly adapted protease cleavage point which results in the ability for the virus to fuse with Furin-presenting host cells

  • This may account for why SARS-CoV-2 has high transmissibility and systemic symptoms compared to other CoV species, although futher data is needed to further establish this link.

• Another potential therapeutic target for COVID-19 is main protease, which processes viral polypeptides into viral proteins within host cells

  • Studies have shown that main protease may be inhibited by ɑ-ketoamide inhibitors.

• Coronavirus species use endoribonuclease to evade host defenses

  • This is done by cleaving replicated viral proteins to dampen the immune reaction

Literature Review:

Every coronavirus has four structural proteins: membrane (M) protein, envelope (E) protein, nucleocapsid (N) protein, and spike (S) protein. Among these, S protein, a glycoprotein, plays the most significant role in mediating viral attachment, fusion, and entry. All CoV S proteins have three domains: extracellular (EC) domain, transmembrane anchor domain, and intracellular tail. The EC contains two active subunits: S1 and S2 (1). The S1 subunit of S protein mediates viral entry by binding a host receptor through a unique sequence of peptides known as the receptor-binding domain (RBD). The S2 subunit then fuses viral and host membranes. In order for viral fusion to occur, host cell proteases must cleave the S protein at the S1/S2 junction. The requisite host proteases necessary for viral fusion are a key factor for determining many clinical details of the virus. Studies of the 2002 SARS-CoV virus have indicated a number of human proteases that activate the virus, many of which are present in the lungs. One notable such cleavage protein is TMPRSS-2, which studies by Hoffman et al. have shown to play a role in the cleavage and fusion of S proteins on Influenza type A, and CoV species to cell membranes of numerous tissue types. This may be an attractive target for therapeutic intervention for COVID-19, as TMPRSS-2 is expressed ubiquitously and is largely considered dispensable to cellular function. (22) A currently licensed medication exists that inhibits TMPRSS-2 function: camostat mesylate, which has potential for off-brand use in COVID-19. In addition to TMPRSS-2, a bioinformatics study from Wang et al. indicates that the novel SARS-CoV-2 virus has the insertion of four additional residues between S1 and S2, resulting in the insertion of a furin cleavage site between residues 682 and 685 that is unique to SARS-CoV-2. Furin protease is expressed in many organ systems, including the lung, GI tract, alimentary tract, and reproductive tissue. This is likely at least partially responsible for SARS-CoV-2 ability to produce systemic infection and may also play a role in the virus’ dramatically enhanced transmissibility compared to other betacoronavirus species (2). Furin has particularly high expression on human alveolar type 2 cells, which may help explain the predominance of respiratory symptoms in COVID-19. (23) In addition to variance in the S1/S2 junction, a study by Tai et al. showed that the RNA binding domain (RBD) on the S1 subunit of SARS-CoV-2 recognizes and strongly binds Angiotensin Converting Enzyme II (ACE2) on host cells, quite similarly to the behavior of SARS-CoV S protein. It was further shown that purified recombinant SARS-COV-2 RBD exhibits stronger binding to cell-associated and soluble ACE2 receptors than virus-associated ACE2 RBD, suggesting a possible avenue of treatment against COVID-19 infection. In addition, pseudoviral infection studies indicated that antibodies against SARS-CoV infection produced strong cross-neutralization of SARS-CoV-2 (3). Another study by Luan et al. further elaborated that the N82 variant of ACE2 showed a closer contact with the SARS-CoV-2 RBD than the M82 variant, indicating further optimization of an ACE2-related agent for treatment of COVID-19 (4).

Surface proteins are necessary for viral binding and survival. However, another potential therapeutic target is the main protease (Mpro). This protein is responsible for processing viral polypeptides within the host cell. Zhang et al. have shown that α-ketoamide inhibitors halt crucial proteases of alphacoronaviruses, betacoronaviruses, and enteroviruses, and that the inhibition of this protease blocks viral replication. Because there are no human proteases with similar cleavage sites, the risk of human toxicity is low (5). Despite this, further work on designing these drugs is necessary for adequate treatment of COVID-19 infection.

A paper from Hackbart et al. suggests that all members of the coronavirus family encode endoribonuclease, that evades host defenses by cleaving 5’-polyuridines from replicated viral proteins, dampening immune response (6). This may play a role in SARS-CoV-2 pathogenesis, and may additionally be a target of future antiviral therapies. In addition, other studies have shown that SARS-CoV-2 undergoes unusually quick mutations compared to virus species due to an error-prone RNA polymerase. Despite this, it is not believed that the virus is prone to rapid shifts in transmissibility or pathogenesis. Instead, this suggests that longitudinal study of the virus is necessary to protect public health. (24)

Summary and Literature Review written by Rohin Gawdi 3/29/2020.