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SARS-CoV-2: Structure, Proteins, and Pathogenesis of the New Coronavirus

by | Mar 21, 2021 | Coronavirus | 0 comments

  1. Introduction
  2. SARS-CoV-2 Structure
  3. Spike protein
  4. Pericapside protein
  5. Membrane protein
  6. Nucleocapsid protein
  7. Non-Structural Proteins
  8. Viral Pathogenesis
  9. Inflammatory Response
  10. References


For over a year now, the world’s attention has been focused on COVID-19, the respiratory infection caused by the new Coronavirus SARS-CoV-2, and the ensuing pandemic.

The epidemiological data at the moment say that: SARS-CoV-2 is present in over 200 countries around the world, has infected around 113 million people worldwide (February 2021), and 2.5 million of them have died.

SARS-CoV-2 is a virus that mainly affects the respiratory tract, causing symptoms such as cough, cold, fever, and, in severe cases, breathing difficulties. Sometimes, it can also induce systemic inflammation, causing sepsis, heart failure, and multi-organ dysfunction.

SARS-CoV-2 infection is particularly dangerous for individuals over 60, for those with chronic diseases (e.g., diabetes, coronary artery disease), and people receiving immune system depressants (e.g., chemotherapy, immunosuppressants).

This article aims to analyze the structure, genome, and proteins of SARS-CoV-2, and provide basic information on the pathogenesis of the virus.

To explore:

Coronavirus 2019-nCoV: How to Recognize First Symptoms

Structure of SARS-CoV-2

As is done by SARS-CoV-2: Structure, Genome and Protein

As an example of a beta-coronavirus, SARS-CoV-2 is a single-stranded RNA virus with pericapsid (envelope).

The pericardium is a kind of envelope around the head of some viruses; it consists of phospholipids and glycoproteins.

SARS-CoV-2 has a genome of 29,881 nitrogen bases, which encodes 9,860 amino acids.

This genome is subdivided into genes for structural proteins and genes for non-structural proteins.

The genes for structural proteins encode for spike protein (abbreviated in S), pericapsid protein (abbreviated in E, envelope), membrane protein (abbreviated in M), and nucleocapsid protein (abbreviated in N).

As its name suggests, structural proteins help to form the SARS-CoV-2 structure.

The genes for non-structural proteins, on the other hand, encode for proteins, such as protease similar to 3-chymotrypsin, papain-like protease, or RNA polymerase RNA-dependent. Whose functions are regular and direct the processes of virus replication and assembly.

Below is a description of the individual structural proteins, focusing on S protein and non-structural proteins.

Spike protein

SARS-CoV-2 Spike Protein Structure

The spike protein (or S protein) of SARS-CoV-2 (and of all known Coronaviruses) plasters the virus’s outer surface. Forming those characteristic bumps that give the New Coronavirus the crown’s appearance (from which, precisely, the term “Coronavirus” derives).

The spike protein weighs 180-200 kDa (kiloDalton) and consists of 1,273 amino acids.

Spike consists of two major amino acid components, called S1 subunits (14-685) and S2 subunits (686-1.273):

The S1 subunit hosts a sequence of amino acids known as RBD (British acronym that stands for “Receptor Binding Domain.”

Which is a binding domain to the receptor), which is crucial to binding the virus to the host’s cells (the human being).

Subunit S2, on the other hand, is the site of amino acid sequences (melting peptide, HR1, HR2, a transmembrane domain, and cytoplasmic domain). The final function is to facilitate the fusion and entry of the virus into the host cells.

At the native state (i.e., when the virus is not infecting anyone), the spike protein is in the form of an inactive precursor. However, when the virus encounters a potential organism to infect, it immediately passes to an active form:

  • The proteases of the target cells trigger the activation process (so the host activates it!), which “break” the spike and form the S1 and S2 subunits.

How Does SARS-CoV-2 Spike Protein Work

The SARS-CoV-2 spike protein function is complex. The article in question aims to simplify it as much as possible to be understandable to readers.

The spike protein is crucial for initiating the host infection process; In other words, it is the weapon that the New Coronavirus uses to cause the infection known as COVID-19.

spike’s infection process can be divided into two parts:

  • The link to the host cell. It is the stage in which the virus attacks and binds to the cells of the organism, which then infects.
  • The fusion of the viral membrane (in the essence of the virus) with the host cell membrane. This is the stage in which the virus enters the cells of the attacked organism and spreads its genome to it.

Link to host cells

The spike protein binds host cells through the RBD sequence of the S1 subunit.

Scientific studies have shown that the RBD sequence binds to the host cells by an interaction with the ACE2 receptor on the surface of the plasma membrane of the cells themselves.

ACE2 is an enzyme and is homologous of ACE, the protein used to convert angiotensin 1-9.

In humans, ACE2 is found, mainly on the surface of the plasma membrane of cells of organs such as lungs, intestines, heart, and kidneys.

Once the S1 subunit is bound to ACE2, the S-protein begins to change conformation. This event is intended to promote the fusion phase and the entry of the virus into the host cell.

The binding to ACE2 and the resulting conformational change are two fundamental aspects for realizing the vaccine against SARS-CoV-2 and for understanding the mechanisms of antigenicity and immune response of the host.

However, there is a problem that needs to be considered: mutations in the S1 subunit and, in particular, the RBD sequence, could change the way the conformational change develops; as a result, this could affect the antigenic characteristics and the effectiveness of vaccines (to learn more about the topic, we recommend reading the article on variants of SARS-CoV-2).

Host Cell Merger

The spike protein implements the fusion of the virus to the host cell through the amino acid sequences of the S2 subunit.

The virus fusion process takes place on the wave of the conformational change of the S-protein induced by the binding between the RBD and the host’s ACE2 receptor: spike’s conformation change, in fact, approaches the viral membrane to the plasma membrane of the host cell, up to the interaction, the membrane fusion and, finally, the swallowing of the infectious virus.

Once the viral genome is inside the host cell, the virus begins its replication. The infection process can be considered complete.

Pericapside’s protein

Also known as E proteins, the SARS-CoV-2 pericapsid proteins contribute to the formation of the pericardium.

They are a group of tiny proteins made up of only 75-109 amino acids.

Despite their small size, E proteins play an extremely significant functional role: they can support the assembly and release of virions.

In microbiology, the mature virus particle is called a virion. Its nucleic acid (DNA or RNA) is enclosed in a protein capsule called a capsid.

Studies have shown that the E-protein of SARS-CoV-2 is a viroporin, which, once in the host cell, goes to localize on the membrane of the Golgi apparatus and endoplasmic pattern to promote assembly and release of virions.

A viroporin is a viral protein that acts as a membrane channel within the host’s cells.

The E protein of SARS-CoV-2 is very similar to that of SARS-CoV, while it exhibits some differences compared to MERS-CoV.

Membrane protein

Membrane proteins (or M proteins) are the most abundant structural proteins in SARS-CoV-2.

They have an amino acid sequence of about 220 elements.

The M protein of SARS-CoV-2 covers various functions:

  • Defines the shape of the pericardium;
  • By interacting with the E, N, and S proteins, it organizes the virion assembly.

Research has shown that without the M protein, but with all the other structural proteins available, SARS-CoV-2 cannot assemble new virions within the host. This means that M proteins play a key role in this process.

On the other hand, the evidence suggests that:

  • The interaction between M protein and S protein ensures that it is incorporated into new virions;
  • The interaction between M protein and N protein stabilizes the nucleocapsid (that is, the RNA – protein N complex) and promotes final virion assembly.
  • Along with protein E, it contributes to the formation of the pericapsid.

Nucleocapsid protein

The N protein, or nucleocapsid protein, is the only SARS-CoV-2 protein capable of binding to the viral genome.

Not by chance, due to this property, it plays a key role in the process of packaging the viral RNA within the new virions.

The viral RNA – protein N complex is the nucleocapsid.

As anticipated, the N protein action is M protein: the interaction between these two proteins stabilizes the nucleocapsid. It promotes the final assembly of the virions.

It should be noted that protein N studies have shown that N is also involved in the transcription and replication of viral RNA.

Following this discovery, experts began to consider N protein as a possible target for new specific drugs against SARS-CoV-2.

Protein N is highly preserved in Coronavirus: for example, SARS-CoV-2 has an amino acid sequence of 90% compared to that of SARS-CoV.

Non-Structural Proteins

SARS-CoV-2 Non-Structural Protein Origin and Function

The topic of non-structural proteins (abbreviated to “nsp”) by SARS-CoV-2 is quite complex.

So we need simplification to make it easier to understand.

First, the non-structural proteins of SARS-CoV-2 are in total 16 elements.

They are derived from two large proteins called polyprotein 1a (pp1a) and polyprotein 1ab (pp1ab), which in turn are encoded by virus genes known as replicate 1a and 1ab replicate, respectively.

Forming non-structural proteins from the two polyproteins involves the involvement of two specific viral enzymes, called proteases and products from the virus that was early on. These proteases are dedicated to “cut” the polyproteins at specific points, giving rise to individual non-structural proteins.

The strategy of polyproteins (from which smaller proteins derive) is very common among viruses.

Interestingly, before the cutting, the proteins included in the polyproteins are inactive, not functional. They only become functional after protease intervention and splitting from the major amino acid chains.

The main function of SARS-CoV-2 non-structural proteins is to transcribe and replicate viral RNA.

However, it should be noted that these proteins are also involved in viral pathogenesis.

Protease of SARS-CoV-2

Two key non-structural proteins for SARS-CoV-2 are undoubtedly proteases involved in “cutting” out polyproteins and forming proteins useful for viral RNA transcription and replication.

These proteases are known as 3-chymotrypsin-like proteases (abbreviated in 3CLpro) and papain-like proteases (shortened in PLpro).

Because the proteins from which they give rise then serve to spread the infection in the host, the proteases in question are an attractive pharmacological target.

RNA RNA RNA-dependent Polymerase

RNA polymerase RNA-dependent is the non-structural protein of SARS-CoV-2 essential for replicating the viral genome intended for new virions.

This non-structural protein would also be an attractive pharmacological target.

Viral Pathogenesis

How SARS-CoV-2 Causes COVID-19 Infection

SARS-CoV-2 begins the infectious process when, through the spike protein, it manages to invade the host cells.

As described in the S protein chapter, ensuring the entry of the virus into the host organism is the interaction between the spike’s RBD sequence and the ACE2 receptor on the plasma membrane of the cells of the respiratory tract of the host itself.

Upon arrival, SARS-CoV-2 “appropriates” the host’s ribosomes and uses them to transcribe its genome to RNA and create the proteins necessary for the replication of the same genetic material and the assembly of new virions.

Based on the above, non-structural proteins play a key role in the transcription and replicating of viral RNA.

With the transcription and replication of the viral genome, SARS-CoV-2 spread to the host, giving rise to the actual infectious disease.

At this stage, the virus acts on the host organism both with a cytoid activity (i.e., that kills the cells) and with immune-mediated mechanisms.

About cytoid activity, evidence suggests that SARS-CoV-2 induces apoptosis (cell death) and cell lysis. In more detail, it has emerged that the virus produces syncyzes within the infected cell and causes the rupture of the apparatus of Golgi, after its replication.

About immune-mediated mechanisms, research has shown that SARS-CoV-2 involves both the innate and adaptive immune systems (antibodies and T-lymphocytes).

Why is SARS-CoV-2 more infectious than the SARS Coronavirus?

SARS-CoV, the Coronavirus responsible for SARS, also invades host cells using the interaction between RBD and the ACE2 receptor present on respiratory tract cells.

However, there is an important difference between this type of link and the one made by SARS-CoV-2:

  • the RBD sequence of the Coronavirus responsible for COVID-19 has much more affinity to ACE2. It binds to it much more efficiently, which is far more effective in invading host cells.

Scientific studies have shown that the difference in interaction described above is due to a different amino acid composition between SARS-CoV RBD and SARS-CoV-2 RBD. In particular, there are two amino acid regions with important differences.

This difference in affinity explains several aspects:

  • The reason why SARS-CoV-2 is greater than SARS-CoV;
  • The reason that drugs and vaccines targeted the SARS-CoV RBD sequence and that appeared to be effective are not suitable against SARS-CoV-2.

What is R0?

Also known as the “basic reproduction number,” R0 represents the average number of secondary infections produced by each infected individual in a completely susceptible population. I.e., never coming into contact with the newly emerging pathogen).

This parameter measures the potential transmissibility of an infectious disease.

Inflammatory Response

SARS-CoV-2 and Cytokine Release

Following the entry of SARS-CoV-2, the immune system of the infected host organism becomes active.

At this point, the immune system elements (e.g., T lymphocytes) reach the site of infection and attack the virus.

In most people, the above process is successful, eliminating the virus from the body and allowing the individual to recover.

In several cases, however, it happens that the infectious disease takes more severe connotations and that SARS-CoV-2 stimulates an aberrant immune response.

The present case found that the virus caused an overproduction of pro-inflammatory cytokines (e.g., interleukin-1, interleukin-2, interleukin-6, etc.) to accumulate in the lungs, eventually damaging the lung parenchyma.

Pro-inflammatory cytokines result from the activity of certain cells of the immune system.

Under normal conditions, they serve to regulate the immune response, inflammation, and hemopoiesis.

Also, clinical data and other research have shown that the overproduction of pro-inflammatory cytokines. Seen in the presence of a severe infection with SARS-CoV-2 may extend to other organs (e.g., heart). Causing dysfunction, and have repercussions on the coagulative processes, inducing thrombi formation.

When SARS-CoV-2 triggers an overproduction of extended pro-inflammatory cytokines, experts call the phenomenon the term “cytokine storm syndrome”.


  • Ahmad Abu Turab Naqvi, Kisa Fatima, Taj Mohammad, Urooj Fatima, Indrakant K. Singh, Archana Singh, Shaikh Muhammad Atif, Gurao Hariprasad, Gulam Mustafa Hasan, and Md. Imtiaz Hassan (October 101, 2020) Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim Biophys Acta Mol Basis Dis; 1866(10): 165878.
  • Yuan Huang, Chan Yang, Xin-Feng Xu, Wei Xu, and Shu-wen Liu (03 august 2020) Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacological Sinica Volume 41, pages1141-1149.
  • Muge Cevik, clinical lecturer, Krutika Kuppalli, Jason Kindrachuk and Malik Peiris (23 October 2020) Virology, transmission, and pathogenesis of SARS-CoV-2. BMJ 371: m3862.

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