SARS-CoV-2 and Covid-19 Vaccines

SARS-CoV-2

Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) carries single-stranded positive sense RNA (+RNA) as its genomic material ^[1]. To gain access to a cell and deposit the viral RNA, a virion attaches itself to the cell by binding the viral spike (S) protein to a specific cell receptor (ACE2).

The viral RNA and the spike (S) protein which will be translated from it are the most important ingredients of the vaccines.

SARS-CoV-2 Pathway

1. The S protein of SARS-CoV-2 binds to a specific (ACE2) host cell receptor.
2. Fusion and entry take place via endocytosis.
3. Breakdown of the containing endosome and viral proteins, and release of genomic RNA.
4. Replication of genomic RNA.
5. Replication and expression of subgenonomic mRNAs.
6. Translation of subgenonomic mRNAs into viral proteins by ribosomes.
7. Fragments of viral proteins display on host cell MHC1 receptors.
8. Endosomal containment of genomic RNA and viral proteins, followed by assembly into new virion.
9. Virion buds via exocytosis.

Vaccines

The objective of any Covid-19 vaccine is to deliver a modified version of the SARS-CoV-2 genomic RNA to ribosomes in the host cell. This modified version only contains the genes for making the S protein — the ribosomes do the job of translating them. It must be stressed that the S protein is not infectious and is merely used as a marker for the immune system to identify.

Currently, the two most widely accepted vaccines for international travel ^[2] are those produced by Oxford-Astrazeneca and Pfizer/BioNTech. It will be seen from the diagrams that the methods of translation, assembly and budding of the S proteins are the same for both vaccines. The major difference between them is that the Pfizer/BioNTech carries RNA and the Oxford-Astrazeneca vaccine carries DNA. The Astrazenaca DNA must be injected into the nucleus and converted (transcribed) to mRNA before proteins can be translated, whereas the RNA carried by Pfizer/BioNTech can start translation as soon as it escapes from the endosome.

Oxford-Astrazeneca Vaccine

This vaccines employs a harmless, engineered chimpanzee adenovirus as its vector.

How is it harmless?

All infectious genes are stripped from the DNA during the production process with the result that it cannot be used to replicate neither adenoviruses (as there are no longer any genes that can encode them in the DNA) nor SARS-CoV-2 proteins (excepting the S protein, the only protein the genes in the DNA can encode).

Why a chimpanzee adenovirus?

Adenoviruses, which cause cold-like symptoms, routinely infect humans. Consequently, the immune system has many defences against them. Using a human adenovirus as a vector for a vaccine would therefore mean that there would be a strong chance of it being destroyed before it was able to enter a cell, rendering the vaccine useless. Using a chimpanzee adenovirus, unknown to the immune system, provides a much greater chance of the vaccine being able to enter a cell and do its work.

How is it engineered?

All adenoviruses carry DNA as the genomic material. The viral RNA from SARS-CoV-2 is first extracted and then reverse transcribed ^[3] back into DNA. This DNA then replaces the adenovirus DNA, after, as previously mentioned, all genes save those that encode the S protein have been removed.

Viral DNA and the host cell nucleus

It is important to emphasise that although the DNA will eventually be inserted into a host cell's nucleus it will not integrate with the host cell's DNA.

1. The adenovirus fibre binds with the cell's adenovirus receptor and fusion takes place via endocytosis.
2. The endosome carries the adenovirus into the cytosol. The fibres detach and the endosome dissolves, releasing the capsid.
3. The capsid is transported to the nucleus.
4. The capsid injects its DNA through a nuclear pore into the nucleus.
5. Viral DNA is transcribed into messenger RNA (mRNA).
6. Translation of S (spike) protein by ribosomes.
7. Fragments of S protein display on the host cell MHC1 receptors.
8. Endosomal containment of S protein.
9. The endosome is transported to the cell surface.
10. S protein exits the cell via exocytosis.

2) Pfizer/BioNTech LNP mRNA Vaccine

LNPs (lipid nanoparticles) do not bind to cell receptors but rather mimic the appearance of membrane-friendly molecules which allows them access to the cell via endocytosis. ^[4].

The LNP vector carries positive sense mRNA as its genomic material. This mRNA only codes for the spike (S) protein. The viral mRNA does not enter the host cell nucleus.

1. Fusion takes place via endocytosis.
2. The endosome carries the LNP into the cytosol. Endosome and lipid bilayer dissolve, releasing the positive sense RNA.
3. Translation of S (spike) protein by ribosomes.
4. Fragments of S protein display on the host cell MHC1 receptors.
5. Endosomal containment of S protein.
6. The endosome is transported to the cell surface.
7. S protein exits the cell via exocytosis.

Immune responses

In this section I first cover the immune response to the vaccine itself and then the immune response to a system that has received the vaccine.

Note: what follows is a simplified account of the workings of the immune response, in particular omitting much of the work of the innate immune system and highlighting the workings of the adaptive immune system instead.

Immune response to a vaccine

The purpose of any vaccine is to stimulate an immune response which will be remembered by the immune system and which will fight off any later infection.

A

S proteins have exited the cell. A cytotoxic T-cell and a B-cell, both part of the adaptive immune system, are present, along with a macrophage, an antigen presenting cell belonging to the innate immune system. Macrophages patrol the extracellular space looking for potential pathogens. A helper T-cell, responsible for coordinating the activities of the adaptive immune system is nearby.

1. A macrophage digests the S protein and exposes a fragment on its receptor.
2. A helper T-cell binds its receptor to the macrophage receptor holding the S protein fragment.

B

The helper T-cell is activated on binding with the macrophage.

1. Helper T-cell activation results in the secretion of a flood of cytokines (chemical messengers) which target the helper T-cell itself. The cytokines also target and stimulate
2. the cytotoxic T-cell to bind to the host cell MHC1 receptor, and
3. the B-cell receptor to attach to the S protein.

C

Note: memory cells (T and B) are cells of the adaptive immune system which stay in the system, ready to intercept a specific antigen.

1. Clonal proliferation of Helper T-cells and Helper memory T-cells.
2. Clonal proliferation and activation of memory and cytotoxic T-cells, which emit granzymes and perforins to destroy the infected cell.
3. Clonal proliferation and activation of B-cells and memory B-cells.
4. Maturation of B-cells into plasma B-cells (antibody factories).

Post-vaccination Immune Response

In this scenario an already vaccinated person is attacked by SARS-CoV-2.

1

1. Mature B-cells (plasma cells) produce antibodies which bind to the S protein of the invading virions rendering them unable to bind to host cells.
2. Antibody binding also signals to macrophages to attack the virions.
3. Antibodies block the virion's access to the S protein receptor (ACE2) denying access to the cell's interior.

2

Note: the first seven steps are identical to those of the SARS-CoV-2 Pathway, above.

If a viral particle manages to evade the antibodies produced by the plasma cells and is able to enter the host cell, the following scenario might take place:

1. The S protein of SARS-CoV-2 binds to a specific (ACE2) host cell receptor.
2. Fusion and entry take place via endocytosis.
3. Breakdown of the containing endosome and viral proteins, and release of genomic RNA.
4. Replication of genomic RNA.
5. Replication and expression of subgenonomic mRNAs.
6. Translation of subgenonomic mRNAs into viral proteins by ribosomes.
7. Fragments of viral proteins display on host cell MHC1 receptors.
8. A cytotoxic T-cell binds to the fragment of the S protein presented on the MHC1 receptor. This stimulates the production of granzymes and perforins which destroy the infected cell.

The Role of Adjuvants in Vaccines

Adjuvants (not shown in the diagrams) ^[5] are substances in the vaccines which stimulate cell-mediated immune responses.

Adjuvants require something of a balancing act: they need to induce a strong immune response which will attract the attention of cells from the innate immune system. However, the response must not be so strong that the cell is destroyed (or self-destructs) before the protein fragment on the MHC1 receptor is identified and analysed by the adaptive immune system.