Coronavirus vaccines

My goal in this page isn't to address the health benefits of the vaccines, or to suggest that one is better than the other. Instead, I want to describe how they work on a molecular level, and try to connect that explanation to some concepts that you’ve already learned.

To describe these different approaches, I’m going to rely mainly on two sources:

Both of these publications have a lot to offer, but neither is exactly suited to my goals for Bio 6B, so I’m going to mix and match. Before you read this page, I recommend that you watch the following video:

I also highly recommend this one:

Vaccines stimulate immunity

Traditional vaccination works by injecting a person with an antigen to stimulate an adaptive immune response. The antigen could be in the form of a heat-killed or otherwise weakened virus, or simply viral proteins. Newer vaccine technologies rely on using nucleic acids to instruct cells to produce a viral antigen themselves.

In the case of SARS-CoV-2, the virus that causes Covid-19, most efforts have been focused on the viral spike protein as an antigen, because that’s the protein by which the virus attaches to cells. Blocking or this antigen, or using it to attack and destroy the virus, can prevent the virus from causing disease.

The adaptive immune response uses antigen receptors, which bind to specific antigens; these receptors come in two different styles:

  • Antibodies (immunoglobulins) are antigen receptors secreted into body fluids as part of the humoral immune response. Antibodies can function in two different ways. In neutralization , antibodies attach to viral surface antigens, preventing viruses from entering cells. In opsonization , antibodies label the viral antigens, causing the virus to be destroyed by phagocytosis.
  • T cell receptors are antigen receptors on the surface of T cells, and function in the cell-mediated adaptive immune response. These receptors only react to antigens that are displayed on the surface of host cells, either as a result of infection or antigen presentation by phagocytes that have absorbed and destroyed viruses.

In the race for coronavirus vaccines, much emphasis has been placed on the development of vaccines that stimulate the production of neutralizing antibodies, but other aspects of the immune response are likely to be equally important.

How immunity works

Before looking at vaccine mechanisms, it makes sense to examine the body's immune response when infected by the virus itself.

Nature vaccine basics  Image credit: Nature.

The goal of a vaccine is to provide antigens that stimulate an effective immune response, without the disease itself. There are a variety of different approaches to this.

Protein vaccines

The most obvious approach to vaccine design would be to simply inject the antigen itself -- for example, a piece of the coronavirus spike protein. This approach presents some challenges, though. Naked proteins tend to not be very effective in stimulating immune responses, though, so protein-based vaccines must use additional mechanisms to improve the response. This diagram shows two approaches:

Nature protein vaccines

  Image credit: Nature.

In the upper graphic, the spike protein itself is the main ingredient of the vaccine,  along with some adjuvants — substances added to a vaccine to improve the immune response.

In the lower graphic, copies of the spike protein are added to a virus-like particle, which includes a membrane-like shell, but no genetic material. The particle is taken into antigen-presenting cells by phagocytosis, and the cell cuts up the spike protein into small peptides (using its proteasomes) and displays them on MHC proteins on the cell surface.

Proteins aren’t necessarily easy to manufacture, so the usual approach to protein vaccines is to insert the appropriate gene into cultured cells and have the cells produce the protein in a large controlled-environment container called a bioreactor. In some cases, insect cells are used, as they provide a workable eukaryotic cell that can be grown in a liquid medium. Later, the protein is isolated for use in the vaccine.

Novavax is producing a protein-based vaccine against SARS-CoV-2.

Virus-based vaccines

Perhaps the most traditional approach is to use a weakened version of the virus itself. Multiple research groups have worked on this approach for SARS-CoV-2. One of the challenges with this approach is to develop a method that reliably prevents the virus from causing infection, but keeps it intact enough to stimulate an appropriate immune response. The main approaches are to either genetically modify the virus, or weaken it with heat or chemicals.

Nature viral vaccines

  Image credit: Nature.

Another major challenge of this approach is producing sufficient quantities of virus. Viruses can only be grown in cells, again (like protein vaccines) requiring the use of large-scale bioreactors.

Influenza (flu) vaccines have traditionally been made by growing the virus in chicken eggs, purifying the virus, and inactivating or weakening it. It’s a long process, and it requires vaccine makers to start far in advance of the flu season. Since flu virus strains differ from year to year, the vaccine makers are often in the position of producing a less-than-ideal vaccine as the virus evolves during the vaccine production process. Another influenza vaccine approach uses cell cultures instead of eggs as bioreactors, which offers some advantages.

Sinopharm, Sinovac, and Bharat Biotech are making vaccines based directly on the SARS-CoV-2 virus.

Viral vector vaccines

Viruses can be excellent tools for eliciting immune responses, but there’s one big problem with the SARS-CoV-2 virus: if it’s not handled properly, it can cause Covid-19. Rather than using coronavirus itself as part of the vaccine, some developers are using other viruses as vectors to carry coronavirus genes into cells.    

Nature viral vector vaccine

Image credit: Nature.

The goal of these approaches is to induce the body’s cells to produce coronavirus spike proteins, without actually using the coronavirus.

Two approaches are shown in the graphic. The replicating viral vector is based on a weakened measles virus, to which a part of the coronavirus spike gene has been added. The virus infects cells and replicates slowly, but doesn’t cause measles because it contains multiple weakening mutations. This might sound like a crazy approach, but the weakened measles virus has been used for many years as a measles vaccine, so its safety is thoroughly proven.

The non-replicating approach uses an adenovirus, similar to some viruses that cause colds. In the vaccine version, some genes have been altered so the virus can’t reproduce at all. This makes it a safe vehicle, but also reduces its effectiveness.

In both these approaches, viruses are used to do what they do best: infect cells and insert their own genomes. Nucleic acid vaccines are designed to achieve a similar goal, but without the virus.

Johnson & Johnson, Oxford-AstraZeneca, Gamaleya (Sputnik V) and  are making adenovirus-based vaccines against SARS-CoV-2.

Nucleic acid vaccines

The protein-based vaccines require large bioreactors in which cells produce the proteins. Nucleic acid vaccines are based on a different idea: what if your own cells could be the bioreactor?

Nature nucleic acid vaccine

Image credit: Nature.

Nucleic acid vaccines insert either DNA or RNA into vaccinated cells, inducing the cells to produce viral antigens. In this respect, they are similar to virus-based vaccines, but they lack the extra genes, proteins, and membranes associated with viruses. This means that they can’t possibly cause the disease (which is a remote possibility with weakened viruses). It also means that an alternate approach is needed to get the nucleic acid into the cell. Two approaches have been used: DNA and RNA vaccines.

DNA vaccines

To me, the DNA vaccine approach illustrated here looks a lot like the pGLO experiment in Bio 6B. A small, circular DNA molecule is inserted into cells, the DNA replicates within the cell, and specific genes are expressed. 

DNA vaccines are slightly more complex than RNA vaccines. Since it's DNA, the nucleotide sequence must first be transcribed to RNA before an antigen can be produced by translation. This means that the DNA vector must enter the nucleus, whereas RNA vaccines only need to enter the cytoplasm. Important challenges for DNA vaccines include:

  • Transformation: In the example above, electroporation is used to get the DNA vector into the cell. A pulse of electricity is used to create temporary openings in cell membranes, so DNA can enter. This technique is commonly used in bacterial cell transformation; it works better than the chemical transformation technique that we normally use to get the pGLO plasmid into E. coli in the 6B lab. Alternatively, liposomes can also be used with DNA vaccines.
  • DNA replication: DNA vaccine vectors are typically constructed as plasmids , circular DNA molecules containing an origin of replication that allows the vector to be copied within the cell. The circular nature of the DNA facilitates replication and reduces the chances that exposed DNA ends will trigger the DNA damage response. Like a plasmid, the nucleotide sequence must contain an origin of replication to allow the DNA to be replicated.
  • Transcription: DNA vaccine vectors must contain a promoter for the gene that encodes the antigen (in this case, the spike protein). Researchers choose promoters that will be highly active in a wide range of cells; in some cases, these promoters are derived from viruses. 
  • Translation: As with RNA vaccines, once the antigen mRNA is produced and exported to the cytoplasm, the cell's ribosomes produce the protein.

Inovio is working on DNA vaccines.

RNA vaccines

In principle, an RNA vaccine against Covid-19 is simply the messenger RNA encoding all or part of the viral spike protein. The mRNA is inserted into human cells, where it is translated by the cell's ribosomes and other translation machinery. The mRNA sequence contains an open reading frame (ORF) plus short untranslated regions at the 5' and 3' ends. It doesn’t need a promoter, because it’s already RNA; no transcription is needed.

The RNA vaccine method is simple in principle, but it does present some challenges:

  • RNA doesn't enter cells easily. RNA molecules are negatively charged and very large, so they won't cross membranes on their own. To solve this problem, RNA molecules are often coated in lipid coats (liposomes or lipid nanoparticles ), which can fuse with cell membranes and allow the RNA to enter the cell.
  • mRNA has a short lifetime. Modifications to the nucleotide sequence may increase the lifetime of a messenger RNA molecule, but it's still likely that cells will only be producing the antigen for a relatively short time. If the vaccine is successful, the cells must produce enough antigen to elicit a strong immune response.
  • Foreign RNA (such as a vaccine or a virus) may be attacked by the innate immune system. In some cases, RNA vaccines use modified nucleotides that reduce the chance of RNA destruction and increase the lifetime of the RNA.

This approach has led to the most widely used coronavirus vaccines in the US. RNA vaccines for other diseases had already been developed and researched before the current pandemic, but hadn’t gone through their final testing and approval because the demand didn’t seem to be high enough. In retrospect, this seems a bit short-sighted.

Here is an alternate graphic of an RNA vaccine:

NYT RNA vaccine

Image credit: New York Times.

This one emphasizes the fact that the cell that takes in the vaccine ends up presenting the antigen on its surface. In the upper nucleic acid vaccines graphic, the antigenic proteins are shown being released from the vaccinated cell and taken up by antigen-presenting cells. Both of these events happen; in both cases, the antigen is a chopped-up fragment of the spike protein that is displayed on the cell surface by MHC proteins.

Moderna and Pfizer-BioNTech are producing RNA-based vaccines.

Advantages of nucleic acid vaccines

They can be developed very quickly. The first SARS-CoV-2 genome sequence was published to an international virology server by Chinese scientists in early 2019. By this time, it was already clear that an emerging epidemic was underway in Wuhan. Within hours of the publication of the genome sequence, scientists at U.S. biotech companies had analyzed the sequence and begun to design vaccines. They began by searching the sequence for ORFs and figuring out which proteins they encoded (having completed the Open Reading Frames in pGLO assignment, you might have some idea how to do this). Taking advantage of previously published information about coronaviruses (much of which was learned during the earlier SARS and MERS epidemics), they could focus on the spike protein, the viral attachment point. They designed the first vaccine over the weekend. The process of vaccine testing for safety and efficacy still takes a long time, but the first candidate vaccines for Covid-19 were available in record time. As new SARS-CoV-2 variants appear, it may be necessary to create vaccines with modified RNA sequences to match the new variants; this kind of tweaking wouldn’t be possible with older vaccine technologies.

Nucleic acid vaccine production can also be scaled up quickly, since it doesn't rely on the cell culture or egg methods of traditional vaccines. This could be important for emerging diseases (defined as "new" viruses such as Covid-19) but also for viruses such as influenza, which are always around but evolve rapidly. Instead of designing and producing an influenza vaccine far in advance, the vaccine could be produced after it becomes clear which viral types are most abundant in a given year.

The first time I prepared a lesson on Covid-19 vaccines was in Spring 2020. At that time, I wrote:

Will nucleic acid vaccines help us overcome the Covid-19 pandemic? Will they even turn out to be safe and effective in humans? At this point, nobody knows. 

Well, we know that now. In the race to develop safe and effective vaccines, many approaches have been tried, and several have succeeded. RNA vaccines in particular seem to be providing a much-needed tool for addressing an ever-evolving set of pathogens. Whether it’s the next strain of coronavirus, or another virus altogether, it won’t be long before we need to apply these tools to a new threat to human health.

Compare & contrast

I’ve presented several approaches to vaccine development on this page, but all have certain things in common: 

  • The immune system must be presented with an antigen. In all these examples, the antigen is a fragment of the spike protein. Other proteins could have been used as targets, but the spike protein was chosen partly because it’s essential for viral attachment. This makes it likely that antibodies binding to this antigen will neutralize the virus.
  • The antigen must be presented on the surface of cells to stimulate an effective response. Even when a vaccine is based on injecting viral antigens, those protein fragments must be taken into cells and displayed in order to induce a strong immune response.
  • In all cases, the proteins are synthesized by ribosomes in some kind of cells. Protein-based vaccines use insect or other cells in large bioreactors, while virus-based and nucleic acid vaccines rely on inserting genes and allowing the vaccinated person’s own cells to produce the proteins. There’s no other reasonable way to manufacture proteins; technology hasn’t caught up with nature in this respect. 

On the other hand, the different vaccine technologies described on this page use different methods to produce and deliver the antigens. In each case, some combination of biology and technology is required to get macromolecules (proteins or nucleic acids) across membranes and into cells.


Terms & concepts

  • Antigen
  • Antigen receptors: antibodies and T cell receptors
  • Antigen presenting cells
  • Lipid nanoparticles or liposomes
  • MHC (major histocompatibility complex) proteins
  • Neutralization vs. opsonization
  • Phagocytosis in vaccine function
  • Protein vaccine
  • Vaccine
  • Virus-based vaccine (weakened or inactivated coronavirus)
  • Viral vector vaccine (virus other than coronavirus)
  • Virus-like particle

Review questions

  1. Compare and contrast RNA and DNA vaccines, in terms of what features are needed in the nucleic acid sequences. 
  2. RNA viruses have specific features that allow their RNA to enter cells. How do RNA vaccines solve this same problem?
  3. Why is the spike protein used as the antigen for coronavirus vaccines?

References & further reading


mRNA vaccines, explained . Vox. Outstanding intro. 7 minutes.

Inside the Lab That Invented the COVID-19 Vaccine. It's Okay to be Smart. 12 minutes. Describes some interesting science behind the development of mRNA vaccines. 

Vaccines. This video is part of an MIT course on Covid. Scroll  down the page to Lecture 10: Kizzmekia Corbett, “Vaccines.” Corbett is a researcher who carried out some of the foundational work on the structure of the spike protein, which was essential for vaccine development. 56 minutes and more detail than you need for this class, but it's an interesting look at the research.

Covid-19 vaccines

The race for coronavirus vaccines: a graphical guide (Nature). An excellent graphic guide to vaccine mechanisms; I've used some of the graphics in this page.

How Nine Covid-19 Vaccines Work . Corum and Zimmer, The New York Times. An outstanding set of brief graphic articles describing the various vaccines. Includes links to separate pages on the individual vaccines. The site allows only a limited number of article views for free.

COVID-19 vaccine . Wikipedia. Describes the vaccine types featured on this page.

RNA vaccines

How mRNA Technology Could Change the World. Thompson, 2021. An excellent, easy-reading look at the development and future of mRNA vaccines. Thompson makes the point that the seemingly rapid development of mRNA vaccines was built on a foundation of research that began long before Covid-19.

RNA vaccines: a novel technology to prevent and treat disease . Hubaud, Harvard.

Influenza vaccines

How Influenza (Flu) Vaccines Are Made . CDC. Describes egg-based, cell-based, and recombinant flu vaccines.

Influenza Vaccine Production and Design. NIH.


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