Currently, several vaccines for COVID-19 are undergoing clinical trials. They are based on a variety of innovative technological platforms, several of which have never been used in any licensed vaccine. This post analyzes five of them, and presents a layman explanation of their principles of operation.

Introduction

The purpose of a vaccine is to train the body to quickly recognize and fight pathogens (troublemakers). In most cases, the immune system is able to take care of this on its own, but even so several days are necessary before the body is able to fight off a novel pathogen. Vaccines shorten this timespan and increase the strength of the response.

Traditional vaccines were made with killed or weakened pathogens. New emerging platforms alleviate the need of dealing with pathogens when making a vaccine by synthesizing only the necessary antigens (parts of the pathogen). These synthetic antigens can be delivered to the relevant parts of the immune system in a variety of ways. I want to stress this point: different vaccines can be produced for the exact same antigen by using a different delivery technology. Three of the five vaccines described below use the same antigen, but a different method for delivery.

Most vaccines follow a similar path: after injection, they float outside cells until they are picked up and internalized by professional antigen presenting cells. These cells will degrade the antigen and present pieces of it on their surface. At the same time, they migrate in the lymph nodes, the training ground for (some of) the fighters of the immune system. Once there, naive lymphocytes will be exposed to the antigen presenting cell. Lymphocytes that recognize the antigen are activated and leave the lymph node, hunting for anything that looks like that antigen.

COVID-19 is a disease caused by the novel coronavirus, or SARS-CoV-2. Emerged in the last months of 2019, by April 2020 it caused lockdowns and curfews all around the world. Viruses employ several mechanisms to infect cells and hijack their facilities to produce and release copies of the virus. The novel coronavirus presents on its surface a spike that recognizes and binds to cells expressing a particular receptor called ACE2, normally used to control blood pressure.

Vaccines for COVID-19 aim at activating B cells, a kind of lymphocyte that produces antibodies when it meets its cognate antigen (the antigen it recognized on the professional antigen presenting cell). These antibodies look like the ACE2 receptor and trick the virus into binding to them instead of other cells in the body. Anything tagged by an antibody will eventually be eaten, digested and disposed of by macrophages.

There are currently five vaccine candidates in clinical trials (and there will probably be more when you read this article). They all use fairly recent technologies that are actively under research, some of which have never been featured in a licensed vaccine for the masses.1 In this post I summarize what I learned about these technologies, as they were new to me. A disclaimer is, therefore, in order: in spite of my best efforts, what I say might be inaccurate and/or incomplete, and the references might not be the most appropriate, so take all of this with a grain of salt. I certainly cannot make any kind of educated guess on which vaccine has the best chance to succeed.

mRNA-1273

Follow-up: The authors have relased a pre-print on bioRxiv2 giving more details on the vaccine and its evaluation in phase I and II clinical trials.

Developed by Moderna and tested in clinical trial NCT04283461, mRNA-1273 is a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine that encodes for a full-length, prefusion stabilized spike (S) protein of SARS-CoV-2.

As explained above, the Spike (S) protein is used by the coronavirus to hook the ACE2 receptor and enter into the cell. When this happens, the S protein will fold and pull the virus to the cell surface so that the two membranes can merge. In order to block SARS-CoV-2, antibodies must target the S protein before it binds to ACE2, therefore it is fundamental to train them using its prefusion form. On its own, however, this configuration is quite unstable, which means that S proteins delivered as part of a drug might break down before they have a chance to educate the immune system. In this vaccine, therefore, the S protein is slightly modified to keep in the desired prefusion configuration. A method to do so was reported for SARS’s spike protein,3 and I presume this could work for the novel coronavirus without too many changes.

Unfortunately, mRNA is also unstable and would be quickly degraded before it could be picked up by the antigen presenting cells. This is where nanoparticles come into play: they are spherical shells that insulate the mRNA from the dangerous environment outside cells. These sturdy structures last long enough to be found by antigen presenting cells, but once inside they can be easily disassembled and expose their payload. The shell is made from lipids (“oily/fatty substances”) because they are non-toxic, and a solid form allows to control how quickly the drug is released.4

3d model of a solid lipid nanoparticle

A three dimensional visualization of a solid lipid nanoparticle. The drug is represented as double-stranded DNA helixes, in green. The orange spheres constituting the surface are lipids.

Image credit: Precision Nanosystems (no affiliation).

Once inside cells, the mRNA antigen is copied, and some of these copies are then presented on the surface of the cell. When this happens in professional antigen presenting cells, lymphocytes are trained to recognize the antigen, and can start hunting for it.

Ad5-nCoV

From CanSino Biologics Inc. and tested in clinical trial NCT04313127, Ad5-nCov is a recombinant adenovirus type 5 vector that expresses the S protein.

Adenoviruses are fairly common, so much so that a considerable portion of people have been unknowingly infected and recovered at some point in their lives. Their natural infective capabilities can be exploited to deliver vaccines or other types of drugs. Adenoviruses, especially of type 5, are well understood and frequently used to treat a wide variety of diseases.5 6

a picture of adenovirus particles

An image of adenovirus particles.

Image credit: Drugs and Diseases Reference Index - Adenovirus.

This is done by genetically engineering the virus to either (a) display selected antigens on its surface or (b) produce copies of the desired drug when it infects a cell. The description of the clinical trial makes me guess that Ad5-nCov follows the latter option. Adenoviruses can be further modified to remove their replication capabilities, so that upon infection only the desired drug is produced. This is done in most modern adenovirus-based therapies.

INO-4800

By Inovio Pharmaceuticals and tested in clinical trial NCT04336410, INO-4800 is a DNA plasmid encoding the S protein delivered by electroporation.

DNA plasmids are ring-shaped DNA molecules.7 8 They encode the antigen of interest, in this case again SARS-CoV-2’s spike protein, together with some elements that stimulate and facilitate copying the antigen. Antigens encoded in DNA vaccines must be copied into RNA, which is then copied again to produce a new instance of the antigen. Antigens in RNA vaccines, being already made of RNA, can skip the first copying step altogether. However, the DNA plasmids reside in the cell nucleus, which means that new copies of the antigen can be produced even a long time after the RNA is discarded.

picture of plasmids

False color image of DNA plasmids from E. Coli.

Image credit: Science photo library.

Electroporation is a procedure that makes it easier for the plasmids to enter inside cells.9 After delivery of the vaccine, brief electrical pulses are applied to the area of injection. These pulses create small temporary holes in the surface of nearby cells, thanks to which the plasmids can enter. This can increase the effectiveness of the vaccine by orders of magnitude.

LV-SMENP-DC

Proposed by the Shenzhen Geno-Immune Medical Institute, it is evaluated in clinical trial NCT04276896. That page explains it well:

Based on detailed analysis of the viral genome and search for potential immunogenic targets, a synthetic minigene has been engineered based on conserved domains of the viral structural proteins and a polyprotein protease. The infection of Covid-19 is mediated through binding of the Spike protein to the ACEII receptor, and the viral replication depends on molecular mechanisms of all of these viral proteins. This trial proposes to develop and test innovative Covid-19 minigenes engineered based on multiple viral genes, using an efficient lentiviral vector system (NHP/TYF) to express viral proteins and immune modulatory genes to modify dendritic cells (DCs) and to activate T cells

Unlike the vaccines discussed above that only used the spike protein, the antigen in this vaccine is created by joining together several pieces of the coronavirus. These pieces come from its structural proteins, i.e. the parts that make up its external shell. The “SMENP” in the vaccine name is an acronym from the five structural proteins: spike, membrane, nucleocapsid, envelope and protease.

Conserved domains are parts of the virus that rarely change because of mutations. Mutations are one of the main mechanisms that viruses use to avoid recognition by the immune system. Some parts, however, cannot change, because are essential for the functioning of the virus. By comparing the hundreds of published coronavirus genomes, it is possible to find regions with few mutations that are still recognizable by the immune system, and create an artificial antigen based on them. This technology is actually the main focus of my PhD. If you want to know more, you can read the two papers10 11 I have worked on until now.

The antigen in this vaccine is delivered through modified dendritic cells. Dendritic cells are one of the main professional antigen presenting cells described in the introduction of this post. The other vaccines count on them to eventually pick up the antigen and present it to lymphocytes. This vaccine takes an entire different route: specific kinds of cells are harvested from the patient, stimulated to grow into dendritic cells, forcefully modified to present the engineered antigen, then injected into the patient so that they can do their own thing.12 Using lentiviruses to modify the dendritic cells is an especially effective strategy.13 Lentiviruses incorporate their DNA with the DNA of the cells they infect, so that for this vaccine these dendritic cells are continuously producing and presenting the synthetic minigene derived from the coronavirus. For good measure, some T cells are activated in the lab and delivered to the patient together with the modified dendritic cells. Note, however, that the modified dendritic cells can activate B cells once delivered to the patient, so this vaccine can be used for prevention, too.

a picture of inactivated and activated dendritic cells

An image showing immature (left) and activated (right) dendritic cells. Immature dendritic cells look for antigens to display, while activated dendritic cells are actively displaying antigens on their surface.

Image credit: Drugs and Diseases Reference Index - Adenovirus.

Pathogen-specific aAPC

From the same developers as the previous vaccine, and tested in clinical trial NCT04299724, this vaccine is quite similar from the previous one. Instead of growing dendritic cells from cells harvested from the patient, here they try to use artificial antigen presenting cells. The hope is to avoid the need to harvest cells from the patients that should receive the vaccine, and instead use universal, pre-made antigen presenting cells.14 This would make the vaccine much easier to produce and deliver. Some of these artificial cells are grown by modifying suitable cells, but many alternatives that are not based on cells at all are being explored.

Conclusion

As you realized, a wide variety of technologies is being tested. Most of them are fairly new and under active development. Another challenge facing vaccine developers is comparing the results of the clinical trials to establish the best vaccine.15 I am looking forward to reading the results of these clinical trials. Without a doubt, these findings will spur considerable enthusiasm towards successful technologies and accelerate their application to other diseases.

If you want to stay informed about these developments, I found articles in Nature Reviews Immunology and Drug Discovery, as well as Nature News Feature a very interesting source of news that are particularly accessible and clearly explained. In particular, The race for coronavirus vaccines: a graphical guide16 is a good complement to this blog post, with beautiful images explaining the same biological processes involved.

Bibliography

  1. Le, T. T. et al. The COVID-19 vaccine development landscape. Nature Reviews Drug Discovery (2020) doi:10.1038/d41573-020-00073-5. ↩

  2. Corbett, K. S. et al. SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness. http://biorxiv.org/lookup/doi/10.1101/2020.06.11.145920 (2020) doi:10.1101/2020.06.11.145920. ↩

  3. Kirchdoerfer, R. N. et al. Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Scientific Reports 8, (2018). ↩

  4. Mehnert, W. & Mäder, K. Solid lipid nanoparticles. Advanced Drug Delivery Reviews 64, 83–101 (2012). ↩

  5. Wold, W. S. M. & Toth, K. Adenovirus Vectors for Gene Therapy, Vaccination and Cancer Gene Therapy. Curr Gene Ther 13, 421–433 (2013). ↩

  6. Zhang, C. & Zhou, D. Adenoviral vector-based strategies against infectious disease and cancer. Human Vaccines & Immunotherapeutics 12, 2064–2074 (2016). ↩

  7. Kutzler, M. A. & Weiner, D. B. DNA vaccines: ready for prime time? Nature Reviews Genetics 9, 776–788 (2008). ↩

  8. Gary, E. N. & Weiner, D. B. DNA vaccines: prime time is now. Current Opinion in Immunology 65, 21–27 (2020). ↩

  9. Khan, A. S., Broderick, K. E. & Sardesai, N. Y. Clinical Development of Intramuscular Electroporation: Providing a “Boost” for DNA Vaccines. in Electroporation Protocols (eds. Li, S., Cutrera, J., Heller, R. & Teissie, J.) vol. 1121 279–289 (Springer New York, 2014). ↩

  10. Graph-Theoretical Formulation of the Generalized Epitope-based Vaccine Design Problem ↩

  11. Joint epitope selection and spacer design for string-of-beads vaccines ↩

  12. Sabado, R. L., Balan, S. & Bhardwaj, N. Dendritic cell-based immunotherapy. Cell Research 27, 74–95 (2017). ↩

  13. He, Y., Zhang, J., Mi, Z., Robbins, P. & Falo, L. D. Immunization with Lentiviral Vector-Transduced Dendritic Cells Induces Strong and Long-Lasting T Cell Responses and Therapeutic Immunity. The Journal of Immunology 174, 3808–3817 (2005). ↩

  14. Kim, J. V., Latouche, J.-B., Rivière, I. & Sadelain, M. The ABCs of artificial antigen presentation. Nature Biotechnology 22, 403–410 (2004). ↩

  15. Callaway, E. Scores of coronavirus vaccines are in competition — how will scientists choose the best? Nature (2020) ↩

  16. Callaway, E. The race for coronavirus vaccines: a graphical guide. Nature 580, 576–577 (2020). ↩