CRISPR – the original „vaccine” and what it can teach us about fighting viral infections

By Monika Berezowska

Clustered Regularly Interspaced Short Palindromic Repeats – six words that rapidly gained popularity in 2015 and according to Google Trends overtook even Drake’s hit single – “Hotline Bling”. This phrase however dates back to 2004 and initially had little to do with its current applications.

First used in the context of yoghurt production, CRISPR was observed by Rodolphe Barrangou – a researcher working for a Danish food company. He received a number of complaints from clients buying cell cultures to use for processing milk into yoghurt. Occasionally the bacterial cultures were killed by a viral infection during delivery. To fix this problem he looked into the differences between cells from cultures that resisted infection and the ones destroyed by it. One of the differences he noticed was that the survivor cells in a DNA region with many identical repetitions had one more, followed by a short sequence coming directly from the genome of the virus that caused trouble. 

To test the hypothesis whether CRISPR is a result of exposure to a new pathogen, bacteria were exposed to a known phage and after the content of their CRISPR gene loci was compared. It turned out that the exposed bacteria, which developed immunity to the virus in fact had one more spacer in that plasmid region and it mimicked the genetic make-up of the virus (Barrangou, 2007).

This was the first piece of evidence suggesting that CRISPR might be an immune system. As further experiments confirmed, bacteria use a system of incorporating a part of a pathogen’s genome into their own plasmids. That way they gain the ability to use it as a guide to recognize the pathogen in the future and cut any genetic material inserted by it. Cleaving viral DNA by introducing a double-stranded break leads to its degradation and prevents further spread of infection. (Gasiunas, 2012)

Effectively, all these short fragments that keep getting incorporated when a bacterium comes across a new phage remain in its genome and provide a certain display off all the pathogens it is immune against – almost like a vaccination book! In that sense CRISPR is a more primitive acquired immunity system used by prokaryotes and some archaea (Horvath, 2010). 

Naturally the human body fights viral infections by recognizing the pathogen, producing antibodies in the B cells that will bind to the virus and prevent it from entering cells and replicating further. Therefore, to treat diseases like SARS-CoV-2 blood plasma of convalescent patients can be used as it contains high level Covid-19 specific antibodies. (Joyner et al., 2021)

According to a recent study on 3082 hospitalized patients, in early treatment with plasma of varied antibody concentrations the risk of dying from Covid-19 infection decreased as the number of antibodies increased. The group who received the most antibody dense plasma was at a 34% lower risk compared to the patients who received scarcer antibodies. This analysis is one of many confirmations that an infusion of antibody-rich plasma is an efficient method of protection against severe SARS-CoV-19 disease.  

The reason why patients needed transfusions of antibodies is that their bodies didn’t produce enough of their own. The process of antigen exposure, developing all the right kinds of T and B cells to produce large number of antibodies lasts about up to 14 days. 

Because of how complex the process of stimulating the production of a new kind of antibodies is, the levels of antibodies produced after B-cells that are first familiarized with a new pathogen are also relatively low and only begin to increase exponentially after re-exposure (Riddell, 2020). This is precisely why the vast majority of available vaccines require multiple doses to stimulate an immune response strong enough to give reliable protection.

After the initial encounter with a new virus there is a large variety of so-called antigen-presenting cells and other intermediates involved on the way to the development of the proper, pathogen-specific memory B-cells. Only a fraction of affected B cells gains this important role and the capabilities that come with it. Once a population of memory B-cells is established when they encounter the virus again, they will rapidly divide and produce large numbers of antibodies. The process of developing them however is far from immediate, often slower than the progress of the viral infection which is why some people develop severe symptoms before their natural response against the disease stops the virus in its tracks.   

If we could however act faster this could potentially not only benefit the well-being of an individual but also help manage the spread of viral diseases, limit their outbreaks and provide a useful tool to fight pandemics. CRISPR as an immune system operating on a molecular level targets the viral load, which is the bulk of the problem behind infectious diseases, in a very direct way. Supposedly its protection could be achieved in a much shorter timeframe then the one offered by the myriad of white blood cells. Whether present in a human cell as a preventative method or administered to combat the spread of viral infection it seems to have potential to be an effective, programmable anti-viral. Experimentally CRISPR has been successfully used to inhibit a variety of human viruses (Frieje, 2019). It also shows potential use in diagnostics and vaccine development and is expected to become an irreplaceable tool in the fight against future infectious diseases (Ding, 2021).      

Imagine that a virus is a ticking-time bomb! It’s only a matter of time until it explodes and infects thousands of cells around. You can try to combat it the way the human immune system does – recruit a team of specialist sappers, engineer new equipment for them and try to train them before it’s too late. You might also tackle it the way CRISPR would – grab a pair of scissors and cut off the fuse. You know what a bacterium would do, and they have been around much longer than us.   


Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A. & Horvath, P. (2007) CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science. 315 (5819), 1709-1712. Available from: Available from: doi: 10.1126/science.1138140. 

Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 109 (39), E2579-86. 

Horvath, P. & Barrangou, R. (2010) CRISPR/Cas, the Immune System of Bacteria and Archaea. Science. 327 (5962), 167-170. Available from: Available from: doi: 10.1126/science.1179555. 

Joyner, M. J., Carter, R. E., Senefeld, J. W., Klassen, S. A., Mills, J. R., Johnson, P. W., Theel, E. S., Wiggins, C. C., Bruno, K. A., Klompas, A. M., Lesser, E. R., Kunze, K. L., Sexton, M. A., Diaz Soto, J. C., Baker, S. E., Shepherd, J. R. A., van Helmond, N., Verdun, N. C., Marks, P., van Buskirk, C. M., Winters, J. L., Stubbs, J. R., Rea, R. F., Hodge, D. O., Herasevich, V., Whelan, E. R., Clayburn, A. J., Larson, K. F., Ripoll, J. G., Andersen, K. J., Buras, M. R., Vogt, M. N. P., Dennis, J. J., Regimbal, R. J., Bauer, P. R., Blair, J. E., Paneth, N. S., Fairweather, D., Wright, R. S. & Casadevall, A. (2021) Convalescent Plasma Antibody Levels and the Risk of Death from Covid-19. The New England Journal of Medicine. 384 (11), 1015-1027. 

Freije, C. A., Myhrvold, C., Boehm, C. K., Lin, A. E., Welch, N. L., Carter, A., Metsky, H. C., Luo, C. Y., Abudayyeh, O. O., Gootenberg, J. S., Yozwiak, N. L., Zhang, F. & Sabeti, P. C. (2019) Programmable Inhibition and Detection of RNA Viruses Using Cas13. Molecular Cell. 76 (5), 826-837.e11. 

Riddell, N. E. (2020) Immune Responses: Primary and Secondary. 

Ding, R., Long, J., Yuan, M., Jin, Y., Yang, H., Chen, M., Chen, S. & Duan, G. (2021) CRISPR/Cas System: A Potential Technology for the Prevention and Control of COVID-19 and Emerging Infectious Diseases. Frontiers in Cellular and Infection Microbiology. 11 639108. 

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