Reverse Vaccinology: from a dream to reality

Bhavna Karnani

Bhavna Karnani

Bhavna is a young researcher at the National Institute of Molecular Genetics (INGM) in Milan, Italy. Her Alma Mater is the Florida Institute of Technology from which she graduated with honors in Biochemistry. She continued her education at ETH Zurich where she gained a Microbiology and Immunology master degree with research experience centered on human nutrition, food microbiology and biochemistry. She is now actively involved in the research of human regulatory T-cells in cancer.

Vaccines have eradicated some of the deadliest infectious diseases known to man, yet scientists have been challenged by the inability to create vaccines for all pathogens in the past. Recently, scientists have focused on the DNA of microbes to help develop vaccines by using a technique called “Reverse Vaccinology”. This efficient and cost-effective approach is expected to revolutionize vaccine development in the 21st century and is also being used as a promising approach for the treatment of cancer and antibiotic resistance.

The era of Classical Vaccinology

Prior to the 18th century, life expectancy was between 20 and 30 years of age. With healthier sanitation practices and the use of antibiotic drugs and vaccines, life expectancy has significantly increased to about 85 years. While vaccines have rendered deadly diseases such as smallpox, polio and measles essentially nonexistent, it is no secret that researchers still face challenges when it comes to developing vaccines for every pathogen that causes disease. As previously described in ‘’The rise of the 21st century anti-vaxxer epidemic’’, the human body must be instructed to recognize antigens from microbes such as bacteria, fungi and viruses. Antigens are toxins or foreign molecules belonging to the pathogen or invader that the immune system recognizes as non-self, thanks to the innate and adaptive immune systems. The innate immune system is the first response at the site of an infection and attacks anything foreign it comes into contact with. On the other hand, the adaptive immune system is an acquired immunity that takes time to develop as it needs to be ‘taught’ to recognize pathogens that the innate immune system cannot swiftly handle. Vaccines work because they produce an immune memory allowing the body to immediately recognize the microbe and quickly fight back when it comes into contact with it in the future.

Types of Classical Vaccines

The four types of vaccine that are commonly administered include: live-attenuated, inactivated, toxoid and conjugate vaccines. The MMR vaccine is an example of a live-attenuated vaccine, which contains a weakened live form of the virus. This type has some drawbacks, especially for individuals with a weakened immune system, as it could mount a strong adverse reaction to the vaccine. Inactivated vaccines, as the name suggests, contain inactivated or dead forms of the microbe such as the Hepatitis A vaccine. Because this vaccine does not yield such a strong protective response as the live-attenuated type, booster shots are typically administered to maintain protection throughout life. Toxoid vaccines represent a completely different approach. A toxoid is a chemically modified toxin from a pathogenic microorganism that does not actually cause the disease itself, but is still capable of mounting an effective immune response against the disease. The tetanus vaccine, for example, contains the inactivated tetanus toxin produced by the bacteria Clostridium tetani. Last but not least, there are conjugate vaccines that target parts of the microbe, such as polysaccharide molecules found on bacterial cell surfaces or viral capsids that coat viruses. Conjugate vaccines like the one against Streptococcus pneumoniae, contain a weak polysaccharide antigen coupled to a stronger protein antigen. Polysaccharides antigens are weak because they are not recognized by adaptive immune cells responsible for creating immune memory. Having said that, when polysaccharides are connected to proteins, with the latter being recognized by such cells, the immune response becomes a lot stronger and long-lasting.

Vaccination. Photo @ Pixabay.

The grueling journey of vaccine development

Developing vaccines can be quite an expensive and time-consuming task, but probably the most challenging aspect of vaccine development is finding the right antigen, one that will have a long-lasting effect on the human immune system. The majority of vaccines that have been developed up until today have followed a classical vaccinology approach. In the 19th century, the French microbiologist Louis Pasteur developed a rationale for classical vaccinology to treat diseases. Pasteur proposed three steps that had to be followed to ensure protection against a pathogen. First, the microbe causing the disease had to be ‘isolated’ then ‘inactivated’ and finally ‘reinjected into the host’ (1). With these rules in place, it was understood that scientists had to first grow the pathogen in specialized biosafety laboratories or find antigens that would mount a strong immune response. In the past, the most time-consuming part of vaccine development was isolating, inactivating and understanding the behavior of microbes. In pharmaceutical research institutions, antigen-candidates must be first tested in animal models like rodents before being tested in humans. Mice and rats have biological, behavioral and genetic similarities to humans, and often develop symptoms observed in the human disease, which makes them ideal for animal models. However, a common drawback with this approach is that often, the same microbe that is able to inflict disease in humans may not cause disease in these animals. To make matters worse, sometimes the pathogen simply does not survive in rodents, which can complicate animal studies. Therefore, alternative methods to bypass these challenges have been required. Nevertheless, when animal models do work, vaccines must undergo several rounds of clinical trials before they can be considered safe to enter the clinics and be administered to people. Unfortunately, this process can easily take longer than a decade to complete and there is no guarantee that a vaccine will be approved until the very end of the study.

The major flaws of Classical Vaccines

While numerous vaccines have been developed using classical methods, this straight-forward approach hasn’t worked for all infections. A perfect example of this is the development of a vaccine for Meningococcus B (MenB). This bacterium notoriously caused the B-serotype meningitis outbreak in Princeton University back in 2013 and is responsible for 50% of the meningococcal meningitis worldwide. As previously mentioned, vaccines work because they prime the body to produce antibodies against the foreign threat before the threat is encountered in nature. In the case of Meningococcus B, the antigen presented on the bacterial surface is a self-antigen, a molecule that is identical to that of a sugar molecule present in humans (1, 2). Since developing a vaccine that will only inflict harm to the human body is never an option for any scientist or medical practitioner, an alternative solution had to be found. Vaccine developers had to dream big, think outside of the box and utilize different approaches if they wanted to develop a vaccine for MenB… and they did just that.

The birth of Reverse Vaccinology

By the late 80’s, the first conjugate vaccine against meningitis had been developed using new techniques to strengthen the antigenic responses in individuals (1). Additionally, a powerful tool came from the ability to access the genomes of microorganisms, which was made available in 1995 when Craig Venter published the first genome of a living organism (3). This technological revolution paved the way for scientists to move beyond the rules of Pasteur, which were challenging and time-consuming. The new technique was called ‘Reverse Vaccinology’ and was developed in 2000 by current Chief Scientist and Head of External R&D at GlaxoSmithKline Rino Rappuoli. Here, the process of vaccine discovery starts on the computer using the genetic information of a pathogen, rather than growing the pathogen itself (2). In the last decade, Rappuoli has shown that by sequencing the genome, we are not only able to learn about evolution and our ancestry, but we can also use this novel technique to find suitable targets for developing vaccines that will fight against a broad range of diseases like cancer, antibiotic resistance and AIDS (1, 4). With reverse vaccinology, scientists are now able to sequence the genome of a pathogen allowing the prediction of all antigens, independent of their abundance or their immunogenicity during infection. Moreover, this technique can also select for antigens that can mount immune responses in humans as well as in rodents, which can ensure the success of using animal models in the early stages of vaccine development. This not only saves money, but also time, which is of the essence when preventing an epidemic from emerging. What’s more, at least 15 suitable antigen candidates are often found to be unique to the pathogen, meaning they are not present in the human genome (2). Having so many suitable antigens has allowed us to exploit non-conventional parts of the immune system and increase the probability, rate and efficacy of obtaining a fully functioning vaccine (2). Impressively, thirteen years later through reverse vaccinology, a fully functioning MenB vaccine had been approved for use in individuals (6).

Reverse Vaccinology as a promising approach to treat cancer

But it doesn’t end there. With reverse vaccinology, scientists are not only trying to find novel targets for infectious diseases, but are also using this efficient approach to treat non-communicable diseases such as certain forms of cancer. While the prevalence of infectious diseases, such as diphtheria and measles, have drastically declined across the globe, there has been an increase in heart-related diseases, cancer and autoimmune diseases such as type-1 diabetes. In fact, non-communicable diseases have risen at an alarming rate and have become an important factor in the number of lives lost as described in “Reshaping the gut is the secret to successful weight-loss”. With the fascinating approach of reverse vaccinology, scientists hope to sequence the genome of cells in healthy tissue and compare it to those found in tumors, in order to identify new mutations that could allow earlier detection and treatment of cancer. Moreover, reverse vaccinology is already being used to combat parasitic infections and find new targets to combat antibiotic resistance and HIV infection. Reverse vaccinology is a technique that continues to evolve, and researchers remain hopeful that by combining biological methods with computer-based modeling, a prosperous and healthier future lies ahead of us.


Bhavna Karnani



  1. Sette, A. and Rappuoli, R., “Reverse vaccinology: developing vaccines in the era of genomics”, Immunity, 2010
  2. Rappuoli, R., “Reverse Vaccinology”, Current Opinion in Microbiology, 2000
  3. Fleischmann, RD. et al. “Whole-genome random sequencing and assembly of Haemophilus influenzae Rd”, Science, 1995
  4. Rappuoli, R., “Reverse Vaccinology”, Current Opinion in Microbiology, 2000
  5. Rappuoli, R. and Aderem, A., “A 2020 Vision for vaccines against HIV, tuberculosis and malaria”, Nature, 2011
  6. Masignani, V. et al. “The development of a vaccine against Meningococcus B using Reverse Vaccinology”, Front. Immun., 2019
Received: 29.07.19, Ready: 29.08.19, Editors: XZ, RG.

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