How Vaccines Work: From Lab to Shots
Now that it’s autumn again and everyone is getting sick left and right with various infections, it’s time to remember vaccination. I take it rather seriously. I had a bad case of flu a decade ago that almost killed me (the town’s hospital was quarantined due to some outbreak) that left me with long-lasting gifts like shortness of breath and constant fatigue; then COVID came and made everything worse. Was ‘lucky’ to get it before the vaccine was available, courtesy of relatives who did not believe in the pandemic. Now four years later I still can’t go up the stairs. Oh well.
I believe that awareness of how exactly vaccines work and how they are produced can help to ease the fear surrounding them. The pandemic and its aftermath showed us that a lot of people either don’t get what vaccines are or are misinformed about their function. And people are afraid of things they don’t understand.
Part 1: The immune system — our line of defense.
The immune system is probably the most complex component in the human body. It is our primary defense mechanism against disease-causing bacteria, viruses, fungi, and parasites. Understanding how the immune system works helps with awareness of how vaccines work and why they are so effective.
The immune system consists of two main components: the innate immune system and the adaptive immune system; these two work together to identify, attack, and eliminate pathogens while remembering them for future attacks. The innate immune system is the first line of defense that responds to invaders within minutes to hours. It reacts to general signs of invasion instead of recognizing a specific pathogen. The key components of the innate immune system can be summarized as:
- Physical barriers (the skin and mucous membranes) that prevent pathogens from entering the body;
- Chemical barriers (tears, saliva, stomach acid, and mucus) that contain enzymes and other chemicals that can destroy pathogens;
- Phagocytes (macrophages and neutrophils) that are specialized white blood cells able to engulf and digest pathogens;
- Natural Killer cells that target and destroy infected or abnormal cells — including cells infected by viruses or transformed into cancer cells;
- Inflammation that involves increased blood flow, swelling, and heat to help isolate and destroy the pathogen. That is why a cut or infected area often becomes red and warms.
On the other hand, the adaptive immune system is the specialized defense line that is highly specific. It takes longer to respond, from days to weeks, but it’s more powerful and precise than the innate immune system. It learns to recognize specific pathogens and remembers them for faster responses in the future. This capability to ‘remember’ is the basis for how vaccines work. The key components of the adaptive immune system include
- B cells, one of two lymphocyte types. B cells are responsible for the production of antibodies — proteins that specifically recognize and bind to antigens (unique markers on pathogens).
- T cells, another type of lymphocyte. There are two primary types of T cells: helper T cells and cytotoxic T cells. Helper T cells activate and direct other immune cells, including B cells and cytotoxic T cells. Cytotoxic T cells just directly kill infected or cancerous cells.
- Antigen Presenting Cells (APCs), such as dendritic cells, capture parts of an invading pathogen and present them to T cells, alerting and educating the adaptive immune system about the specific invader.
The immune response is a coordinated effort between the innate and adaptive systems to recognize, respond to, and remember pathogens. When a pathogen enters the body, the innate system is the first to detect it. Recognition receptors on immune cells recognize structures commonly found on pathogens but not human cells (e.g. glycoproteins, peptidoglycans, double-stranded RNAs). Upon recognition, the innate immune system responds to the pathogens. Phagocytes travel to the site of infection and attempt to digest the pathogens. These cells also release chemical signals (cytokines) that ‘signal for reinforcements’ and cause inflammation.
APCs capture pieces of the pathogen and move to the lymph nodes where they present the antigens to T cells. As T cells recognize the presented antigen, they become activated and start multiplying. Helper T cells then release signals that stimulate B cells and cytotoxic T cells. Now B cells start producing antibodies that specifically target the pathogen, and cytotoxic T cells start searching for and destroying infected cells. Antibodies produced by B cells can circulate through the body and bind to pathogens. These antibodies can combat the infection in several ways: directly block the pathogen’s ability to infect cells, mark the pathogen for destruction by other immune cells (by opsonization), and activate complement proteins in the blood that help to destroy pathogens by creating holes in their membrane. After the infection is cleared, some B and T cells become memory cells that can remain in the body for years, available for a rapid response if the body is infected by the same pathogen again. This memory formation is what vaccines are trying to invoke.
Part 2: Vaccines, how do they work?
Vaccines utilize the natural power of the immune system’s memory. Vaccines trigger an immune response without causing illness by introducing a harmless part of the pathogen, such as a protein or a weakened version. The immune system then begin producing memory cells that can deal with the real pathogen if encountered later. Here we will look into our two examples: the MMR vaccine and the mRNA COVID-19 vaccines.
The MMR vaccine protects against three dangerous infections: measles, mumps, and rubella. None of them have a cure or specific treatment. You are most likely vaccinated against all three, either as a complex vaccination or separately. Measles caused 2.6 million deaths per year before immunization, now it’s down to 136,000 deaths in 2022 — mostly children from areas with low rates of vaccination. Rubella, another infection that can lead to serious complications such as encephalitis and miscarriage, has been successfully eliminated from 84 out of 195 countries, thanks to the vaccine. Reading the complication list for mumps made me appreciate the availability of vaccine — mumps virus infections can result in inflammation of breasts, meninges, brain, pancreas, kidneys…
The MMR vaccine uses live attenuated viruses — weakened versions of the viruses that cause these diseases. The weakened viruses are not strong enough to cause the full-blown disease but are able to stimulate the immune system. When the vaccine is administered, the body activates an immune response as if the virus were a real threat. The immune system produces antibodies and memory cells that recognize the measles virus. So if a vaccinated person encounters the actual measles (or mumps, or rubella) virus, their immune system will be ready to neutralize it before it can cause illness.
The COVID-19 pandemic led to the rapid development of a new type of vaccine using messenger RNA (mRNA) technology, but the research in mRNA vaccines has been ongoing since the 1990s. The Pfizer-BioNTech and Moderna COVID-19 vaccines were among the first mRNA vaccines to be widely used. So how did these companies develop the vaccines so fast? BioNTech and Moderna were founded in 2008 and 2010, respectively, to advance the development of mRNA biotechnologies. COVID-19 vaccines were the first approved mRNA vaccines due to the emergency caused by the pandemic, but they are not the first developed mRNA vaccines.
Unlike traditional vaccines that use inactivated or attenuated viruses, mRNA vaccines deliver a small piece of genetic material into cells. This mRNA ‘tells’ cells to produce the spike protein, a harmless piece of the virus that causes COVID-19. This spike protein is what the virus uses to enter human cells. When the cells produce the spike protein, they ‘teach’ the immune system to recognize it as a threat — the immune system then makes antibodies and memory cells specific to the viral protein. The ‘memory’ of the pathogen can last for years, decades, or even a lifetime — depending on the pathogen and the type of immune response.
Part 3: Vaccine design.
The first step in vaccine development is to understand the biology of an emerging pathogen. Scientists sequence the pathogen’s genome and look into it to identify its proteins and understand how it interacts with human cells. This helps researchers to choose the target for a vaccine — typically a component essential for the pathogen’s ability to cause disease that the immune system can easily recognize. The vaccine design evolved, too.
Going back to the measles vaccine, its development began in the 1950s with the isolation of the measles virus. The virus was cultured in different cell lines in the lab, it was gradually weakened through repeated passages in non-human cells — a process known as attenuation. This attenuated virus then became the foundation for the first measles vaccine. This approach targeted the entire virus in a weakened form, meaning that the immune system could recognize multiple viral components. Such broad recognition is why the vaccine provides long-lasting immunity after one or two doses. A more refined vaccine version has since been developed and used worldwide to reduce measles cases.
When SARS-CoV-2 virus emerged in late 2019, researchers quickly sequenced the virus’s genome. The spike protein that is responsible for binding to human cells and initiating infection was found to be the central component. The spike protein binds to the ACE2 receptor in human cells, and blocking this interaction would prevent the virus from infecting the cells. With the development of COVID-19 vaccines came the first approved mRNA vaccines. Instead of using a live virus or viral protein, the vaccine delivers genetic instructions to our cells to produce a piece of the spike protein. This is sufficient to trigger an immune response without exposing the body to the virus.
Part 4. Clinical tests and trials
Vaccine production is a complicated process that starts after a vaccine candidate has been designed. It involves rigorous testing and refinement to ensure the safety and effectiveness of the vaccine; the process typically takes years to develop a vaccine from lab research to large-scale clinical trials. Accelerated production and approval of COVID-19 vaccine took 1.5 years due to the emergency caused by pandemic.
Before any vaccine can be administered to humans, it must undergo preclinical testing. This phase involves testing the vaccine candidate in cells and animal models to obtain information on its safety, ability to provoke an immune response, and effectiveness. Often animal models such as mice, ferrets, or non-human primates are used because they demonstrate a close approximation of how humans might respond to the vaccine — researchers investigate how the animal’s immune systems react to the vaccine and whether the animals are protected from infection when later exposed to the pathogen. In this stage, different dosages, formulations, and delivery methods are tested before moving into clinical trials if the vaccine shows promising results.
Clinical trials are conducted in three phases, and they are designed to assess the optimal parameters of the vaccine in humans. These trials are highly regulated by government agencies to make sure that all safety standards are met. Each phase of clinical trials is based on the results of the previous phase, and the number of participants increases as the vaccine progresses through the stages.
Phase 1 trials are the first step in testing the vaccine in humans. These trials are typically small (20–100 volunteers). The goal is to evaluate the safety of the vaccine and to determine the correct dosage that will be used in future trials. Participants in Phase 1 trials are usually healthy individuals, and the trial seeks to determine whether the vaccine is safe for humans, how does the human body react to the vaccine, and what is the optimal dose to provoke an immune response without causing unwanted effects. Scientists measure the immune response by looking at antibody levels and T-cell activation. As an example, here is a snippet from Moderna’s Phase 1 study of mRNA vaccine against coronavirus:
The Phase 1 study is evaluating the safety and immunogenicity of three dose levels of mRNA-1273 (25, 100, 250 μg) administered on a two-dose vaccination schedule, given 28 days apart. A total of 45 healthy adults will be enrolled in the study. Participants will be followed through 12 months after the second vaccination. The primary objective is to evaluate the safety and reactogenicity of a two-dose vaccination schedule of mRNA-1273. The secondary objective is to evaluate the immunogenicity to the SARS-CoV-2 S protein.
The results of the Phase 1 were reported:
The mRNA-1273 vaccine induced anti–SARS-CoV-2 immune responses in all participants, and no trial-limiting safety concerns were identified. These findings support further development of this vaccine.
If the vaccine successfully passes Phase 1, it moves into Phase 2 trials, where it is tested in a larger group of participants. This phase further looks into the vaccine’s safety and starts changing focus to efficacy. Participants in Phase 2 trials are usually more diverse in age and health conditions to help researchers understand how different populations may respond to the vaccine. In this phase, the scientists aim to gather more data on the vaccine’s safety and side effects in broader population groups and to refine the dosing regimen, including the possibility of booster doses, if the immune response does not last long.
Phase 2 results of the Moderna vaccine were:
Vaccination with mRNA-1273 resulted in significant immune responses to SARS-CoV-2 in participants 18 years and older, with an acceptable safety profile, confirming the safety and immunogenicity of 50 and 100 µg mRNA-1273 given as a 2 dose-regimen.
Phase 3 clinical trials are the final and most extensive phase of testing before a vaccine can be considered for approval. In this stage, the vaccine is tested in thousands of participants. These trials are designed to confirm the vaccine’s effectiveness in preventing the disease and to monitor for any rate of side effects that may not have been detected in earlier phases. This phase typically involves a randomized, double-blind, placebo-controlled trial. In other words, participants are randomly assigned to either the vaccine group or the placebo group neither the participants nor the researchers know who is receiving the vaccine and who is receiving the placebo, and the comparison between the two groups allows scientists to determine the true effect of the vaccine by comparing disease rates between the vaccinated group and the placebo group. During this phase, participants are followed over time, and their health outcomes are carefully tracked. Researchers measure how many people in the vaccinated group contract the disease compared to the placebo group, and the efficacy rate based on the comparison determines whether the vaccine will be approved for public use.
High efficacy rates in Moderna’s Phase 3 trials helped with rapid emergency authorization:
The trial enrolled 30,420 volunteers who were randomly assigned in a 1:1 ratio to receive either vaccine or placebo (15,210 participants in each group)… The mRNA-1273 vaccine showed 94.1% efficacy at preventing Covid-19 illness, including severe disease. Aside from transient local and systemic reactions, no safety concerns were identified.
But even after a vaccine is approved for public use, the process isn’t over. Post-approval monitoring is needed to ensure that the vaccine remains safe and effective as it is distributed to millions of people. It involves ongoing surveillance to detect any side effects that may have appeared during clinical trials. Regulatory agencies, healthcare providers, and vaccine manufacturers are all in collaboration to continue the evaluation of the vaccine’s performance in real-world settings.
For example, the rollout of COVID-19 vaccines led to the detection of rare side effects, such as myocarditis in younger people following mRNA vaccines and blood clotting disorders associated with some viral vector vaccines. Such findings allowed public health authorities to change vaccination recommendations and maximize safety.
Part 5: Manufacturing and purification
After a vaccine has successfully passed through clinical trials and has been approved, the production has to be scaled up to meet the demands. This process can be complex, especially for modern vaccines, which require precise conditions to manufacture on a larger scale. Ensuring that every dose is safe and consistent is also critical. The production of mRNA vaccines is probably the most complex to scale up, given its nature; as in the future we will encounter more and more mRNA vaccines, I’ll use its production as an example.
The first step in manufacturing is the synthesis of the mRNA sequence in large quantities. Scientists use DNA templates that contain the code for the viral protein, special enzymes are used to transcribe the DNA into mRNA, copying the natural process that occurs in cells. This synthetic mRNA is highly specific and must be carefully designed — it may not code for the correct protein otherwise. After synthesis, the mRNA is purified from contamination and impurities.
Purification process is needed to ensure that each dose is safe and free from any contaminants or impurities that could harm the recipients. Vaccines are introduced into our bodies — so even smallest amount of contamination can pose health risks. When vaccines are produced, they undergo multiple chemical and biological processes. Some substances used in these processes, such as reagents and enzymes, are necessary for the production but are not meant to be part of the final product. These unwanted byproducts may cause unintended reactions in vaccine recipients and reduce vaccine’s effectiveness — purification ensures that the only thing left in the vial is the vaccine.
The method of purification depends on the type of vaccine produced, but usually methods include techniques like filtration, chromatography, and ultracentrifugation. Filtration involves passing the solution containing vaccine through a series of filters designed to remove cell debris and other unwanted materials; this method is especially important for the removal of bacterial contaminants. Chromatography is a more complex technique that separates the vaccine’s active components from impurities based on their chemical properties. Ultracentrifugation is another common method that uses high-speed spinning to separate particles based on their size and density.
The mRNA is delivered into the cells using lipid nanoparticles. Lipid nanoparticles are small bubbles of fat that encapsulate the mRNA and protect it from degradation. Without these particles, the mRNA would be destroyed before it could reach the cells. In large-scale manufactoring, the mRNA is mixed with lipids under specific conditions to form the nanoparticles; any variation in the size or structure of the lipid particles could affect how the vaccines works, so strict quality control is necessary. The product is ready to be formulated into individual vaccine doses when the encapsulation of mRNA is finished.
Filling and packaging must be precise because any deviations can affect the vaccine’s stability or dosage accuracy. Each vial must contain the right amount of vaccine so that everyone receives a consistent dose. The mRNA vaccines are sensetive to temperature, so manufacturers add stabilizers to help preserve the vaccine. The vaccine must also be stored and transported at extremely low temperatures to prevent degradation.
Part 6: Delivery to the body
Now that a vaccine has been developed, tested, and manufactured, the next step is to deliver it to individuals in a way that ensures it will be effective. The most common method of vaccine delivery is injection, either into the muscle, under the skin, or directly into the bloodstream.
For most vaccines, including the mRNA, the standard delivery is through an intramuscular injection. The muscle tissue contains dendritic cells that are crucial for detecting viruses and bacteria. Upon injection of the vaccine, these dendritic cells capture the vaccine components and start the activation of the immune system. Muscles also contain a rich blood supply, which allows efficient transport of vaccine components throughout the body, thus ensuring quick response and recognition of the antigens or viral proteins introduced by the vaccine. Furthermore, the muscle tissue absorbs a rather large volume of vaccine fluid, causing less discomfort during injection.
The process of immune system activation is slightly different for mRNA vaccines. Once the mRNA is injected into the muscle, it is taken up by muscle and dendritic cells near the injection site. These cells receive the mRNA instructions and start producing the spike protein — this process mimics a natural viral infection. The production of the spike protein causes the immune reaction: T cells are activated, and B cells will start producing antibodies. Memory cells are created in this process too, and they will remain in the body ready to start a strong immune response if the person encounters the virus in the future.
Final words
The COVID-19 pandemic happened when I was in the middle of studying for my biochemistry and molecular biology degree, so viruses and vaccines were a hot topic for discussion for a short while. My undergrad university tried its best to interest students in virology and promote awareness of what a pandemic might become… for around a month. Then they used the pandemic as an excuse to kick students off campus, cancel scholarships, and charge outrageous amounts for piss-poor quality pre-recorded online lectures, while student advisors and lecturers went MIA for two whole years. I got inspiration for this article because that university had the audacity to send out a questionnaire asking me to rate how my life is going two years after graduation, and how the pandemic period affected my studying. Four years too late, but we truly were all in this together.
Thank you for reading!
References
- https://www.ncbi.nlm.nih.gov/books/NBK279364/
- https://www.sigmaaldrich.com/NO/en/applications/pharmaceutical-and-biopharmaceutical-manufacturing/vaccine-manufacturing/mrna-vaccines-process-manufacturing
- https://www.pfizer.com/science/coronavirus/vaccine/manufacturing-and-distribution
- https://pubmed.ncbi.nlm.nih.gov/23600866/
