Issue 21 Understanding Science

Clinical Trials – Part Three: Vaccines in Clinical Trials

🕒 25 min

“Our primary mission is life critical. Our goal is very clear: to address the gross inequities in child health still existing in the world today. Life or death for a young child too often depends on whether he is born in a country where vaccines are available or not.”

Nelson Mandela, addressing the Vaccine Fund Board 2003 meeting in Johannesburg

The last topic in the series on medical research and clinical trials is related to studies on vaccines and, what better example to explain vaccines research than the recent Covid-19 pandemic. Similar to pharmaceutical products, vaccines trials occur in 3-4 phases (Phase I-III pre-marketing authorization and Phase IV after the vaccine is licensed).

In reality, vaccines can be both prophylactic (serve to prevent a disease) and therapeutic (serve to treat the existing disease). They can be given to healthy individuals and to patients that suffer from a disease, depending on the design and the disease. Vaccines can be administered in several ways, intramuscularly, subcutaneously and there are even oral vaccines and nasal spray vaccines. In addition, newer technologies are investigating transdermal patches as a vessel for vaccines, to avoid the discomfort of getting an injection. Also, the vaccines are usually administered in a syringe but this can be a prefilled syringe for which administration can be done immediately, or first, the vaccine would need to be prepared, the syringe filled, and then administrated.

When we talk about vaccines, mostly we think of vaccines to prevent communicable diseases or those that can be transferred from person to person. Examples are infectious diseases caused by a pathogen: cholera, typhoid, hepatitis, influenza (flu), malaria, tuberculosis, tetanus, and COVID-19. In contrast, non-communicable diseases represent usually chronic, individual diseases such as cancers, cardiovascular diseases, and diabetes. They cannot be spread from person to person by bodily fluids, breathing in the virus, or being bitten by an insect.

Here, for simplicity, the focus will be on prophylactic vaccines as well as communicable diseases. The previous article (Clinical Trials – Part Two: Clinical Trials) explains the general ways clinical trials are performed and this is largely also applicable to vaccines.

Vaccines clinical trials: what is special compared to other trials?


As explained above, communicable diseases are caused by a pathogen – a virus, bacterium, fungus, or parasite. Each pathogen is biologically and chemically different, for example, bacteria are very different from viruses and fungi are very different from either of them. Once our bodies are confronted by a pathogen for the first time, they will react to components of that pathogen by creating antibodies. The component that causes the production of antibodies is called an antigen. Since the antibody production is not immediate, the body initially becomes sick and often this is when we start having symptoms. However, since the antibodies are being produced, the next time the body is confronted by the same antigen, the body will have already built immunity to prevent that particular disease and associated symptoms.

The immune system is a complex platform and there are additional components that contribute to overall protection against a certain disease together with antibodies. Immunity in its nutshell can be innate or adaptive (acquired). Innate immunity is the immunity we are born with, with organs, tissues, and cells protecting us (e.g., skin, white blood cells), whereas adaptive immunity is acquired through life. Adaptive immunity can be active (naturally acquired when facing pathogens or artificially through vaccination) and passive (naturally acquired through someone else, e.g., via breastfeeding, or artificially acquired from a medicine, e.g., antibody infusion). Vaccination, as such, is offering a shortcut to obtain adaptive immunity against a certain pathogen before even facing it for the first time, and often has far fewer side effects and inconvenience than getting a disease.

Figure 1 Innate and adaptive immunity (adapted from

Vaccine ingredients // types of vaccines // doses

Vaccines can contain various ingredients and can be given in single or multiple doses depending on which pathway of the adaptive immune system they need to activate and whether they have the capability for a durable immune response.

As an example, influenza or flu is one of the pathogens for which it is infamously difficult to create a universal vaccine that would protect against flu in general, no matter how much it changes every year. The problem in the development of such a universal, “supraseasonal” vaccine, as opposed to the seasonal vaccine, is laying in the biology of the virus. The flu virus consists of 8 segments of single-stranded RNA – which is its genetic material, and once it infects the cell, each flu virus releases its 8 RNA segments into a cell, where the production of new virus particles occurs. There may be errors in the process:

  1. Antigenic drift: the production is erroneous causing mutations in newly created RNA segments that will randomly pack into new flu viral particles. These RNA segments ultimately serve as a template to produce several enzymes and proteins that finally create 2 surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA). HA and NA are the actual antigens that the body will create antibodies against. The virus uses HA to enter the cell and NA to escape the cell once the new virus particles are packed and ready to be spread. You are probably familiar with H1N1 – these letters come from the two proteins mentioned above (the numbers mark different HA and NA types, which can be abundant in e.g., birds but are limited in humans). Over time these small mutations can accumulate and result in a different HA and NA on the surface and therefore, antigenically the flu virus may be too different from the one our antibodies are familiar with. Our immune system may not be able to recognize such a virus because it is too different. That is why we get sick from flu multiple times in our lifetime.
  2. Antigenic shift: sometimes major changes occur, resulting in new HA or NA unknown to humans. Often, this happens when an animal virus gains the capability to infect humans. A known case is a swine flu from 2009 when avian, human, and swine viruses mixed and gained the ability to infect humans.

These may present some of the reasons why it is difficult to come up with a universal, multi-year vaccine, given that the flu virus changes frequently and yearly. That being said, many companies/sponsors are trying to dig deeper into the biology of influenza and are coming up with technologies and different targets that may help with achieving a more robust flu vaccine.

Vaccine components

What is important for a vaccine is to activate the body’s immune system. To achieve that, each vaccine has to consist of at least one or several components capable of triggering the desired effect:

  • Antigen

Every vaccine contains a component to activate the immune response so that the next time body is faced with the same pathogen, it can recognize it and not get sick. This is usually a small part of the disease-causing agent (bacteria or virus) or can be a weakened form of a pathogen, that will trigger the immune system but not cause disease.

  • Preservatives

Preservatives help to keep the vaccine safe from contamination. Some vaccines are packaged in single-use vials or pre-filled syringes meant to be administered directly to one person. Such vaccines do not necessarily need preservatives. However, vials that contain multiple doses for several people need to be safe for repeated use and preservatives there serve to prevent contamination once the vaccine gets in contact with the air. The commonly used preservative is 2-phenoxyethanol, which is proven safe to be used in vaccines and other products, given it has low toxicity in humans.

  • Stabilizers

Stabilizers serve to prevent chemical reactions from happening in the vial and can be sugars, proteins, gelatin, or amino acids.

  • Surfactants

Surfactants keep vaccines homogeneous and uniform, as they prevent clumping. They are commonly used in food too, for example, in ice cream.

  • Residuals

Residuals are substances present in a very small amount (measured in parts per million or parts per billion) in the vaccine as a trace of the manufacturing process. For example, seasonal flu vaccines are produced in eggs and because of that, a final vaccine may contain traces of egg protein, which are in such small quantities that vaccines are even safe to be administered to people with egg allergies.

  • Diluent

Normally, vaccines need to be in a certain concentration which defines the correct dose to be administered. Vaccines are either already prepared in such a concentration or sometimes need to be prepared before administration. To achieve the desired concentration, diluents are used. The most common one is a saline solution.

  • Adjuvants

Besides antigen, the vaccine can contain another active component to enhance its activity. These are adjuvants and they serve to improve the immune response to the vaccination, by stimulating a local immune response or even components of cellular immunity. The most commonly used adjuvant is based on aluminum salts, but there are also new, more complex platforms being used. Notably, aluminum is found in food and our environment and the amount used in vaccine is entirely safe for humans.

How are vaccines developed?

Starting dose and schedule

Vaccines, like other pharmaceutical medical products, are developed based on preclinical and clinical research, as described in Parts 1 and 2 of this article series (Clinical Trials – Part One: Medical Research and Clinical Trials – Part Two: Clinical Trials). The main challenge with vaccines, as opposed to drugs, is that the starting dose is usually difficult to determine, given the lack of appropriate models. Vaccines are biological products so toxicity, pharmacodynamics, and pharmacokinetics as such may not be applicable measures to support the choice of dose. Moreover, the regulatory guidance when it comes to First-Time-in-Human vaccine application is scarce and often vague. Both EMA and FDA guidance on First-in-Human clinical trials are focused on investigational medicinal products, irrespective of whether they are biological, biotechnological, or chemical entities. However, vaccines come with their own particularities as biological products and there is currently no specific guidance on how to choose the starting dose for clinical application. The ICH provides very general guidance.

For the starting dose of drugs, an approach based on toxicity in the relevant animal model specifically on the no-observed-adverse-effect level (NOAEL). Since vaccines are complex in terms of exposure and long-term effects as well as non-specific adverse events, NOAEL may not be the best approach. The alternative approach is to use a calculation based on the minimal-anticipated-biological-effect level (MABEL), being the dose level at which a minimal biological effect in humans is expected by in vitro or in vivo data. It is based on the occurrence of any biological effect, not only toxicity, and usually yields a much lower dose compared to the NOAEL. Now, the problem is that with vaccines, even if a biological effect exists, it is often unknown whether this effect will translate into an any or adequate protection against the disease, especially if for a given disease a correlate of clinical protection does not exist = a threshold through which we know/expect a vaccine to protect against a given disease either by preventing a pathogen to enter the cell and replicate or by preventing symptoms and shedding (infecting other people).

If a new vaccine is developed against a disease against which there is already a vaccine, this would make the development easier, as there may be a way to compare new results with previously established safety, efficacy and immunogenicity data. If there are no vaccines against a given disease, a risk-based approach is used to help with determining a starting dose. What can be also helpful is the use of the animal model, provided that it is as similar to humans as possible, infected with the same pathogen naturally, and have similar symptoms of the disease. This is a very long and exhaustive process, including clinical and non-clinical considerations. Beyond the starting dose, there is also a need to establish whether a possible vaccine would have a durable effect or only a short-term effect (seasonal vaccine for instance) requiring repeating dosing (booster). Depending on that, a few doses and schedules may be tested in Phase I/II of clinical development.

Beyond the complexity, what is reassuring is that a vaccine is usually considered to be a very safe product. The adverse events reported in clinical trials are usually mild and transient. That said, there have been rare occasions of severe side effects and even occurrences of death. Examples are:

  • In 1955 there was a Cutter incident with a polio outbreak when insufficiently inactivated batches of polio vaccine caused an outbreak of polio due to the presence of wild-type poliovirus strains. 40,000 children developed mild polio, 200 were permanently paralyzed and 10 died.
  • In 1967, in 4 clinical studies investigating the respiratory syncytial virus (RSV) vaccine, infants and toddlers immunized with a formalin-inactivated vaccine experienced an enhanced form of RSV disease characterized by high fever, bronchopneumonia, and wheezing after getting infected by wild-type RSV virus later. Hospitalizations were frequent, and two immunized toddlers died. In this case, instead of protecting the children, the vaccine was the cause of then unknown VAERD (vaccine-associated enhanced respiratory disease). This was only occurring in children who were immunized before contracting wild-type virus (seronegative). Generally, humans get infected by RSV until the age of two. To date, this presents a problem in the development of a vaccine for seronegative children, who are usually the most vulnerable population that suffers from RSV infections.
  • Recently, since the COVID-19 pandemic started in March 2020 and several vaccines against SARS-CoV-2 developed, there was much media coverage about vaccines’ side effects. Although quite rare, there have been reports of serious and severe vaccine adverse events, even deaths. These, although infrequent, are being researched and scientists are investigating the possible mechanisms of action to understand how to make vaccines even safer.

The natural disease can in many cases cause much more discomfort, long-term symptoms, and even death. That is, of course, relevant when looking at the vaccine risk/benefit profile. In addition to investigating the risk/benefit on an individual level, given that vaccines often prevent communicable diseases, herd immunity is also a relevant factor, i.e., whether a certain level of vaccination in a population provides protection overall (you may have heard in the news that “we need to achieve a certain percentage of herd immunity” for protection). Hence, it is important to understand that the benefit of the large population may be more relevant than rare risks on an individual level when looking at the outcomes and the risk/benefit profile.

Outcomes/endpoints of the vaccine clinical studies

The side effects of vaccines can be collected and monitored either in a clinical trial setting or in a real-life setting after the vaccine obtained licensure and can be used in a given market. An adverse event is any undesirable experience associated with the use of a medical product in a person. 

In the clinical setting, after vaccination, usually, the following adverse events are collected from participants:

  • Solicited adverse events (AEs) or reactogenicity – a collection of the prespecified adverse events obtained after each vaccination for a short amount of time, as most of them are expected to be transient – usually in a form of daily questions to check occurrence or absence of:
    1. Local solicited AEs: pain/tenderness of the location where the vaccine is administered; redness/erythema; swelling
    2. Systemic solicited AEs: headache, myalgia, arthralgia, gastrointestinal issues/diarrhea/nausea, fever, fatigue/tiredness

For example, a participant can be asked daily to report the occurrence of headache and pain at the administration site in their vaccination diary for 10 days after vaccination.

  • Unsolicited AEs – any non-serious adverse event to be reported in the specified time, for example, back pain starting at 15 days post-vaccination.
  • Serious AEs (SAEs) – any untoward medical occurrence – serious AE resulting in:
    • Death,
    • Is life-threatening,
    • Emergency visit or hospitalization excluding elective procedures,
    • Persistent or significant disability/incapacity,
    • Congenital anomaly/birth defect,
    • Requires intervention to prevent permanent impairment or damage.

They are usually collected throughout the entire study.

Often, medically-attended AEs (MAAEs) are also collected as well as potential immune-mediated diseases (pIMDs). Each AE can be attributed to a grading of severity, usually based on FDA Toxicity Grading Scale for Healthy Adult and Adolescent Volunteers Enrolled in Preventive Vaccine Clinical Trials. Mild AEs that do not influence everyday activities belong to grade 1, those which partially prevent everyday activities are grade 2 and those which significantly impair everyday life belong to grade 3. Moreover, for each AE, the investigator and sponsor can try to determine if this event is likely to be related to the vaccine or not. For example, someone who had a car accident that resulted in a foot fracture 3 days after vaccination will have this reported as an AE. Now, the foot being fractured is clearly not causally associated with the vaccination, but the car accident may have been caused by a person feeling nauseous or ill as a vaccine side-effect. Also, note that laboratory parameters pre- and post-vaccination can be monitored for any worsening or change in cell counts (platelets, white blood cells, etc.).

Apart from side effects, immunogenicity is usually investigated based on blood samples: humoral immunity (neutralizing antibodies, B-memory cells) and cellular immunity (T-cells). This is to investigate if a vaccine induces an immune response, possibly indicating that there may be a certain level of protection against the disease. The pre-and post-vaccination levels are investigated and based on change from baseline, the next steps are determined.

The safety, reactogenicity, and immunogenicity, as well as dose and schedule determination based on clinical trial results, are usually evaluated in Phase I/II. Phase III generally continues the investigation of the safety profile given that a large number of people are being exposed to the vaccine, but it also looks at the efficacy, and the power of the vaccine to protect against diseases. Usually, this is looking at how many people experience a disease after vaccination in groups that received a vaccine vs. the group that receives a placebo. Other Phase III studies can look at the non-inferiority of a vaccine being co-administered with another vaccine vs. separate administration, there may be vaccine production lots comparisons or end-of-shelf-life studies and, expansions to more special populations: pregnant women, children, or immunocompromised individuals.

All these represent objectives and endpoints and based on them = the success of a clinical trial, program, and vaccine is determined. In the end, this is how the benefit/risk of a given vaccine is observed, and based on that outcome, the vaccine may or may not be authorized for use in the market.

Vaccine platforms

When it comes to platforms that today’s vaccines are based on, they differ based on disease, the desired immunological effect, and the practicality of development. These are the following:

  • Inactivated vaccines

When a pathogen is inactivated or killed in a laboratory with heat, radiation, or chemicals and used in a vaccine, we are talking about inactivated vaccines. Examples are polio and flu vaccines. They are shown to work well in humans and can be produced on a reasonable scale. However, since the pathogen has to be grown in the lab safely and then killed/inactivated, this can take a long amount of time. Remember for example, that the flu virus is grown in eggs, hence the egg protein can be residual in such a vaccine. Often, these vaccines do not offer long-term protection, so booster shots are needed.

  • Live-attenuated vaccines

When a pathogen is weakened, but not killed completely, we are referring to live-attenuated vaccines. This is a reasonably similar technology to inactivated vaccines. The best example is the MMR(V) vaccines – measles, mumps, and rubella (and varicella). Since it contains weakened, but still living virus particles, it may not be appropriate for use in people with a weakened immune system. They often provide long-lasting immunity.

  • Messenger RNA (mRNA) vaccines

mRNA vaccines have been researched for a very long time and only recently have seen the light of day. The benefit of the vaccine is that it is not carrying a living organism, but a genetic material – instruction to create proteins antigens against which the immune system will start building protection. Their manufacturing time is very short and uncomplicated, as it is based on a known genetic sequence. The only example at the time being is the vaccine against COVID-19.

  • Subunit, recombinant, polysaccharide, and conjugate vaccines

These types of vaccines contain a component of a pathogen, for example, a protein, sugar, or larger parts of a virus/bacterium. They can be safely used on everyone, including immunocompromised, but they may not offer long-lasting protection. Examples are pneumococcal vaccines, vaccines against human papillomavirus (HPV), etc.

  • Toxoid vaccines

Toxoid vaccines are those based on toxins that the pathogen produces and that cause disease. The immune response is then activated based on the presence of the toxin, not the pathogen itself. A booster vaccination is needed for protection. An example is diphtheria/tetanus vaccine.

  • Viral vector vaccines

This type of vaccine contains a different virus as a vessel to deliver a component of the pathogen causing the disease to the host and therefore, induces an immune response against that component. The vessel virus (called a vector) is safe and does not cause any disease itself. Its mission is to present the component of another pathogen to the host so that the body can protect against that virus/bacterium. The ebola vaccine is one example.

As mentioned above, vaccines can be administered in various ways, mostly by injection in either fatty tissue (subcutaneous) or muscle (intramuscular). Some existing vaccines are intranasal (nasal spray flu vaccine) and oral (oral drops rotavirus vaccine).

COVID-19 vaccine development

Until recently, the public has not been directly exposed to the preclinical and clinical development of drugs and vaccines. This completely changed in 2020. In December 2019, a new virus was identified in Wuhan, China, and since then it has spread worldwide. On March 11, 2020, the pandemic was declared. As of April 10, 2022, the pandemic had caused more than 498 million cases and 6.17 million deaths, making it one of the deadliest in history.

Immediately upon the pandemic being declared, several companies started working on the possible treatments and prevention strategies. While it may seem that the development of such medicinal products, including vaccines, was extremely short, compared to the standard development, the truth is that this was a global effort on many levels. To be that fast, the use/testing of old and new technologies, new unprecedented collaborations, political and economic willingness, and regulatory approval focus were required. When it comes to preclinical and clinical research, the mission was to do things in parallel as much as possible, while not compromising quality and safety.

Normally, to develop a new vaccine, approximately a decade is needed, although more recently, irrespective of COVID-19, these timelines have been reduced. Even so, the delivery time of some COVID-19 vaccines was extreme and it took less than 12 months to have the product ready. Not surprisingly, many wonder how that was possible and whether any shortcuts were taken.

The first answer lies in the nature of the pandemic itself. The last notable pandemic was the 1918-1920 Spanish flu, which infected half a billion people around the world, killing 20 to 100 million. At that time, the technology, funding, and resources, including the scientific acumen, were not on the same level as today. Today, the combination of science and technology, communication and collaboration, luck, and willingness made it possible to develop these vaccines. The technologies used, including mRNA, have been researched for decades, despite a concrete product based on such technologies missing. When it comes to clinical development, there was no compromise on safety and quality, but some phases and parts were done in parallel to save time. Luckily, the research yielded positive results, and the regulators committed to reviewing the results in an unprecedentedly short time. One must understand that for standard development, all these steps take time, sometimes even years. This is not to say other diseases are less relevant or that there it was easier for COVID-19 to get approvals. The main difference is that the global threat was present and without the willingness and dedication of stakeholders involved, we would still not have any vaccines. What helped as well is that there was a keen interest of the public and the recruitment in clinical trials was very fast. In addition to that, since the virus was spreading fast, it was relatively easy and quick to establish vaccine efficacy for tested vaccines.

The key components of fast vaccine development during the COVID-19 pandemic were:

  1. Manufacturing at risk
  2. Streamlined regulatory approval
  3. Prioritization
  4. Global efforts
  5. Funding

Types of COVID-19 vaccines

At the moment, in different geographies, different vaccines may be administered, depending on regulatory approvals obtained. In the US, 3 are fully approved or have emergency use authorization (EUA) status: Comirnaty/BNT162b2 (manufacturer BioNTech/Pfizer), Spikevax/mRNA-1273 (manufacturer Moderna) and Janssen COVID-19/Ad26.COV2.S (manufacturer Janssen pharmaceutical company of Johnson & Johnson) vaccines. In Europe, in addition to those three, Nuvaxovid/Covovax/NVX-CoV2373 (manufacturer Novavax) and Vaxzevira/Covishield/AZD1222 (manufacturer Oxford/AstraZeneca) are approved for use. Elsewhere, Sputnik V/Gam-Covid-Vac (manufacturer Gamaleya), Convidecia/Ad5-CoV (manufacturer CanSino Bio), BBIBP-CorV (manufacturer Sinopharm), CoronaVac (manufacturer SinoVac) BBV152/Covaxin (manufacturer Bharat Biotech) may be used.

The details of the 5 most used vaccines in the US and EU can be seen below (the colors correspond to the technology used).

Figure 2 Comparison of leading COVID-19 vaccines (the efficacy varies due to varying circumstances, time period of studies being performed, and circulating virus variants)

So, where does this leave us? The COVID-19 vaccines did not fully stop the pandemic, but they helped us manage it and slow down the spread, together with social distancing and the use of masks. The main goals of vaccination, together with other measures, were to prevent the disease from spreading and to lower the incidence of severe disease symptoms and hospitalization. During this pandemic, science showed that it can deal with the challenge.

Despite that, there are other factors coming into play that may determine the success of future medicines and vaccines. The whole COVID-19 vaccine development process was visible to the public and media. Since the development of medicinal products is a very complex process, with mistakes and constant updates, for the general audience it may seem messy and not actually scientific, as they would normally see only the end result.

Most scientists are actually happy that transparency and visibility are becoming more relevant and that the general public is getting involved. That being said, further education on the process is needed, to minimize the unnecessary scrutiny. While challenges, questions, and public interest is completely justified, there needs to be a balance between reasonable and unreasonable criticism. And yes, there is a lot we still do not know, but that is fine. We all need to work together to ensure the best and most needed products are coming to the market. And we all need to ensure that people will understand their development and want to use them.

The future of vaccine development is bright, yes, but it does not only depend on scientific achievements and technology. Dialogue, acceptance, and understanding are also needed to bridge the existing gaps in scientific knowledge and process transparency when it comes to the general audience. In the end, despite all efforts in achieving lean and fast development, we can be only as successful as the general public “allows” it.

“Alone we can do so little; together we can do so much.”

Helen Keller


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