Limitations to their effectiveness, nevertheless, exist.^[35] Sometimes, protection fails for vaccine-related reasons such as failures in vaccine attenuation, vaccination regimens or administration.^[36]

Failure may also occur for host-related reasons if the host’s immune system does not respond adequately or at all. Host-related lack of response occurs in an estimated 2–10% of individuals, due to factors including genetics, immune status, age, health and nutritional status.^[36] One type of primary immunodeficiency disorder resulting in genetic failure is X-linked agammaglobulinemia, in which the absence of an enzyme essential for B cell development prevents the host’s immune system from generating antibodies to a pathogen.^[37][38]

Host–pathogen interactions and responses to infection are dynamic processes involving multiple pathways in the immune system.^[39][40] A host does not develop antibodies instantaneously: while the body’s innate immunity may be activated in as little as twelve hours, adaptive immunity can take 1–2 weeks to fully develop. During that time, the host can still become infected.^[41]

Once antibodies are produced, they may promote immunity in any of several ways, depending on the class of antibodies involved. Their success in clearing or inactivating a pathogen will depend on the amount of antibodies produced and on the extent to which those antibodies are effective at countering the strain of the pathogen involved, since different strains may be differently susceptible to a given immune reaction.^[40] In some cases vaccines may result in partial immune protection (in which immunity is less than 100% effective but still reduces risk of infection) or in temporary immune protection (in which immunity wanes over time) rather than full or permanent immunity. They can still raise the reinfection threshold for the population as a whole and make a substantial impact.^[42] They can also mitigate the severity of infection, resulting in a lower mortality rate, lower morbidity, faster recovery from illness, and a wide range of other effects.^[43][44]

Those who are older often display less of a response than those who are younger, a pattern known as Immunosenescence.^[45] Adjuvants commonly are used to boost immune response, particularly for older people whose immune response to a simple vaccine may have weakened.^[46]

The efficacy or performance of the vaccine is dependent on several factors:

• the disease itself (for some diseases vaccination performs better than for others)
• the strain of vaccine (some vaccines are specific to, or at least most effective against, particular strains of the disease)^[47]
• whether the vaccination schedule has been properly observed.
• idiosyncratic response to vaccination; some individuals are “non-responders” to certain vaccines, meaning that they do not generate antibodies even after being vaccinated correctly.
• assorted factors such as ethnicity, age, or genetic predisposition.

If a vaccinated individual does develop the disease vaccinated against (breakthrough infection), the disease is likely to be less severe and less transmissible than in unvaccinated cases.^[48][49]

Important considerations in an effective vaccination program:^[50]

1. careful modeling to anticipate the effect that an immunization campaign will have on the epidemiology of the disease in the medium to long term
2. ongoing surveillance for the relevant disease following introduction of a new vaccine
3. maintenance of high immunization rates, even when a disease has become rare

Some vaccines contain live, attenuated microorganisms. Many of these are active viruses that have been cultivated under conditions that disable their virulent properties, or that use closely related but less dangerous organisms to produce a broad immune response. Although most attenuated vaccines are viral, some are bacterial in nature. Examples include the viral diseases yellow fever, measles, mumps, and rubella, and the bacterial disease typhoid. The live Mycobacterium tuberculosis vaccine developed by Calmette and Guérin is not made of a contagious strain but contains a virulently modified strain called “BCG” used to elicit an immune response to the vaccine. The live attenuated vaccine containing strain Yersinia pestis EV is used for plague immunization. Attenuated vaccines have some advantages and disadvantages. Attenuated, or live, weakened, vaccines typically provoke more durable immunological responses. Attenuated vaccines also elicit a cellular and humoral response. However, they may not be safe for use in immunocompromised individuals, and on rare occasions mutate to a virulent form and cause disease.^[57]

Some vaccines contain microorganisms that have been killed or inactivated by physical or chemical means. Examples include IPV (polio vaccine), hepatitis A vaccine, rabies vaccine and most influenza vaccines.^[58][59]

Toxoid vaccines are made from inactivated toxic compounds that cause illness rather than the microorganism.^[59] Examples of toxoid-based vaccines include tetanus and diphtheria.^[59] Not all toxoids are for microorganisms; for example, Crotalus atrox toxoid is used to vaccinate dogs against rattlesnake bites.^[60]

Rather than introducing an inactivated or attenuated microorganism to an immune system (which would constitute a “whole-agent” vaccine), a subunit vaccine uses a fragment of it to create an immune response. One example is the subunit vaccine against hepatitis B, which is composed of only the surface proteins of the virus (previously extracted from the blood serum of chronically infected patients but now produced by recombination of the viral genes into yeast).^[61] Other examples include the Gardasil virus-like particle human papillomavirus (HPV) vaccine,^[62] the hemagglutinin and neuraminidase subunits of the influenza virus,^[59] and edible algae vaccines. A subunit vaccine is being used for plague immunization.^[63]

Certain bacteria have a polysaccharide outer coat that is poorly immunogenic. By linking these outer coats to proteins (e.g., toxins), the immune system can be led to recognize the polysaccharide as if it were a protein antigen. This approach is used in the Haemophilus influenzae type B vaccine.^[64]

Outer membrane vesicles (OMVs) are naturally immunogenic and can be manipulated to produce potent vaccines. The best known OMV vaccines are those developed for serotype B meningococcal disease.^[65][66]

Heterologous vaccines also known as “Jennerian vaccines”, are vaccines that are pathogens of other animals that either do not cause disease or cause mild disease in the organism being treated. The classic example is Jenner’s use of cowpox to protect against smallpox. A current example is the use of BCG vaccine made from Mycobacterium bovis to protect against tuberculosis.^[67]

Genetic vaccines are based on the principle of uptake of a nucleic acid into cells, whereupon a protein is produced according to the nucleic acid template. This protein is usually the immunodominant antigen of the pathogen or a surface protein that enables the formation of neutralizing antibodies. The subgroup of genetic vaccines encompass viral vector vaccines, RNA vaccines and DNA vaccines.^[65]

Many innovative vaccines are also in development and use.

• Dendritic cell vaccines combine dendritic cells with antigens to present the antigens to the body’s white blood cells, thus stimulating an immune reaction. These vaccines have shown some positive preliminary results for treating brain tumors^[76] and are also tested in melanoma.^[77]
• Recombinant vector – by combining the physiology of one microorganism and the DNA of another, immunity can be created against diseases that have complex infection processes. An example is the RVSV-ZEBOV vaccine licensed to Merck that is being used in 2018 to combat ebola in Congo.^[78]
• T-cell receptor peptide vaccines are under development for several diseases using models of Valley Fever, stomatitis, and atopic dermatitis. These peptides have been shown to modulate cytokine production and improve cell-mediated immunity.
• Targeting of identified bacterial proteins that are involved in complement inhibition would neutralize the key bacterial virulence mechanism.^[79]
• The use of plasmids has been validated in preclinical studies as a protective vaccine strategy for cancer and infectious diseases. However, in human studies, this approach has failed to provide clinically relevant benefit. The overall efficacy of plasmid DNA immunization depends on increasing the plasmid’s immunogenicity while also correcting for factors involved in the specific activation of immune effector cells.^[80]
• Bacterial vector – Similar in principle to viral vector vaccines, but using bacteria instead.^[65]
• Antigen-presenting cell^[65]
• Technologies which may allow rapid vaccine deployment in response to a novel pathogen include the use of virus-like particles^[81] or protein nanoparticles.^[82]
• Inverse vaccines are vaccines that train the immune system to not respond to certain substances.

While most vaccines are created using inactivated or attenuated compounds from microorganisms, synthetic vaccines are composed mainly or wholly of synthetic peptides, carbohydrates, or antigens.^{[citation needed]}

When two or more vaccines are mixed in the same formulation, the two vaccines can interfere. This most frequently occurs with live attenuated vaccines, where one of the vaccine components is more robust than the others and suppresses the growth and immune response to the other components.^[86]

This phenomenon was noted in the trivalent Sabin polio vaccine, where the relative amount of serotype 2 virus in the vaccine had to be reduced to stop it from interfering with the “take” of the serotype 1 and 3 viruses in the vaccine. To accomplish this, the doses of serotypes 1 and 3 were increased in the vaccine in the early 1960s.^[87] It was also noted in a 2001 study to be a problem with dengue vaccines, where the DEN-3 serotype was found to predominate and suppress the response to DEN-1, -2 and -4 serotypes.^[88]

Vaccines typically contain one or more adjuvants, used to boost the immune response. Tetanus toxoid, for instance, is usually adsorbed onto alum. This presents the antigen in such a way as to produce a greater action than the simple aqueous tetanus toxoid. People who have an adverse reaction to adsorbed tetanus toxoid may be given the simple vaccine when the time comes for a booster.^[89]

In the preparation for the 1990 Persian Gulf campaign, the whole cell pertussis vaccine was used as an adjuvant for anthrax vaccine. This produces a more rapid immune response than giving only the anthrax vaccine, which is of some benefit if exposure might be imminent.^[90]

Vaccines may also contain preservatives to prevent contamination with bacteria or fungi. Until recent years, the preservative thiomersal (a.k.a. Thimerosal in the US and Japan) was used in many vaccines that did not contain live viruses. As of 2005, the only childhood vaccine in the US that contained thiomersal in greater than trace amounts was the influenza vaccine,^[91] which is currently recommended only for children with certain risk factors.^[92] Single-dose influenza vaccines supplied in the UK do not list thiomersal in the ingredients. Preservatives may be used at various stages of the production of vaccines, and the most sophisticated methods of measurement might detect traces of them in the finished product, as they may in the environment and population as a whole.^[93]

Many vaccines need preservatives to prevent serious adverse effects such as Staphylococcus infection, which in one 1928 incident killed 12 of 21 children inoculated with a diphtheria vaccine that lacked a preservative.^[94] Several preservatives are available, including thiomersal, phenoxyethanol, and formaldehyde. Thiomersal is more effective against bacteria, has a better shelf-life, and improves vaccine stability, potency, and safety; however, in the US, the European Union, and a few other affluent countries, it is no longer used as a preservative in childhood vaccines, as a precautionary measure due to its mercury content.^[95] Although controversial claims have been made that thiomersal contributes to autism, no convincing scientific evidence supports these claims.^[96] Furthermore, a 10–11-year study of 657,461 children found that the MMR vaccine does not cause autism and actually reduced the risk of autism by seven percent.^[97][98]

Beside the active vaccine itself, the following excipients and residual manufacturing compounds are present or may be present in vaccine preparations:^[99]

• Aluminum salts or gels are added as adjuvants. Adjuvants are added to promote an earlier, more potent response, and more persistent immune response to the vaccine; they allow for a lower vaccine dosage.
• Antibiotics are added to some vaccines to prevent the growth of bacteria during production and storage of the vaccine.
• Egg protein is present in the influenza vaccine and yellow fever vaccine as they are prepared using chicken eggs. Other proteins may be present.
• Formaldehyde is used to inactivate bacterial products for toxoid vaccines. Formaldehyde is also used to inactivate unwanted viruses and kill bacteria that might contaminate the vaccine during production.
• Monosodium glutamate (MSG) and 2-phenoxyethanol are used as stabilizers in a few vaccines to help the vaccine remain unchanged when the vaccine is exposed to heat, light, acidity, or humidity.
• Thiomersal is a mercury-containing antimicrobial that is added to vials of vaccines that contain more than one dose to prevent contamination and growth of potentially harmful bacteria. Due to the controversy surrounding thiomersal, it has been removed from most vaccines except multi-use influenza, where it was reduced to levels so that a single dose contained less than a microgram of mercury, a level similar to eating ten grams of canned tuna.^[100]

Vaccines developed for multinational distribution via the United Nations Children’s Fund (UNICEF) require pre-qualification by the WHO to ensure international standards of quality, safety, immunogenicity, and efficacy for adoption by numerous countries.^[104]

The process requires manufacturing consistency at WHO-contracted laboratories following Good Manufacturing Practice (GMP).^[104] When UN agencies are involved in vaccine licensure, individual nations collaborate by 1) issuing marketing authorization and a national license for the vaccine, its manufacturers, and distribution partners; and 2) conducting postmarketing surveillance, including records for adverse events after the vaccination program. The WHO works with national agencies to monitor inspections of manufacturing facilities and distributors for compliance with GMP and regulatory oversight.^[104]

Some countries choose to buy vaccines licensed by reputable national organizations, such as EMA, FDA, or national agencies in other affluent countries, but such purchases typically are more expensive and may not have distribution resources suitable to local conditions in developing countries.^[104]

In the European Union (EU), vaccines for pandemic pathogens, such as seasonal influenza, are licensed EU-wide where all the member states comply (“centralized”), are licensed for only some member states (“decentralized”), or are licensed on an individual national level.^[106] Generally, all EU states follow regulatory guidance and clinical programs defined by the European Committee for Medicinal Products for Human Use (CHMP), a scientific panel of the European Medicines Agency (EMA) responsible for vaccine licensure.^[106] The CHMP is supported by several expert groups who assess and monitor the progress of a vaccine before and after licensure and distribution.^[106]

Under the FDA, the process of establishing evidence for vaccine clinical safety and efficacy is the same as for the approval process for prescription drugs.^[110] If successful through the stages of clinical development, the vaccine licensing process is followed by a Biologics License Application which must provide a scientific review team (from diverse disciplines, such as physicians, statisticians, microbiologists, chemists) and comprehensive documentation for the vaccine candidate having efficacy and safety throughout its development. Also during this stage, the proposed manufacturing facility is examined by expert reviewers for GMP compliance, and the label must have a compliant description to enable health care providers’ definition of vaccine-specific use, including its possible risks, to communicate and deliver the vaccine to the public.^[110] After licensure, monitoring of the vaccine and its production, including periodic inspections for GMP compliance, continue as long as the manufacturer retains its license, which may include additional submissions to the FDA of tests for potency, safety, and purity for each vaccine manufacturing step.^[110]

In India, the Drugs Controller General, the head of department of the Central Drugs Standard Control Organization, India’s national regulatory body for cosmetics, pharmaceuticals and medical devices, is responsible for the approval of licences for specified categories of drugs such as vaccines and other medicinal items, such as blood or blood products, IV fluids, and sera.^[111]

Until a vaccine is in use amongst the general population, all potential adverse events from the vaccine may not be known, requiring manufacturers to conduct Phase IV studies for postmarketing surveillance of the vaccine while it is used widely in the public.^[104][110] The WHO works with UN member states to implement post-licensing surveillance.^[104] The FDA relies on a Vaccine Adverse Event Reporting System to monitor safety concerns about a vaccine throughout its use in the American public.^[110]

According to the World Health Organization (WHO), the biggest barrier to vaccine production in less developed countries has not been patents, but the substantial financial, infrastructure, and workforce requirements needed for market entry. Vaccines are complex mixtures of biological compounds, and unlike the case for prescription drugs, there are no true generic vaccines. The vaccine produced by a new facility must undergo complete clinical testing for safety and efficacy by the manufacturer. For most vaccines, specific processes in technology are patented. These can be circumvented by alternative manufacturing methods, but this required R&D infrastructure and a suitably skilled workforce. In the case of a few relatively new vaccines, such as the human papillomavirus vaccine, the patents may impose an additional barrier.^[125]

When increased production of vaccines was urgently needed during the COVID-19 pandemic in 2021, the World Trade Organization and governments around the world evaluated whether to waive intellectual property rights and patents on COVID-19 vaccines, which would “eliminate all potential barriers to the timely access of affordable COVID-19 medical products, including vaccines and medicines, and scale up the manufacturing and supply of essential medical products”.^[126]

The companies with the highest market share in vaccine production are Merck, Sanofi, GlaxoSmithKline, Pfizer and Novartis, with 70% of vaccine sales concentrated in the EU or US as of 2013.^[136]: 42 Vaccine manufacturing plants require large capital investments ($50 million up to $300 million) and may take between 4 and 6 years to construct, with the full process of vaccine development taking between 10 and 15 years.^[136]: 43 Manufacturing in developing countries is playing an increasing role in supplying these countries, specifically with regards to older vaccines and in Brazil, India and China.^[136]: 47 The manufacturers in India are the most advanced in the developing world and include the Serum Institute of India, one of the largest producers of vaccines by number of doses and an innovator in processes, recently improving efficiency of producing the measles vaccine by 10 to 20-fold, due to switching to a MRC-5 cell culture instead of chicken eggs.^[136]: 48 China’s manufacturing capabilities are focused on supplying their own domestic need, with Sinopharm (CNPGC) alone providing over 85% of the doses for 14 different vaccines in China.^[136]: 48 Brazil is approaching the point of supplying its own domestic needs using technology transferred from the developed world.^[136]: 49

Notable developments in vaccine delivery technologies have included oral vaccines. Early attempts to apply oral vaccines showed varying degrees of promise, beginning early in the 20th century, at a time when the very possibility of an effective oral antibacterial vaccine was controversial.^[138] By the 1930s there was increasing interest in the prophylactic value of an oral typhoid fever vaccine for example.^[139]

An oral polio vaccine turned out to be effective when vaccinations were administered by volunteer staff without formal training; the results also demonstrated increased ease and efficiency of administering the vaccines. Effective oral vaccines have many advantages; for example, there is no risk of blood contamination. Vaccines intended for oral administration need not be liquid, and as solids, they commonly are more stable and less prone to damage or spoilage by freezing in transport and storage.^[140] Such stability reduces the need for a “cold chain“: the resources required to keep vaccines within a restricted temperature range from the manufacturing stage to the point of administration, which, in turn, may decrease costs of vaccines.

A microneedle approach, which is still in stages of development, uses “pointed projections fabricated into arrays that can create vaccine delivery pathways through the skin”.^[141]

An experimental needle-free^[142] vaccine delivery system is undergoing animal testing.^[143][144] A stamp-size patch similar to an adhesive bandage contains about 20,000 microscopic projections per square cm.^[145] This dermal administration potentially increases the effectiveness of vaccination, while requiring less vaccine than injection.^[146]

A common issue with animal vaccination is that it interferes with immunological tests as both infection and vaccination can result in antibodies against an antigen being made. To solve this issue, special marker vaccines are created using pathogen strains carrying at least one epitope less than the equivalent wild microorganism. An accompanying diagnostic test that detects the antibody against that epitope assists in identifying whether the animal has been vaccinated or not. They are also called “DIVA vaccines”.^[149]

The first marker vaccines and companion diagnostic tests were developed by J. T. van Oirschot and colleagues at the Central Veterinary Institute in Lelystad, The Netherlands.^[150][149] They found that some existing vaccines against pseudorabies (also termed Aujeszky’s disease) had deletions in their viral genome (among which was the gE gene). Monoclonal antibodies were produced against that deletion and selected to develop an ELISA that demonstrated antibodies against gE. In addition, novel genetically engineered gE-negative vaccines were constructed.^[151] Along the same lines, DIVA vaccines and companion diagnostic tests against bovine herpesvirus 1 infections have been developed.^[149][152]

The DIVA strategy has been applied in various countries to successfully eradicate pseudorabies virus from those countries. Swine populations were intensively vaccinated and monitored by the companion diagnostic test and, subsequently, the infected pigs were removed from the population. Bovine herpesvirus 1 DIVA vaccines are widely used in European BoHV-1 control and eradication programmes.^[153]

First generation vaccines are whole-organism vaccines – either live and weakened, or killed forms.^[168] Live, attenuated vaccines, such as smallpox and polio vaccines, are able to induce killer T-cell (T_C or CTL) responses, helper T-cell (T_H) responses and antibody immunity. However, attenuated forms of a pathogen can convert to a dangerous form and may cause disease in immunocompromised vaccine recipients (such as those with AIDS). While killed vaccines do not have this risk, they cannot generate specific killer T-cell responses and may not work at all for some diseases.^[168]

Second generation vaccines were developed to reduce the risks from live vaccines. These are subunit vaccines, consisting of specific protein antigens (such as tetanus or diphtheria toxoid) or recombinant protein components (such as the hepatitis B surface antigen). They can generate T_H and antibody responses, but not killer T cell responses.^[40]

RNA vaccines and DNA vaccines are examples of third generation vaccines.^{[168][169][170]} In 2016 a DNA vaccine for the Zika virus began testing at the National Institutes of Health. Separately, Inovio Pharmaceuticals and GeneOne Life Science began tests of a different DNA vaccine against Zika in Miami. Manufacturing the vaccines in volume was unsolved as of 2016.^[171] Clinical trials for DNA vaccines to prevent HIV are underway.^[172] mRNA vaccines such as BNT162b2 were developed in the year 2020 with the help of Operation Warp Speed and massively deployed to combat the COVID-19 pandemic. In 2021, Katalin Karikó and Drew Weissman received Columbia University’s Horwitz Prize for their pioneering research in mRNA vaccine technology.^[173]

The idea of vaccine production via transgenic plants was identified as early as 2003. Plants such as tobacco, potato, tomato, and banana can have genes inserted that cause them to produce vaccines usable for humans.^[178] In 2005, bananas were developed that produce a human vaccine against hepatitis B.^[179]