Antibodies and vaccination

An antibody (immunoglobulin) is a Y-shaped quaternary protein secreted by plasma cells. The structure is exquisitely matched to its function — binding one specific antigen and recruiting other components of the immune system.

Four polypeptide chains. Each antibody consists of two heavy chains (longer, ~450 amino acids) and two light chains (shorter, ~220 amino acids), held together by disulfide bonds between cysteine residues. The four chains together form the characteristic Y-shape.

Variable region (V region). At the tip of each of the two arms of the Y, the amino acid sequence differs between different antibody molecules. The variable regions of one heavy + one light chain together form an antigen-binding site (paratope) that is precisely complementary in shape and chemistry to a specific antigen (the epitope). Each antibody therefore has two identical antigen-binding sites — so a single antibody can bind two antigens.

Constant region (C region). The rest of the molecule (the lower arms and the stem) has a constant amino acid sequence for all antibodies of a given class (IgG, IgM, IgA, etc.). The constant region:

• Determines the antibody class (IgG, IgM, IgA, IgD, IgE — differ in heavy-chain constant regions).
• Is recognised by phagocyte Fc receptors during opsonisation.
• Activates complement proteins to lyse bacteria.
• Allows antibodies to cross the placenta (IgG) or be secreted into mucus (IgA).

Hinge region. Between the two arms and the stem is a flexible hinge region that allows the two binding sites to point in slightly different directions. This flexibility lets one antibody bind two pathogens at different distances apart — essential for agglutination.

Five antibody classes (you do not need all in detail for 9700, but should know IgG and IgM):

• IgG — most abundant in blood; crosses placenta giving newborns passive immunity from mother.
• IgM — first antibody made in primary response; a pentamer (5 Y-shapes joined) so very efficient at agglutination.
• IgA — secreted into mucus, saliva, breast milk.
• IgE — bound to mast cells; mediates allergic reactions.
• IgD — on naive B-cell surfaces; function less well understood.

Antibodies do not directly kill bacteria — they mark, block or clump pathogens, and recruit other parts of the immune system to do the killing. The five main mechanisms:

1. Agglutination (clumping). Each antibody has two binding sites, so one antibody can bind antigens on two separate pathogens at once. Multiple antibodies bind multiple pathogens, forming clumps. Clumped pathogens:

• Are physically too large to enter host cells.
• Are easily engulfed by phagocytes (one engulfment now removes many pathogens).
• Are immobilised if they were swimming free.

2. Neutralisation (blocking). Antibodies bind to the part of the pathogen (or its toxin) that would attach to host cells, blocking the interaction. Examples:

• Antibodies to influenza haemagglutinin block the virus from binding to respiratory epithelial cells.
• Antibodies to cholera toxin prevent the toxin from entering epithelial cells, so no diarrhoea.
• Antibodies to tetanus toxin (tetanus antitoxin) prevent the toxin from binding to neurones.

3. Opsonisation (marking for phagocytosis). Antibodies coat the pathogen surface. Phagocyte Fc receptors recognise the antibody constant region, so antibody-coated pathogens are engulfed much more efficiently than naked ones. 'Opson' = 'preparing for swallowing'.

4. Complement activation. Antibody-coated bacteria activate the complement cascade in plasma. The cascade ends with a membrane attack complex (MAC) that punches pores in the bacterial cell-surface membrane. Water enters the bacterium by osmosis, the cell bursts (osmotic lysis), and the bacterium dies. Complement components also serve as opsonins and as chemoattractants for phagocytes.

5. Antibody-dependent cell-mediated cytotoxicity (ADCC). Antibody-coated cells (parasites, virus-infected cells, cancer cells) are recognised by natural killer (NK) cells via Fc receptors. NK cells release perforin and granzymes that induce apoptosis in the target. ADCC is the main way the immune system handles large parasites that cannot be phagocytosed.

6. Immobilisation. Antibodies bound to bacterial flagella prevent the bacterium from swimming, slowing its spread.

Monoclonal antibodies are a population of identical antibodies, all secreted by a single clone of B cells, all specific for one antigen / one epitope. (A normal immune response produces polyclonal antibodies — a mixture from many different B-cell clones recognising different epitopes on the same antigen.)

Production — the hybridoma technique (Köhler & Milstein, 1975 — Nobel Prize 1984):

1. Inject mouse with antigen. A laboratory mouse is injected with the target antigen. Over weeks, it mounts a normal immune response — B cells proliferate, including some that produce the desired antibody.
2. Extract B cells from spleen. Spleen B cells are isolated. Each B cell makes one specific antibody, but B cells cannot be cultured for long outside the body — they would die in days.
3. Fuse with myeloma cells. B cells are fused with myeloma cells (cancerous B-line cells that divide indefinitely) using polyethylene glycol or electrofusion. The fused cell is called a hybridoma.
4. Select hybridomas. A selective medium (HAT medium) kills unfused myeloma cells, leaving only hybridomas. Hybridomas are screened to find single clones producing the desired antibody.
5. Culture and harvest. The chosen hybridoma is cultured at scale (in flasks or bioreactors). Antibody is harvested from the culture medium.
6. Humanisation. For clinical use, mouse antibodies are usually 'humanised' — mouse constant regions are replaced with human ones to reduce immune rejection (the suffix '-omab' = mouse, '-ximab' = chimeric, '-zumab' = humanised, '-umab' = fully human).

Uses of monoclonal antibodies:

Diagnosis.

• Pregnancy tests — monoclonal antibodies against hCG (human chorionic gonadotrophin, secreted by the placenta). Two antibodies in the test strip — a mobile dye-labelled antibody and a fixed capture antibody — sandwich hCG and produce a coloured line.
• Cancer markers — antibodies to PSA (prostate cancer), CA-125 (ovarian cancer), CEA (colon cancer) detect these proteins in blood.
• ELISA tests for HIV antibodies (and many other infections).
• Blood typing.

Drug delivery (targeted therapy). An antibody specific for a tumour-cell antigen is conjugated to a cytotoxic drug. The antibody finds the tumour cells; the drug kills them while sparing healthy tissue. Examples:

• Trastuzumab (Herceptin) — targets the HER2 receptor on some breast cancers. Used both alone and conjugated to chemotherapy (T-DM1).
• Rituximab — targets CD20 on B-cell lymphomas, marking them for destruction by complement and ADCC.
• Antibody-drug conjugates (e.g. trastuzumab emtansine, brentuximab vedotin) deliver chemotherapy directly to tumour cells.

Immunotherapy. Monoclonal antibodies that block tumour 'immune-checkpoint' receptors (e.g. pembrolizumab targeting PD-1) release the immune system to attack cancers.

Treatment of other diseases.

• Anti-TNF antibodies (infliximab, adalimumab) — treat rheumatoid arthritis and Crohn's disease.
• Bevacizumab — blocks VEGF, slowing tumour blood vessel growth.
• Monoclonal antibodies to SARS-CoV-2 spike protein — used as treatment in COVID-19 (e.g. sotrovimab).

Vaccination introduces antigens from a pathogen into the body in a form that does not cause disease, triggering a primary immune response and producing memory cells. On later real exposure, memory cells mount a rapid, large secondary response that clears the pathogen before symptoms develop.

Types of vaccine:

1. Live attenuated — a weakened (live but non-virulent) form of the pathogen. Replicates briefly in the host, giving strong, long-lasting immunity often from a single dose. Examples: MMR (measles, mumps, rubella); oral polio vaccine; BCG (TB); yellow fever. Drawbacks: cannot be given to immunocompromised people; small risk of reversion to virulence.
2. Killed (inactivated) — the pathogen is killed (heat, chemicals) so it cannot replicate but its antigens remain. Examples: some flu vaccines, hepatitis A, typhoid (injectable). Often needs multiple doses + boosters; safer but generally less potent than live attenuated.
3. Subunit / recombinant — uses only fragments of the pathogen (purified antigens). Examples: HPV vaccine (uses virus-like particles of capsid protein); hepatitis B vaccine (uses surface antigen produced in yeast). Safe and well-defined; often requires adjuvants and boosters.
4. Toxoid — uses an inactivated toxin rather than the whole pathogen. The body produces antitoxin antibodies. Examples: tetanus, diphtheria.
5. mRNA vaccines — newest type, contain synthetic mRNA encoding a pathogen antigen (e.g. SARS-CoV-2 spike protein). The mRNA is taken up by host cells, translated to produce the antigen, which triggers an immune response. Examples: Pfizer-BioNTech and Moderna COVID-19 vaccines. mRNA itself does not enter the nucleus or alter DNA; it is rapidly degraded after translation.
6. Viral vector vaccines — use a harmless virus (e.g. adenovirus) engineered to carry a gene for a pathogen antigen. Examples: Oxford/AstraZeneca COVID-19 vaccine; Ebola vaccines.

Why vaccines work — the primary response.

When the vaccine antigen is administered, the immune system recognises it as non-self. Rare B and T lymphocytes whose receptors are complementary to the antigen undergo clonal selection and clonal expansion. Some daughter cells become plasma cells (producing modest antibody levels), but crucially others become memory B cells and memory T cells that persist for years.

Because the antigen is non-disease-causing, the person does not become ill (though mild side-effects such as fever or local swelling reflect normal immune activation).

Real exposure later. When the real pathogen is encountered, memory cells respond rapidly. Clonal expansion is much faster, antibody concentration rises within days to a high peak, and the pathogen is eliminated before symptoms — the person is immune.

Boosters repeat the antigen at intervals to maintain memory-cell numbers, particularly for vaccines whose immunity wanes (e.g. tetanus every 10 years).

Immunity can be classified along two axes — active vs passive and natural vs artificial:

	Natural	Artificial
Active	Infection by the pathogen → own antibodies + memory cells	Vaccination → own antibodies + memory cells
Passive	Mother → baby (antibodies via placenta IgG + breast milk IgA)	Injection of antibodies (antitoxin, monoclonal therapies)

Active immunity means the body makes its own antibodies and memory cells. It is slow to develop (primary response, 5-10 days) but long-lasting (years to decades) because memory cells persist.

Passive immunity means ready-made antibodies are received from another source. Protection is immediate but short-lived (weeks to months) because no memory cells are formed and the antibodies eventually break down. Examples:

• Natural passive: IgG antibodies cross the placenta giving the newborn protection for the first few months; IgA in breast milk gives gut protection.
• Artificial passive: injection of antibodies as treatment — tetanus antitoxin given to someone with a contaminated wound; anti-venoms; monoclonal antibodies for COVID-19; rabies post-exposure prophylaxis.

Why vaccination is active. Even though the antigen is delivered artificially, the body still makes its own response — so vaccination is artificial active immunity.

Herd immunity (population immunity) is the indirect protection of unvaccinated / susceptible individuals that occurs when a high enough proportion of the population is immune (by vaccination or prior infection) to a contagious pathogen. With most potential hosts immune, the pathogen cannot find enough susceptible new hosts to spread, so transmission chains break.

The proportion of the population that must be immune depends on how contagious the pathogen is, characterised by the basic reproduction number $R_0$ — the average number of new infections caused by one infectious person in a fully susceptible population. The herd immunity threshold is approximately $1 - 1/R_0$.

Disease	$R_0$	Herd immunity threshold
Measles	12-18	~95%
Pertussis	12-17	~94%
Smallpox	5-7	~80%
Polio	5-7	~80%
COVID-19 (original)	~3	~67%
COVID-19 (Omicron)	~8-12	~88-92%

Herd immunity is essential because:

• It protects vulnerable individuals who cannot be vaccinated — newborns, the immunocompromised, those with severe allergies to a vaccine component.
• It is the route to eradication: smallpox was eradicated globally (1980) by sustained vaccination achieving herd immunity in every region.
• It reduces hospital admissions, deaths and the chance of new resistant strains arising.

When herd immunity fails. If vaccination coverage falls below the threshold, the disease returns. Examples:

• Measles outbreaks in Europe and the USA from 2015 onwards, driven by falling MMR coverage linked to anti-vaccination misinformation (largely from a now-discredited 1998 paper).
• Polio outbreaks in countries where conflict has disrupted vaccination (Pakistan, Afghanistan).

Vaccination programmes — success and challenges.

Successes:

• Smallpox — eradicated by WHO in 1980. Key factors: antigenic stability, no animal reservoir, effective vaccine, sustained global commitment.
• Polio — global eradication initiative since 1988 has reduced cases by >99%. Endemic only in Afghanistan and Pakistan as of 2024.
• Measles, mumps, rubella, Hib, pneumococcal, rotavirus — childhood vaccinations have dramatically reduced disease and deaths globally.

Challenges:

• Antigenic variation. Pathogens like influenza undergo antigenic drift (point mutations) and antigenic shift (reassortment) — flu vaccine must be reformulated annually. HIV mutates so rapidly that no effective vaccine exists.
• Cold chain. Many vaccines require refrigeration; remote regions struggle to maintain the cold chain.
• Vaccine hesitancy and misinformation — listed by WHO as one of the top ten threats to global health.
• Cost and infrastructure in low-income countries.
• Animal reservoirs make eradication difficult (e.g. influenza in birds and pigs; M. bovis in cattle).