How does the immune system work?

Your immune system is not one organ. It is an army of cells and a network of places where they are made, trained and gather. We are facing the person, so their right side is on your left.

Every immune cell is born in the red bone marrow, inside the hip bones, breastbone and spine. The marrow makes about 100 billion white cells a day (see SkeletonClear for bones). Some of them, the T cells, travel to the thymus, a small organ behind your breastbone, to be trained. It is biggest around puberty and then slowly shrinks.

Threading through the whole body is a second set of pipes beside the blood vessels: the lymphatic system. Thin lymph vessels collect clear fluid, called lymph, that leaks out of the blood. On its way back, lymph passes through about 600 lymph nodes, bean-shaped filters packed in your neck, armpits, belly and groin. Two ducts pour it back into big veins near your neck (see CirculationClear).

Guard posts sit where germs get in. The tonsils and adenoid watch your mouth and nose. Peyer's patches watch your gut, where trillions of friendly microbes live (see DigestionClear). The spleen, under your left ribs, filters the blood itself.

Most germs never get inside you, because your body is wrapped in walls. Skin is a tough top layer of dead cells, slightly acidic and salty (see SkinClear). Your airways are lined with sticky mucus, and tiny hairs called cilia beat 10–15 times a second to sweep it up to your throat, where you swallow it: the mucus escalator (see RespirationClear). Swallowed germs meet stomach acid strong enough to kill most of them (see DigestionClear). Tears and saliva carry germ-dissolving enzymes too.

When a wall is broken, say by a splinter, the innate immune system answers within minutes. It doesn't need to know which germ it is. Damaged cells and guard cells called macrophages release alarm chemicals. Nearby blood vessels widen and leak: the spot turns red, warm and swollen, and it hurts. That is inflammation, and it is a good sign.

The leaky vessels let neutrophils, the most common white cells, squeeze out of the blood and crawl towards the bacteria. They swallow them whole and digest them inside: phagocytosis, "cell eating". Dead neutrophils and bacteria make pus. If germs get into the blood, the brain can raise your thermostat: a fever helps immune cells work and slows some germs down.

The first responders fight any germ the same way. The adaptive immune system is slower, but it learns the exact shape of this germ, and it remembers. Its soldiers are two kinds of lymphocytes: T cells and B cells. They meet the enemy in your lymph nodes.

1. Catch. A dendritic cell, a scout with long arms, grabs a virus, chops it up and carries the pieces to the nearest lymph node. A piece of a germ that the immune system can recognise is called an antigen.

2. Show. The dendritic cell holds up the antigen for helper T cells to check. You have millions of different T and B cells, each with a receptor of one shape. The one whose receptor fits is switched on and sends out chemical orders.

3. Antibodies. The helper T cell wakes the one B cell whose receptor fits the antigen, like a key in a lock. It multiplies into thousands of plasma cells, each pouring out about 2,000 antibodies a second. An antibody is a tiny Y: its two tips grab the germ, which blocks it and marks it for eater cells.

4. Kill. Viruses hide inside your own cells. Killer T cells spot infected cells by the virus pieces on their surface and make them self-destruct, virus and all.

All this takes about a week the first time, which is why you feel ill for days. The second time, memory makes it far faster.

After a fight, most B and T cells die off, but some stay on as memory cells, sometimes for your whole life. If the same germ comes back, they recognise it at once. Antibodies climb within a day or two, to levels 10 to 100 times higher than the first time, and the germ is usually beaten before you even feel ill. That is immunity.

Catching a disease to get immunity is risky: measles, polio or diphtheria can disable or kill. A vaccine teaches the same lesson safely. It shows your immune system a harmless version of the germ: a killed germ (India's Covaxin), a weakened one (oral polio drops), one piece of it (hepatitis B), or a recipe for one piece (mRNA vaccines). Your body makes memory cells, and at most you get a sore arm for a day.

Vaccines also protect people who can't be vaccinated, like newborns or people on cancer treatment. If enough people are immune, a germ can't find enough new people to spread to, and outbreaks fizzle out: herd immunity. How many is "enough" depends on how contagious the germ is. Its R0 is how many people one case infects when no one is immune; the share needed is 1 − 1/R0. For measles, one of the most contagious diseases, that is about 92–95%.

India's Universal Immunisation Programme, started in 1985, gives free vaccines against 12 diseases to about 2.7 crore babies every year. Pulse Polio drives reached every child, the last case of wild polio in India was in January 2011, and India was certified polio-free in 2014.

Your blood doesn't stay perfectly inside its pipes. In each tiny capillary, blood pressure pushes some watery fluid out through the thin wall into the spaces between your cells: tissue fluid. It brings them food and oxygen. At the far end of the capillary, where the pressure is lower, proteins in the blood pull most of it back in (see CirculationClear).

But not all of it. What is left, about 2–4 litres a day, would pile up and make you puffy. Instead it seeps into lymph capillaries, dead-end tubes whose wall cells overlap like flaps: fluid can get in but not out. Now it is called lymph.

Lymph has no heart to pump it. It is squeezed along by the muscles around the vessels, and valves stop it flowing backwards, so walking and moving speed it up many times. On its way, lymph must pass through lymph nodes. Inside, macrophages eat germs and dead cells, and B and T cells check everything for enemies. Filtered lymph flows on into the thoracic duct and back into a vein near your neck. In the gut, lymph vessels also carry away fats from your food (see DigestionClear).

When germs arrive at a node, its lymphocytes multiply to fight them and the node swells. That is why the "glands" in your neck feel sore and lumpy when you have a sore throat. They usually go down within about two weeks. If a lump stays longer, feels hard, or comes with fevers, night sweats or weight loss, see a doctor.

An immune system has to be strong against germs but gentle with everything else. This chapter explains common problems; it cannot tell you what is going on in your own body. For that, see a doctor.

An allergy is an overreaction to something harmless, like pollen, dust mites or peanuts. Special antibodies (IgE) sit on mast cells, which burst open with histamine: sneezing, itchy eyes, rashes or wheezing. A severe reaction, anaphylaxis, with trouble breathing or a swelling face, is an emergency: call 112 (or 108), and use an adrenaline pen if one was prescribed.

In autoimmune diseases the army attacks your own body. In type 1 diabetes it destroys the insulin-making cells of the pancreas (see PancreasClear); India has more children with it than any other country. In rheumatoid arthritis it attacks the joints.

HIV is a virus that infects the helper T cells, the army's commanders. Without treatment they slowly fall until ordinary germs become dangerous (AIDS). Daily medicines keep the virus down so people live long, healthy lives, and they are free at government ART centres in India. HIV does not spread by touching, hugging or sharing food.

Antibiotics kill bacteria but do nothing to viruses such as colds and flu. Using them when not needed helps resistant bacteria win. Take them only when a doctor prescribes them, exactly as told. And the simple things work: wash your hands with soap for 20 seconds, sleep well (teenagers need 8–10 hours), and keep your vaccines up to date.