Part 2
This next bit depends on whether one accepts the germ theory of disease, i.e., the theory that microorganisms may be the cause of some diseases.
If you don't believe THAT then again we have a major difficulty. Among many others, Anton van Leeuwenhoek(1670s), Ignaz Semmelweis(1840s), Louis Pasteur(1860s)[who worked with viruses but didn't realise what they were], Joseph Lister(1860s), Robert Koch(1870s) and Dmitri Iwanowski(1890s)[who discovered the first virus, tobacco mosaic virus] laid the foundations of what we know today about transmissible diseases.
Again, the evidence today for the germ theory of disease (as opposed to "spontaneous generation" or magic) is as strong today as the evidence for the evolution of species or the laws of thermodynamics or those governing turbulent flow.
There are millions of microorganisms in the world, only a small fraction of which parasitise humans and an even smaller number of which cause human disease. Nevertheless, when you get a boil with staphylococcus aureus, or septicaemia with streptococci, it'll make you very unhappy and maybe dead (lots of people died of blood poisoning from strep infections in the pre-antibiotic days).
But when Pasteur and others started writing about microbes as a cause for disease, many people were incredulous, "how could something so small cause disease?" and they were much mocked with songs about "Microbe, busy microbe!". Poor Semmelweiss was hounded to suicide, even though his introduction of handwashing between patients reduced the death rate among new mothers from 18.27 to 1.27%.
Robert Koch then formulated his postulates, which are four criteria designed to establish a causal relationship between a causative microbe and a disease.
1. The organism must be found in all animals suffering from the disease, but not in healthy animals.
2. The organism must be isolated from a diseased animal and grown in pure culture.
3. The cultured organism should cause disease when introduced into a healthy animal.
4. The organism must be reisolated from the experimentally infected animal.
Koch changed them somewhat later to account for new discoveries, but in all important aspects they still hold true today.
Viruses are a little different. Unlike bacteria, which possess all the machinery needed to reproduce themselves, viruses must "borrow" the host cells transcriptional machinery to reproduce themselves. You can't grow viruses in meat broth, viruses need living cells with intact machinery to reproduce. This makes it harder to culture them, but now almost all viruses can be grown in living culture.
Epidemiology studies how transmissible diseases spread from person to person. Sometimes they can be spread indirectly from person to person like droplet infection with a sneeze. Sometimes they need direct contact with infected material like smallpox (American Indians were once deliberately infected to get rid of them by giving them blankets that had been used by smallpox victims). Sometimes the infective agent has several hosts, like the plague bacillus (flea -> rat -> human) which makes it harder to see the chain.
In a larger sense, epidemiology studies how diseases ebb and flow through a population. Christopher Columbus' men brought back a virulent variant of the spirochaete from America in 1498 and it is possible to trace how travellers spread syphilis across Europe. Tracing the links in the infective chain lead to Typhoid Mary, the asymptomatic carrier of typhoid who infected 47 people during her career as a cook between 1900 and 1907.
In 1977, Grethe Rask, a Danish surgeon who worked in the Congo, went back to Denmark to die after months of illness. She had multiple bizarre infections and died of pneumonia from pneumocystis carinii, a common organism in guinea-pigs that almost never causes illness in people.
As 1981 wore on physicians in the Bay area of San Francisco were used to seeing sexually tranmitted infections - after all, this was the gay centre of America, and in the heady days of gay liberation there were some very promiscuous people around, with dozens of partners a week. But they were all curable, and after taking their pills, plunged back into the fray. But then, strange illnesses started to appear - florid candida, pneumocystis, cryptosporidiosis and more, all unknown in healthy people, and this horde of well-fed, golden, gym-addicted young men were supremely fit. These diseases were normally only ever seen in enfeebled patients who were immunosuppressed by anticancer drugs or for transplants. And they died horribly, eaten up by herpes, unable to eat from the candida that infested their mouths, their lungs strangling on pneumocystis.
Doctors talked about it uneasily, until the trickle of desperately ill men became a stream and the Centre for Disease Control in Atlanta became interested. Now there were cases reported from New York. At first it was thought to be the result of multiple ordinary infections, but that didn't seem to be true. Then it was though to be due to the lubricants used for anal intercourse, but that lucked out. Then the nitrite inhalers used as a recreational drug came under suspicion, but that led to a dead end. The one common factor seemed to be that all the victims were male and gay. And they'd often had sex with someone who'd had sex with another victim.
Finally, in horror, the physicians at CDC had to face the truth - some new transmissible agent was out there that nuked people's immune systems. And the really, really bad news was that it seemed to have a very long incubation time - people were infected and infectious long before they showed any signs of immune deficiency.
So the hunt for the causative agent was on. Bacteria were out, drugs were out, the environment was out, other infections were out, malnutrition was out, so it had to be a virus - but a new virus with very selective behaviour. Selective viruses weren't unknown of course, but this one was special, it targeted the immune system itself. But it was hard to get money for research - not easy to get anyone interested in giving money to look into some wierd faggot disease.
And now there were cases appearing in haemophiliacs, who'd received Factor VIII extracted from many pooled donors. And the gays were socially concious people, who gave blood willingly.
And every day there were more. Cases abroad from foreign gays who'd visited the States and had fun in the bathouses. The first cases in women surfaced. Blood and secretions. Junkies swapping needles. And then the first proven blood transfusion cases, blood given by people who later went down with immune deficiency.
And the band played on.
Eventually of course, after many struggles and false starts and allegations of cheating, the virus was found, by Bob Gallo in America and Luc Montaignier in Paris.
It fulfils Koch's postulates (as Koch himself later modied them) and there is no trace, no scintilla, no smidgen of doubt that once infected with this particular virus (whatever name you want to give it) that the victim's immune system will be gradually eroded over between 2 and 15 years until they develop the opportunistic infections characteristic of the Acquired Immunodeficiency Syndrome.