A new theory about how the Aids epidemic in Africa began points an accusing finger at the medical profession, says Margarette Driscoll

He arrived one evening at dusk in a village close to Lake Victoria. A funeral was in progress. "You could hear the singing and chanting rippling through the banana trees. Many people were visibly ill. They called it 'slim disease'. People would get terrible diarrhoea, become dehydrated and die."

Over the next few days and nights, the chanting of funeral after funeral continued. At Kasensero, a collection of iron and mud shacks on the shore of Lake Victoria, the situation was even worse. Ostensibly a fishing village, Kasensero was a thriving centre for smuggling and prostitution.

More than 100 of its 500 inhabitants were already dead. Hooper says he can still see in his mind's eye the gaunt faces pleading for help. "I had the sense that I was witnessing a major tragedy."

Hooper's instincts were right; some 16m Africans have since died of what we now know to be Aids and the United States has just granted Africa $250m (about £148m) to try to cope with the continuing crisis.

Millions of pounds have been poured into care and research into Aids, but for all the high-powered institutions and brilliant minds involved, we still do not know how the disease began. In the panic-stricken 1980s, as Aids became the "gay plague" in America and Britain, wild theories abounded. Some said Aids was manufactured by the CIA in a germ- warfare experiment that escaped from the laboratory. Others believed the virus had crashed to Earth on the tail of a comet.

In fact, the human immunodeficiency virus (HIV), which causes Aids, is the human version of the simian immunodeficiency virus (SIV), carried by certain types of chimpanzees, to whom it does no harm. The question is, how did it jump the species barrier?

The accepted version is that the virus transmitted itself naturally from primates to people; the so-called "cut hunter theory". This says that, over centuries, while hunting chimps for food, hunters would have been cut or injured and HIV could have been passed through blood-to- blood contact.

Many people might have been affected in this way but, the argument goes, African life expectancy was so short that people died from other causes before the dormant virus sprang to life. Then, in the 1960s and 1970s, increased life expectancy and western tourists - bringing a culture of casual sex with them - conspired to start the virus moving through the population.

In rural Africa, condoms were almost unknown. Rural health workers were unable to sterilise needles between blood tests or vaccinations. And so the contamination spread and continues to do so.

Hooper believed this theory too, until he began researching the history of Aids for a book he was planning in the early 1990s. After a decade of research, he has a much more controversial, not to say sinister, explanation. Hooper believes it likely that Aids is iatrogenic, or doctor-caused, and that it entered the population through trials of an experimental oral polio vaccine in Africa in the 1950s.

Hooper's theory has dropped like a bombshell on the scientific community. Some regard the very idea as outrageous. Dr John Moore, an eminent American immunologist, said Hooper's polio vaccine theory was "only believed by the lunatic fringe . . . sheer unadulterated nonsense". John Oxford, professor of virology at Bart's and the Royal London hospital, was equally scathing. "It's tosh," he said.

A two-day meeting of the Royal Society to discuss the origins of Aids, that was to have taken place last week, has had to be postponed until October, because of the outcry from some scientists at the prospect of the vaccine theory taking centre stage.

But equally eminent others have been intrigued by the theory. Bill Hamilton, the world's leading evolutionary biologist, died earlier this year after a trip to the Congo rainforest where he was trying to collect chimpanzee faeces to test whether chimps in the areas where primates were captured for medical experiments carried the virus. After Hamilton's death, Matt Ridley, a respected science writer, was prompted to read Hooper's book, The River (which has just been issued in paperback), and confessed that he was "shaken to the core" by it. On Tuesday, Ridley will question Hooper at The Sunday Times Hay-on-Wye literary festival.

In the 1950s, there was a race to perfect a viable oral polio vaccine. One of the competitors was Dr Hilary Koprowski, a Polish research biologist who moved to America during the second world war. Koprowski's live polio virus - like that of his main competitors, the great scientists Jonas Salk and Albert Sabin - was grown in a culture made from monkey kidneys.

There are clear records as to which monkeys were used for Sabin and Salk's cultures. But Koprowski's records appear to have been lost. What is known is that he was associated for several years with Camp Lindi, a research centre in the Congo. At least 400 chimps were captured and sent from there to America and Belgium for medical research. It is possible that their kidneys were chopped up and used to create the culture necessary to grow polio. If so, were any infected with SIV? Could it have survived and been present in the final polio vaccine?

Hooper thinks it might. There appears to be a broad correlation between the areas in Africa that saw the first outbreaks of Aids and the places where Koprowski's vaccine, known as Chat, was tested in the 1950s. Other simian viruses, most notably SV40, which is implicated as an accelerator of asbestosis and in some kinds of cancer, have survived the vaccine-making process. SV40 has been screened out since the 1960s.

Hooper says there is compelling circumstantial evidence for his theory. For the "cut hunter" theory there is none. Yet Oxford is adamant that this is the most likely mode of transmission.

"This is a natural world," he says. "This is how viruses get transferred. There is no evidence that chimp kidneys were used to make the vaccine and, even if they were, the virus would never survive the vaccine-making process. Furthermore, you take the live polio and drop it into a child's mouth. We know HIV doesn't affect people by mouth. Salk, Sabin and Koprowski were intelligent, thoughtful people who eradicated a horrible disease. This is a character assassination."

The idea that such a devastating disease might have been caused by science is anathema to doctors and scientists. But Hooper says that, unless we face up to the possibility that something like this could happen, we face doing undreamt-of damage to the human race.

"There are implications for medical and scientific research taking place right now," he says. "We are on the verge of putting animal cells, even animal organs, inside human patients and immunosuppressing them so they won't reject the material. We do not know all the retroviruses present in pigs and baboons. Are we about to open another Pandora's box?

"If so, the effect won't be felt by us but by our children and their children. You only have to look at what happened with BSE. We should try our best to avoid any more disasters."

In the main, he says, the scientific reaction to his theory has been fair. "For the most part, they've said there is not enough evidence yet to prove the theory, but there is a case to answer."

And before long, we may know: the Wistar Institute, under whose auspices Koprowski worked, has recently - after eight years of resistance - released half a dozen archive samples of Chat vaccine and polio virus for independent testing. Researchers will test for SIV and try to determine which type of primate tissue was originally used to make the vaccine.

The tests may not be conclusive because the contention is not that all, or even most, batches were contaminated, and there is no way of knowing if the samples come from batches that were used in Africa. But, if SIV were to be found, it would be important supporting evidence for Hooper's case. The tests should be completed later this summer.

The faecal samples collected by Hamilton on his final trip are also being examined for traces of SIV. Omar Bagasra, an American immunologist, has suggested that scientists go back to the Ruzizi valley, on the borders of Rwanda and Burundi, where a mass-vaccination trial was held in the spring of 1958.

He says that, if it were possible to find people who were given the vaccine in the 1950s, their blood could be tested. If any had developed an immunity to SIV, it would not only implicate the polio vaccine but also, perhaps, help create a vaccine against Aids.

It would also take us nearer the answer to that tantalising question: is Aids a natural disaster or an appalling medical error?

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