The website of the World Health Organisation refers calmly to something called influenza A(H1N1). But the world’s media saw the name swine flu, and perhaps not surprisingly homed in on an intensive pig-rearing facility in Mexico as the outbreak’s source—wrongly, as it turned out. Underneath this reaction lay a feeling that industrial agriculture makes modern pandemics more likely—even though there is almost no evidence for this at all.

The British consumer is usually ambivalent about animal welfare, condemning battery chickens but buying them nonetheless. The BSE crisis in the 1990s led to the slaughter of 4.5m cattle and made public some of the (undoubtedly unsavoury) practices involved in making cheap protein for humans, not least feeding the remains of cattle to other cattle. Since then the environmental movement, with its simplistic view of farming—small equals good, big equals bad—has joined with popular campaigns by Jamie Oliver and Hugh Fearnley-Whittingstall to spread a new hostility towards large-scale farming. To many it seemed intuitively right that something as nasty as a pandemic flu must, somehow, have come from this heart of darkness.

But the facts tell a different story. A study by the respected US Centre for Disease Control and Prevention seems to show that swine flu came from a “triple reassortment” of different flu virus genes—pig, avian and human—and that the pig elements also include a genetic contribution from a European strain of swine flu. Since European pigs rarely, if ever, travel as far as Mexico, the reassortment vessel—the physical body in which these various viruses combined—was likely to be human, not swine. World Health Organisation (WHO) officials think that the first case may have been a young boy in southern California, with no pig contact at all. Ultimately, human beings are more likely to have given influenza A(H1N1) to pigs than the other way round.

Even anti-factory farming groups who might admit that intensive farming wasn’t at fault this time still insist that it is a pandemic accident in the making. They will speculate openly about whether one can ever really trust the word of global food conglomerates, such as the world’s largest pork producer, Smithfield Foods, the owners of the suspect Mexican pig factory. The implication is that a return to cottage production would limit diseases, and improve the health of both man and beast.

Of course, there are bad intensive producers that cut corners by selling battery chickens as free range, packing pigs so closely that they can’t move or adding excessive pink colouring to farmed salmon. But any number of closely gathered animals, human or not, present an opportunity to a microbe. The movement of animals to market always creates opportunities for infection, as we saw with foot-and-mouth disease. Whether inside, as commuters crammed in trains or pigs in rearing units, or outside as festival-goers or free-range chickens, merely having more than one animal in the same place increases the likelihood of disease, particularly a novel one.

Even keeping each pig isolated wouldn’t solve the problem. It would interact with us, and we carry disease too. If it grubs in the ground it finds soil-based bacteria and parasites, while other animals—mice, birds, or foxes for instance—also cast off viruses and bacteria. Despite what activists say about modern factory farming, it’s actually much more likely that a future flu pandemic will begin where humans share their cooking and living quarters with domestic animals, as they do in much of the developing world. Such circumstances were probably the cause of the 261 deaths to date from H5N1 influenza, or avian flu.

Good large-scale producers are only too aware that a virus in their flocks presents the greatest possible threat to their bottom line and pull out all the stops to vaccinate, monitor and prevent the spread of any infection. They know too that ignoring animal welfare regulations risks reputation and livelihood. This is especially true in Britain, where BSE left behind some of the world’s fiercest regulations, along with frequent unannounced inspection by officials from Defra. Big supermarkets also regularly inspect their suppliers—whether their farms are in Britain, Thailand or Brazil—in an effort to stop the reputational risk of disease in their supply chain. And even major pig breeders, such as the Pig Improvement Company, invest in health programmes or, like Smithfield, develop their own swine vaccines.

Cottage industries might look nice, but smallholders are less skilled at spotting disease. Ineffective attempts at at-home treatment often mean that help only arrives when an animal is already sick, or not at all given that a vet’s bill often exceeds an animal’s purchase price many times over. Avoiding treatment in this way allows infection to entrench, and animals near death may be taken to market and sold. In parts of the world where food is scarce, carcasses may not be burnt, but left for scavengers, increasing the risk of cross-species transmission.

Of the 40 or so new diseases that have appeared around the world in the last three decades, almost all have come from animals and jumped to human beings, and all have begun in “cottage” conditions. None, unless you count BSE, were caused by intensive production of animals.

So, while our relationship with animals is likely to be the source of any future pandemic, intensive farming is much less likely to be the culprit than the cottage production so many of us admire. Good and bad keepers of animals will remain, whether they are small or large-scale rearers. The important point is that all must be scrupulous in their husbandry.

The final irony is that making a flu vaccine involves the use of hens’ eggs. One dose needs one egg to make it. Even now, vaccine manufacturers are building up flocks, maintained inside to avoid any cross contamination with wild birds, to produce the 1bn eggs that will be needed for the 1bn flu vaccines that are set to be produced for H1N1. Without intensive production in conditions of immaculate cleanliness, we would have no flu vaccines. And we don’t have cottage farmers to thank for that.