The spread of so-called swine flu, which has caused over 120 deaths globally, has sent public health officials into overdrive.
Industrial farms are said to be a "perfect incubating system"
As thousands fell ill in rural Mexico, those living near the outbreak raised suspicions about large industrial pig farms despite the owners' saying their herds were clean and workers were healthy.
Concerns over the border in the US have also centred on the intensive methods which have transformed pig farming in the past 20 years, Julian O'Halloran reports.
Animal welfare campaigners may see the way pigs are crammed into their pens in industrial farms as cruel, but to some public health experts these pens are also incubators for viruses.
This was the warning in a report published last year by American NGO, the Pew Charitable Trust, which funded a commission to study the possible spread of viruses and pathogens.
The conclusion of the study, which took two-and-a-half-years to produce, was clear: "The continued cycling of viruses and other animal pathogens in large herds or flocks increases opportunities for the generation of novel viruses through mutation... that could result in more efficient human-to-human transmission."
The commission's executive director, Bob Martin, told BBC File on 4 the warning was prophetic, coming a year before this outbreak of flu in Mexico in March.
"The commission was very concerned regarding the concentration of swine. Swine are incredible incubators for viruses - they're susceptible to swine flu, avian flu and human flu."
He added: "They can pass it back to you, the human worker and then back to the pig. They generate the novel virus, as it's called."
Mr Martin said the commission had based its report on research by the Iowa School of Public Health, where one of its commissioners was dean of the school.
"They came and addressed what a perfect incubating system a concentrated animal feeding operation or an industrial farm is for breeding novel flu viruses."
He said the virology experts stated these farms could amplify the spread of flu and add to the problem in another way - by possibly increasing the risk that the virus will also infect humans.
"Many of the industrial farm operation workers are lower-income scale in the US - they don't have access to immediate health care or screening and they would be a bridging population to bring the virus from the industrial farm to the broader population."
However the farming industry believes its methods do not increase the risk of breeding novel flu viruses.
FIND OUT MORE
Listen to File on 4, BBC Radio 4 2000 BST, Tuesday 9 June 2009, repeated 1700, Sunday 14 June 2009.
Dr Liz Wagstrom, scientific expert with the US National Pork Council, insisted that a range of precautions are in place on US farms.
"There are all sorts of influenza viruses, pigs are one of them, birds are one of them, humans are one of them and there is a chance for these recombination events can happen in all three species so that's why we have worked very closely with public health agencies to try to develop a surveillance and response plan to identify emerging viruses and respond to them," she said.
The industry also rejects the term swine flu after meat sales fell following the outbreak of the new flu.
And she said that America's top public health officials now call the virus H1N1.
"We worked closely with scientists and others to question whether this was an appropriate name and people within the scientific bodies came to the conclusion that even though there were pieces and parts of this virus that were consistent with viruses seen in swine, because it was not number one found in pigs and contact with pigs was not associated with infection, it was better renamed," she added.
However, Dr David Morens, director of the National Institute of Allergy and Infectious Diseases near Washington DC, is not convinced.
"It's a swine virus - a virus that's descended from two different pig viruses that have been in pigs for a number of years."
He told File on 4: "If you had asked most virologists last year most would have said it was unlikely that a virus circulating in pigs could jump into humans and cause a pandemic.
"And yet that seems what we're observing now... it certainly is spreading in the direction of being called a pandemic."
He added: "Over the coming months, many public health officials in the world will be discussing these things and undoubtedly more research will need to be done and ask the question what can be done to limit the chance that something like this will happen again.