Shortly after the swine flu became a big media topic, Tom Philpott, food writer at Grist, wrote an article about the possible origins of the flu in Mexico.  Based on his reading of a blog, Biosurveillance, that tracks diseases worldwide. Philpott suggested that there was reason to believe that the flu had originated at a huge hog farm owned by U.S. company Smithfield Foods, the worldest biggest hog farming corporation.

The 950,000 hog farm, called Granjas Carroll, after its local subsidiary, is in La Gloria, a town in the state of Veracruz on the Gulf of Mexico.  The disease emerged in February in La Gloria infecting 1,800 people, 60% of the towns 3,000 residents.   

"Veratect reported local health officials declared a health alert due to a respiratory disease outbreak in La Gloria, Perote Municipality, Veracruz State, Mexico.  Sources characterized the event as a "strange" outbreak of acute respiratory infection, which led to bronchial pneumonia in some pediatric cases."

The Guardian, which also picked up on the story, says that there was much confusion about the cause of the disease.  As the symptoms of swine flu became more widely known later, residents of La Gloria said the symptoms were what they had experienced earlier.  Residents of La Gloria,"as well as some Mexican public-health workers, have pointed to flies congregating on manure piles as a possible vector for the flu". 

Smithfield has said that no pigs of theirs appeared to have symptoms of the disease, although they have not indicated whether the pigs have been tested or not.  It is also apparently possible for pigs to carry the disease without exhibiting the symptoms.  Many have scoffed at the idea that flies can transmit the disease although Philpott says that his research has unearthed a paper written by a team of international scientists that points to an outbreak of bird flu in Kyoto, Japan in 2004 that found that "flies caught in proximity to broiler facilities where the outbreak took place carried the same strains of H5N1 influenza virus as found in chickens of an infected poultry farm".

The research paper referred to by Philpott above points out that untreated animal wastes can indeed carry flu strains and the pathogens including influenza viruses can persist for extended periods of time if left untreated.  "Pathogens can survive in untreated and land-disposed wastes from food animals for extended periods of time—between two and 12 months for bacteria and between three and six months for viruses."

Philpott points out that the volume of animal wastes in the world is huge and growing.  "In the U.S., it is estimated that 238,000 CAFOs produce 314 million metric tons of waste per year, which is 100 times as much biosolids produced by treating human wastewater. Global estimates suggest that 140 million metric tons of poultry litter and 460 million metric tons of swinewaste were produced in 2003, based on data from the Food and Agriculture Organization."

Mike Davis, the author of the Guardian piece cited above, notes several issues of concern arising from this story.  He concludes that the new flu strain, a mix of pig, chicken and human flu, is not likely to be tamed by existing WHO and CDC containment tactics.  We may have dodged a bullet this spring, with the changing of the season, but the bigger problem is what we learn from it to prevent larger flu outbreaks next year or the year after. 

Davis asks what caused this acceleration of swine flu evolution? "Virologists have long believed that the intensive agricultural system of southern China is the principal engine of influenza mutation: both seasonal "drift" and episodic genomic "shift". But the corporate industrialisation of livestock production has broken China's natural monopoly on influenza evolution. Animal husbandry in recent decades has been transformed into something that more closely resembles the petrochemical industry than the happy family farm depicted in school readers. . . . In 1965, for instance, there were 53m US hogs on more than 1m farms; today, 65m hogs are concentrated in 65,000 facilities. This has been a transition from old-fashioned pig pens to vast excremental hells, containing tens of thousands of animals with weakened immune systems suffocating in heat and manure while exchanging pathogens at blinding velocity with their fellow inmates."

How do we deal with an industry that will fight us tooth and nail?  Currently human wastes are monitored and treated in the U.S. and elsewhere but animal wastes are not.  Davis goes on, "This is a highly globalised industry with global political clout. Just as Bangkok-based chicken giant Charoen Pokphand was able to suppress enquiries into its role in the spread of bird flu in southeast Asia, so it is likely that the forensic epidemiology of the swine flu outbreak will pound its head against the corporate stonewall of the pork industry."

I think we better hope that Seattle's own Dr. Raj Shah, the newly nominated Under Secretary of Research, Education and Economics and Chief Scientist at USDA, is up to this job.  He will be in charge of U.S. food safety.  Shah is currently serving as Agricultural Development Director at the Bill and Melinda Gates Foundation.