Am. J. Epidemiol. 174, 10.1093/aje/kwr122 (2011).

http://www.sciencemag.org/content/333/6047/twil.full

What all this means is unclear. It is possible that the new recombinations will make the virus even less dangerous. But the opposite is also possible. It would make sense, therefore, to keep a sharp eye on other pig populations around the world, just in case.“

And from the start of the novel H1N1 outbreak, the USDA has tilted decidedly in the direction of promoting U.S. ag interests. Even though virologists and veterinary scientists have been warning for years that large hog farms create ideal conditions for the generation of dangerous new flu viruses—as this Environmental Health Perspectives article definitively shows—-the USDA still isn’t systematically testing swine herds for H1N1. It continues to rely on a voluntary—and little used—testing program.

Nor is it doing much, from what I can tell, on the problem of MRSA, the antibiotic-resistent staph infection that claims more lives every year than AIDS. MRSA has been pretty definitively linked to factory hog farms—specifically the dubious practice of dosing pigs daily with antibiotics.

If the USDA has been limp in its attempts to examine safety conditions on factory farms, it’s been downright zealous in its efforts to promote the pork industry.”

Novelist-turned-anti-meat-pamphleteer Jonathan Safran Foer made a stark claim about swine flu on The Ellen DeGeneres Show recenly:

“This swine flu that’s now an epidemic, they’ve been able to trace it back to a farm in North Carolina… A hog farm. Nobody knows this. Nobody talks about it. We’ve been told this lie that it came from Mexico.”

Well, the situation is even worse than Foer suggests. Authorities aren’t actually saying the novel strain of swine flu “came from Mexico.” That would be uncomfortable, because it first cropped up there a few miles from vast hog operations run by U.S. pork giant Smithfield.

But they are insisting that “pork is safe”—and doing little or nothing to monitor hog confinements for evidence of infection.

For years before the current outbreak, scientists openly worried that CAFOs (concentrated animal feedlot operations) provided excellent arenas for the generation and spread of dangerous new flu varieties.

Amid a trickle of news and science about swine flu over the past week, I’ve been rethinking my position on the novel H1N1 virus that has now infected millions of Americans (thankfully, so far, in a relatively benign way).

When I first began covering the story in April, I fixated on the question of origin. Had the new virus incubated in the vast hog confinements in Vera Cruz, Mexico? In a village near several large hog buildings there, a mysterious and virulent respiratory disease had broken out—and at least some of the cases were later confirmed have been infected with H1N1.

I still think it was right and proper to note the proximity between the CAFO and the outbreak. But now I think the focus on origins was wrong. Asking when and where this novel H1N1 strain mutated into present form is a bit like trying to identify the first mutant wolf pup that grew into a proper dog. In this context, origin is impossible to identify—and probably not that interesting.

The real question is, which of our practices are creating ideal conditions for the mutation of new swine-flu strains not recognized by human immune systems?

And once we identify those practices, we’d do well to phase them out. True, the current strain of H1N1 is behaving rather tamely—spreading fast but not causing much more damage than regular flu strains. And it has entered a phase of genetic stability—it hasn’t mutated much lately.

But what if it does begin to mutate—and new forms are more deadly, and resistant to Tamiflu? If and when it does begin to mutate, entire new vaccines will have to be generated—further straining a public health system already stretched to the limit by the current vaccine effort.

As anyone reading this already knows, I believe that concentrated animal feedlot operations (CAFOs) create excellent conditions for the mutation of new flu strains: thousands of genetically similar bodies living in close quarters, their immune systems compromised, swapping germs and occasionally coming into contact with human workers.

Almost exactly six months ago, I caused a stir by suggesting a possible link between CAFOs and the new strain of H1N1 swine flu that had just broken out. (See here and here.)

My position generated a certain amount of outrage, even among some commentators not linked to the meat industry. How dare I point to a possible link based on indirect, circumstantial, evidence?

Half a year later, I would love to be able to review results of a rigorous set of tests on CAFOs. I wish I could report that USDA researchers had been showing up on hog confinements and taking swabs; that CAFO workers were being monitored for H1N1 infections or antibodies; that the EPA was looking hard at CAFO cesspools—known as lagoons—to see if they could be possible vectors of infection.

From what I can tell, though, none of that is happening—even with the novel H1N1 virus spreading rapidly and vaccines still in short supply.

Pigs might have spread the current strain of influenza to humans, attracting worldwide attention, but new Canadian-led research suggests that we might have given pigs the flu in the first place, during the 1918 Spanish flu pandemic.

A group of Canadian and U.S. researchers, writing in the May issue of the Journal of Virology, say experimental testing of how pigs responded to the 1918 Spanish flu supports the theory that the virus was passed on from humans to pigs in 1918, during the Spanish flu pandemic.

Both the human influenza virus known as the Spanish flu and a swine respiratory disease occurred at roughly the same time. The first human cases of Spanish flu appeared in spring of 1918 while the first reports of the swine illness were in the fall of that year.

Pigs are seen at the Mober SENC farm in Saint Hughes, Que. south of Montreal in this file photo from Thursday, April 30, 2009. The CANADIAN PRESS

‘This virus most likely has been circulating under the radar in pigs for the better part of 10 years,’ Michael Worobey of the University of Arizona revealed at a meeting

Maggie Fox

Washington — Reuters Last updated on Tuesday, Sep. 15, 2009 01:42PM EDT

The new pandemic H1N1 influenza was circulating undetected in pigs for at least a decade before it jumped to people, and much better surveillance is needed among both pigs and people, an expert said on Tuesday.

Molecular tests show the swine flu virus made a mutational jump as it passed from pigs to humans, which apparently happened recently, Michael Worobey of the University of Arizona told a meeting of flu experts sponsored by the U.S. Institute of Medicine. “This virus most likely has been circulating under the radar in pigs for the better part of 10 years,” Mr. Worobey, who specializes in tracking viruses using a so-called molecular clock, told the meeting.

“Once it jumped into humans it probably circulated for months under the radar. There is lots of room for improvement of our surveillance of swine flu in pigs.”

H1N1 was first detected in April and declared a pandemic in June. It has spread quickly around the world but so far causes moderate illness, to the relief of public health experts. The institute, an independent organization that advises the U.S. government and other bodies on health matters, called the meeting to examine the pandemic and look for ways to better prepare for the next one.

Influenza viruses mutate regularly and are easy to trace using their rate of change, Mr. Worobey said. He collaborated with researchers around the world who dug out samples from freezers. By comparing recent gene sequences to older samples, Mr. Worobey was able to track the evolution of the pandemic.

It is hard to determine where people first became infected, he said, because doctors rarely test patients for influenza and even more rarely are the viruses genetically sequenced. “We could do more for surveillance in humans,” Mr. Worobey said. “If we had been doing that kind of thing, we may have picked up on this new strain a month or two or three before we did.”

It has been five months since the A(H1N1) influenza virus — aka the swine flu — climbed to the top of the global media heap, and with the start of the Northern Hemisphere’s annual flu season just around the corner, the topic is worth revisiting.

If you take only one fact away from this analysis, take this: The U.S. Centers for Disease Control and Prevention (CDC) believes that hospitalization rates and mortality rates for A(H1N1) are similar to or lower than they are for more traditional influenza strains. And if you take two facts away, consider this as well: Influenza data are incomplete at best and rarely cross-comparable, so any assertions of the likelihood of mass deaths are little more than scaremongering bereft of any real analysis or, more important, any actual evidence.