President Obama made a speech yesterday before the National Academy of Sciences – and mentioned the important link between scientific knowledge and our national health and security. According to The White House Blog, Obama said:

Science is more essential for our prosperity, our security, our health, our environment, and our quality of life than it has ever been before.

And if there was ever a day that reminded us of our shared stake in science and research, it’s today.  We are closely monitoring the emerging cases of swine flu in the United States. And this is obviously a cause for concern and requires a heightened state of alert.  But it’s not a cause for alarm.

So, the question is: what does science say about the causes of the current swine flu epidemic?

The first place to start is the Centers for Disease Control and Prevention (CDC), which has a dedicated section on Swine Flu. As of April 27, 1:00 PM ET, there were 40 confirmed cases of swine flu infection in the United States – 7 from California, 28 from New York, 1 from Ohio, and 2 from both Texas and Kansas. This is double the number from yesterday, and more than four times the number of confirmed cases on April 25^th.

Over at the World Health Organization, Director-General Dr. Margaret Chan just raised the level of influenza pandemic alert to Phase 4 – which means that there are “verified human-to-human transmission of an animal or human-animal influenza reassortant virus able to cause ‘community-level outbreaks.’”

The largest unanswered question remains: where are these infections coming from?

During a CDC press briefing on April 26^th, Daniel Steinberger from CBS News asked: “ Can you confirm reports that there may be officials in Mexico who are investigating industrial-scale hog facilities as a potential source, or CAFOs?”

The CDC’s Dr. Anne Shuchat responded:

No, I can’t confirm that. I can say that the U.S. Department of Agriculture is working with other parts of the government on animal sources. You know, were doing that as a routine part of this kind of investigation. We’re at the point where we don’t have information about illness in pigs related to this virus, but that would be a normal thing to be looking into.

This despite the Q&A on the CDC website that says “Swine Influenza (swine flu) is a respiratory disease of pigs caused by type A influenza viruses that causes regular outbreaks in pigs. People do not normally get swine flu, but human infections can and do happen.”

But here’s where things get really strange: this strain of the swine flu virus is not just from pigs.

In an interview with Dr. Mike Hansen, a Senior Staff Scientist with Consumers Union, he said “What’s unique here, is that this is not a straight-up swine flu. This has genetic material from swine, avian, and human influenzas…they haven’t found anything like this in any pigs yet.”

Dr. Hansen pointed out that this might indicate a link to a small mixed farming situation, where pigs and perhaps ducks are kept, rather than a larger industrial farm. “So that means that in a certain ironic sense, the big CAFOs might not be the problem,” Hansen continued. “Until we know more….if we point in that direction too much initially, and that’s not where the flu is coming from, then they can use that to sort of discredit the critics of CAFOs. CAFOs are bad for a number of environmental and human health reasons, and that’s why so many groups are fighting them. What’s good is more ecologically logical agriculture, and CAFOs surely aren’t that. But until we know more we need to be testing both big and small pig farmers.”

Other groups are also making the case that we need to study the problem more aggressively. The nonprofit Food & Water Watch sent a letter today to congressional leaders in the House and Senate, asking them to look into the source of the virus, the pathway for transmission between hogs and humans, and conditions inside hog confinement operations that could foster the growth and mutation of the influenza virus into more virulent strains.

The letter continues:

“Swine flu is not the only impact on public health impact from pork production that is worthy of examination by your committees. Another crucial topic is the discovery of Methicillin-Resistant Staphylococcus aureus (MRSA) in U.S. hog facilities, a finding that follows on the discovery of these antibiotic-resistant bacteria on hog farms in Canada and the Netherlands. A growing body of research is establishing the link between the trend of antibiotic-resistant bacteria and the use of antibiotics in livestock production. In fact, recent studies of E. coli bacteria on operations using non-therapeutic antibiotics find that anywhere from 30 to 80 percent of bacterial samples are resistant to one or more antibiotics. These bacteria can be transmitted from livestock to humans through direct contact between animals and workers or farm families; through human contact with animal waste, which can leach into water sources or be carried by flies; or on the meat that consumers purchase in retail stores.”

Finally, in response to the connections first reported on Grist and the Biosurveillance blog, Smithfield Farm reported in a press release that “Based on available recent information, Smithfield has no reason to believe that the virus is in any way connected to its operations in Mexico.”

According to Meatingplace.com (an on-line community for red meat and poultry processors in North America), Smithfield is “cooperating with Mexican officials to assist the investigation of the possible sources of the outbreak of the disease and will submit samples from its swine herds to the University of Mexico for testing.”

A report in the Guardian links La Gloria, a small town in eastern Mexico 12 miles from the Smithfield plant, as the possible epicenter of the recent outbreak. The article cites that “60% of the town’s population…has been affected.”

Dr. Hansen weighs in: “If 60% of the population of a town near a huge swine facility got sick with this flu and those are among the first cases seen (e.g. close to ground zero), then that really does point a strong finger that something in that area could be the problem.  At the very least, there should be a very specific investigation of the Smithfield facility that involves significant testing of those pigs for swine flu.”

We’ll just have to wait to see how all of this pans out over the coming days. But with the stakes as high as they are, we need to make sure we are following the science of the problem and not let our personal opinions about these controversial topics cloud the facts of this outbreak.