The origin of swine flu

April 27, 2009

in Science, The environment

Fixed-gear bicycle derailleur

I am curious about the origin of the swine flu currently radiating out from Mexico. The CDC thinks it arose from one individual who was superinfected with both human and swine flu varieties, which then exchanged genetic information.

It certainly would not surprise me if this was simply the latest monster disease to emerge from the factory farming of meat. Packing together unhealthy, antibiotic-marinated animals in proximity with human workers is pretty much the most efficient possible incubator for novel pathogens. While it must be acknowledged that even the most responsible forms of agriculture raise risks of disease evolution and transmission, the characteristics of contemporary factory farming make it much more likely. A notable previous example is MRSA: a disease that seems to have emerged from pig farms in the Netherlands, and which now kills more people per year in North America than AIDS does.

[Update: 4 May 2009] Two updates: Firstly, the text on the Wikipedia page for swine flu no longer includes the text about the CDC I mentioned in my original post. The older Wikipedia text is available here.

Secondly, there is now an article in Newsweek that affirms a link between factory farming and the swine flu epidemic. According to the article: “This virus has been evolving for a long time, no doubt aided in its transformation by the ecology of industrial-scale pig farming in North America.”

[Update: 5 November 2009] Six months after the outbreak started, it appears that not much effort is being put into discovering exactly where the virus came from, or how it passed into the human population.

Report a typo or inaccuracy

{ 51 comments… read them below or add one }

. April 27, 2009 at 11:39 am

Flu Pandemic Risk: Swine Flu Monitoring Needed For Farm Workers, Study Says

ScienceDaily (Feb. 15, 2008) — A University of Alberta study recommends that workers on pig farms be monitored as part of influenza pandemic preparedness, after a child on a communal farm in Canada was diagnosed with swine flu in 2006.

“The concern is that swine viral strains could adapt into a form that results in efficient human-to-human transmission,” said Dr. Joan L. Robinson, a professor at the University of Alberta in Edmonton, Canada, a pediatrician at the Stollery Children’s Hospital, and lead author of the study, which was published recently in the journal Emerging Infectious Diseases. Swine flu in humans is “under-recognized in Canada, but it has the capacity to become a problem,” she added. “Early recognition that swine strains are becoming more virulent might expedite both implementation of ideal infection control precautions for symptomatic cases and vaccine development.”

. April 27, 2009 at 11:40 am

Swine Flu Outbreak — Nature Biting Back at Industrial Animal Production?

Officials from the CDC and USDA will soon arrive in Mexico to help investigate the deadly new influenza virus that managed to jump from pigs to people in a previously unseen mutated form that can readily spread among humans.

One of the first things they will want to look at are the hundreds of industrial-scale hog facilities that have sprung up around Mexico in recent years, and the thousands of people employed inside the crowded, pathogen-filled confinement buildings and processing plants.

Industry calls these massive compounds “confined animal feeding operations,” or CAFOs (KAY-fohs), though most people know them simply as “factory farms.” You have seen them before while flying: Long white buildings lined up in tightly packed rows of three, four or more. Within each confinement, thousands of pigs are restricted to indoor pens and grain-fed for market, while breeding sows are kept in small metal crates where they spend most of their lives pregnant or nursing piglets.

In the last several years, U.S. hog conglomerates have opened giant swine CAFOs south of the border, including dozens around Mexico City in the neighboring states of Mexico and Puebla. Smithfield Foods also reportedly operates a huge swine facility in the State of Veracruz, where the current outbreak may have originated. Many of these CAFOs raise tens of thousands of pigs at a time. Cheaper labor costs and a desire to enter the Latin American market are drawing more industrialized agriculture to Mexico all the time, wiping out smaller, traditional farms, which now account for only a small portion of swine production in Mexico.

R.K. April 27, 2009 at 12:59 pm

Is there any evidence, beyond speculation, that this swine flu has anything to do with factory farms?

Matt April 27, 2009 at 5:38 pm

Further to R.K.’s comment, you implicated “antibiotic-marinated” livestock, but isn’t the flu viral (meaning antibiotics would have played absolutely no role in its evolution?) I think the connection is tenuous and speculative.

Milan April 27, 2009 at 5:52 pm

I agree that it’s speculative, though the antibiotic point is not irrelevant because this is a virus. The antibiotics are necessary because the conditions in which the animals live exceed what their immune systems can tolerate. Their necessity is thus a sign that the animals are under considerable stress, implying that they are more vulnerable to non-bacterial diseases than animals living in better conditions would be.

Some other good information is in this linked article.

I am not saying this swine flu is definitely the product of factory farming: just that it is plausible and worth investigating.

. April 27, 2009 at 5:56 pm

Swine-flu outbreak could be linked to Smithfield factory farms

Posted 11:06 AM on 25 Apr 2009
by Tom Philpott

The outbreak of a new flu strain—a nasty mash-up of swine, avian, and human viruses—has infected 1,000 people in Mexico and the U.S., killing 68. The World Health Organization warned Saturday that the outbreak could reach global pandemic levels.

Is Smithfield Foods, the world’s largest pork packer and hog producer, linked to the outbreak? Smithfield operates massive hog-raising operations Perote, Mexico, in the state of Vera Cruz, where the outbreak originated. The operations, grouped under a Smithfield subsidiary called Granjas Carroll, raise 950,000 hogs per year, according to the company Web site.

On Friday, the U.S. disease-tracking blog Biosurveillance published a timeline of the outbreak containing this nugget, dated April 6 (major tip of the hat to Paula Hay, who alerted me to the Smithfield link on the Comfood listserv and has written about it on her blog, Peak Oil Entrepreneur):

“Residents [of Perote] believed the outbreak had been caused by contamination from pig breeding farms located in the area. They believed that the farms, operated by Granjas Carroll, polluted the atmosphere and local water bodies, which in turn led to the disease outbreak. According to residents, the company denied responsibility for the outbreak and attributed the cases to “flu.” However, a municipal health official stated that preliminary investigations indicated that the disease vector was a type of fly that reproduces in pig waste and that the outbreak was linked to the pig farms. It was unclear whether health officials had identified a suspected pathogen responsible for this outbreak.”

. April 27, 2009 at 6:06 pm

Swine Flu Fun Facts
By Maggie Koerth-Baker

Some Thoughts on Factory Farming

So I know that Grist, and a couple of other places, are promoting the theory that the genesis of H1N1 swine flu can be tied directly to factory farming practices. I’m no fan of factory farming, and it definitely has some associated public health dangers, but I’m not yet convinced that this one of them.

First, according to the experts I’ve spoken to, nobody currently knows specifically where H1N1 swine flu comes from. In fact, the information we’re getting out of Mexico seems to have a lot of holes in it, to the point that (as of my writing this) nobody even knows how many supposed swine flu cases/deaths are actually caused by swine flu or what percentage of people infected with swine flu are dying in that country. As Pekosz told me, there’s no evidence one way or the other.

Second, while past pandemic viruses have had connections to farming, they haven’t necessarily been connections to factory farming; but rather small-scale (and, particularly, subsistence level) farming, where animals of several species share close quarters. This is important for the H1N1 swine flu. Pigs seem to provide a particularly good environment for flu viruses to get their gene-reassorting watusi on. But to get that pig/avian/human mix, the most likely candidate would be a pig who’d had close contact with both people and poultry. As I understand it, it’s less likely that a human who works with pigs and chickens separately could pass the avian virus to a pig. And, factory farms, which tend to be single-species outfits, aren’t really great places for pigs and chickens to interact.

Now, I can see some ways around that. Say, if the pigs were sleeping or wallowing in muck that was contaminated with chicken feces or something. I could also be interpreting the facts incorrectly here. But from what I’ve read, and from the researchers I’ve spoken with, it seems more likely that H1N1 would have been created in the communal barn of a small farm, than in a giant hog-only factory farm shed.

R.K. April 27, 2009 at 6:10 pm

Given how politicians reflexively protect the agricultural lobby, strong public pressure to investigate the cause of the outbreak might be the only way to ensure an investigation happens, that it be undertaken seriously, and that the results be made public.

. April 27, 2009 at 7:19 pm

Smithfield Foods Says It Found No Evidence of Swine Influenza at Its Mexican Joint Ventures

SMITHFIELD, Va., April 26, 2009 /PRNewswire-FirstCall via COMTEX News Network/ — Smithfield Foods, Inc. (NYSE: SFD) stated that it has found no clinical signs or symptoms of the presence of swine influenza in the company’s swine herd or its employees at its joint ventures in Mexico.

Those operations are cooperating with Mexican officials to assist it in its 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.

Based on available recent information, Smithfield has no reason to believe that the virus is in any way connected to its operations in Mexico. The company also noted that its joint ventures in Mexico routinely administer influenza virus vaccination to their swine herds and conduct monthly tests for the presence of swine influenza.

Milan April 27, 2009 at 7:20 pm

Unrelated to swine flu:

As an aside, I noticed that the photos from today and yesterday have some geometric similarities:

Merged birds and bicycle

Milan April 27, 2009 at 8:54 pm

The Centers for Disease Control and Prevention have a good Swine Flu page.

Tristan April 27, 2009 at 11:55 pm

Is it immoral for me to hope it originated from the factory farming of meat? Because if it did, that could potentially lead to good consequences in the manner of clamping down on standards and enforcement, and growing opposition towards, factory meat farming.

Milan April 27, 2009 at 11:58 pm

Have mad cow disease, avian flu, foot and mouth disease, all the salmonella and e. coli outbreaks, etc not been enough?

I don’t think most people are capable of being disgusted at our existing food system.

Milan April 28, 2009 at 12:07 am

The whole situation reminds me of Jimmy watching the burning animal carcasses in the opening section of Atwood’s Oryx and Crake: a novel that seems to have more contemporary political relevance by the day.

Tristan April 28, 2009 at 12:10 am

“I don’t think most people are capable of being disgusted at our existing food system.”

It’s very difficult. Although I know many things rationally about our food system, I still don’t find things like packaged salami intuitively gross. I keep wanting to connect this back to Zizek’s description of how ideology functions – it still works even when you don’t believe in it.

Magictofu April 28, 2009 at 10:18 am

From what I’ve heard on radio, we still haven’t found a single pig infected with this virus. In fact it seems that this virus is a chimera made of human, pig and bird flu strains. We only call it swine flu because it has key genes (5 out of 8 if I remember it well) that are generally found on usual swine flu viruses.

As for factory farming, these things are horific enough as they are. I don’t see the need to advance unfounded theories about a probable link between them and this new virus. As a matter of fact, it might even be counterproductive in the long term if this theory turns out to ba fasle.

Magictofu April 28, 2009 at 10:21 am

On the plus side, I would love to see how creationists understand the development of this new virus.

. April 28, 2009 at 11:23 am

With Swine Flu Cases Rising, Borders Are Tightened
The New York Times
Published: April 28, 2009

In Mexico, state health authorities looking for the initial source of the outbreak toured a million-pig hog farm in Perote, in Veracruz State. The plant is half-owned by Smithfield Foods, an American company and the world’s largest pork producer.

Mexico’s first known swine flu case, which was later confirmed, was from Perote, according to Health Minister José Ángel Córdova. The case involved a 5-year-old boy who recovered.

But a spokesman for the plant said the boy was not related to a plant worker, that none of its workers were sick and that its hogs were vaccinated against flu.

Milan April 28, 2009 at 12:18 pm

I don’t see the need to advance unfounded theories about a probable link between them and this new virus. As a matter of fact, it might even be counterproductive in the long term if this theory turns out to ba fasle.

I disagree. Even if it turns out that this flu has nothing to do with factory farming, it still makes sense as a thing to investigate when mysterious new diseases emerge. Not every new illness comes from factory farms, clearly, but enough have done to warrant their place on the list of suspects.

Not checking, because it isn’t certain to be the cause, doesn’t strike me as a sensible approach. That being said, we should obviously make it clearly known that the cause was not factory farming, in those cases where it is determined to be so.

When it comes to public relations, having the general link between factory farming and human disease known seems important. While some people get worked up about the health and comfort of the animals themselves, I think most people are only concerned with the impacts our agricultural practices have on human beings.

Milan April 28, 2009 at 12:21 pm

On the plus side, I would love to see how creationists understand the development of this new virus.

I think I remember the answer to this one. It’s god’s punishment for homosexuality, abortion, etc.

. April 28, 2009 at 3:18 pm

Swine flu and the dramatisation of disease

Frank Furedi

Recent events show that, while society has the scientific know-how to cope with outbreaks of flu, it still sees disease as a harbinger of apocalypse.

Alongside fears about the ‘weaponisation’ of viruses, the internet is awash with rumours about the conspiracy responsible for the current outbreak of swine flu. ‘I find it odd that this recent outbreak of swine flu first appeared in Mexico about the time President Obama was visiting there’, writes one blogger, before asking: ‘Does anyone else find that suspicious?’ And far too many people are replying: ‘Yes.’ Far-right conspiracy theorists describe swine flu as the ‘latest bioterrorism attack by the New World Order’. Left-wing conspiratorial-minded crusaders, meanwhile, blame the Republicans in US Congress for cutting ‘pandemic preparedness’ funds out of Obama’s economic stimulus package. Environmental campaigners point the finger of blame at the big corporations that factory-farm pigs. Everyone seems to have their own version of a Hollywood disaster film, through which they can make sense of the outbreak of flu.

It seems the swine flu outbreak has infected our imaginations, giving shape and tangibility to our anxieties about everyday life. We should give the pigs a rest, and get on with living.

. April 28, 2009 at 3:19 pm

28 April 2009

A food system that kills – Swine flu is meat industry’s latest plague

Mexico is in the midst of a hellish repeat of Asia’s bird flu experience, though on a more deadly scale. Once again, the official response from public authorities has come too late and bungled in cover-ups. And once again, the global meat industry is at the centre of the story, ramping up denials as the weight of evidence about its role grows. Just five years after the start of the H5N1 bird flu crisis, and after as many years of a global strategy against influenza pandemics coordinated by the World Health Organisation (WHO) and the World Organisation for Animal Health (OIE), the world is now reeling from a swine flu disaster. The global strategy has failed and needs to be replaced with a public health system that the public can trust.

What we know about the situation in Mexico is that, officially speaking, more than 150 people have died from a new strain of swine flu that is, in fact, a genetic cocktail of pig, bird and human influenza strains. It has evolved to a form that is easily spread from human to human and is capable of killing perfectly healthy people. We do not know where exactly this genetic recombination and evolution took place, but the obvious place to start looking is in the factory farms of Mexico and the US. Experts have been warning for years that the rise of large-scale factory farms in North America has created the perfect breeding grounds for the emergence and spread of new highly-virulent strains of influenza. “Because concentrated animal feeding operations tend to concentrate large numbers of animals close together, they facilitate rapid transmission and mixing of viruses,” said scientists from the US National Institutes of Health (NIH) in 2006. Three years earlier, Science Magazine warned that swine flu was on a new evolutionary “fast track” due to the increasing size of factory farms and the widespread use of vaccines in these operations. It’s the same story with bird flu. The crowded and unsanitary conditions of the farms make it possible for the virus to recombine and take on new forms very easily. Once this happens, the centralised nature of the industry ensures that the disease gets carried far and wide, whether by feces, feed, water or even the boots of workers. Yet, according to the US Centres for Disease Control and Prevention (CDC), “no formal national surveillance system exists to determine what viruses are prevalent in the US swine population.” The same is true of Mexico.

Magictofu April 28, 2009 at 4:06 pm

Milan, my contention here is that some people suggest that the development of new flu strains is due to small farm operations particularly in poor areas where people live in close contact with animals while others blame large industrial farming practices for the reasons mentionned above. I agree that we need to investigate but disagree with placing an emphasis on one theory instead of the other (or others). At the end, we might even learn that both type of farming practices contributed to the outbreak.

I think it is fair however to assume that our relationships with domesicated animals explain the apparition of many new flu strains.

Milan April 28, 2009 at 4:22 pm

Well put.

We obviously shouldn’t blame industrial farming for consequences it doesn’t cause, not let non-industrial farming off the hook for the problems that exist with it.

While a food system without factory farms is preferable to one with them, it isn’t clearly the case that just moving beyond factory farming is sufficient to produce a food system that protects the environment and human health.

Sarah April 28, 2009 at 10:21 pm

I agree that this is interesting & it’ll be good to see more information emerge (presuming that it does emerge, rather than being smothered as any guilty party might be tempted to do by bribing officials). Speculation from the CBC on much the same lines as above:

Mexican farm swine flu’s ‘ground zero’:residents
Residents in a Mexican community of 3,000 say they believe their town is ground zero for the swine flu epidemic, even if health officials aren’t saying so.

A youth stands outside the home of a child who, according to Veracruz state Gov. Miguel Herrera, survived the swine flu, as he waits with others for Herrera’s arrival to La Gloria village in Mexico’s Veracruz state on Monday.A youth stands outside the home of a child who, according to Veracruz state Gov. Miguel Herrera, survived the swine flu, as he waits with others for Herrera’s arrival to La Gloria village in Mexico’s Veracruz state on Monday. (Alexandre Meneghini/Associated Press)More than 450 residents of La Gloria say they’re suffering from respiratory problems from contamination spread by pig waste at nearby breeding farms co-owned by a U.S. company.

Officials with the company say they’ve found no sign of swine flu on its farms, and Mexican authorities haven’t determined the outbreak’s origin.

The swine flu strain is suspected in at least 152 deaths in Mexico and cases have been confirmed in at least four other countries.

As far back as late March, roughly one-sixth of the residents in the Gulf Coast state of Veracruz began complaining of respiratory infections that they say can be traced to a farm that lies upwind 8.5 kilometres to the north, in the town of Xaltepec.

But Jose Luis Martinez, a 34-year-old resident of La Gloria, said he knew the minute he learned about the outbreak on the news and heard a description of the symptoms: fever, coughing, joint aches, severe headache and, in some cases, vomiting and diarrhea.

“When we saw it on the television, we said to ourselves, ‘This is what we had,’” he said Monday. “It all came from here.… The symptoms they are suffering are the same that we had here.” …

. April 29, 2009 at 1:32 pm

Symptom: swine flu. Diagnosis: industrial agriculture?

Posted 10:09 AM on 28 Apr 2009
by Tom Philpott

Several days after news broke of a possible link between Mexico-based hog CAFOs and the rapid spread of a novel swine-flu strain, what have we learned?

. April 30, 2009 at 2:41 pm

Don’t jump to conclusions on swine flu and pork production

Posted 4:52 PM on 29 Apr 2009
by Merritt Clifton

As a lifelong second-generation vegetarian, and longtime vegan, I would like nothing more, for both humane and environmental reasons, than to see an end to factory farming.

Yet in exposing and attacking the many and often grotesquely obvious excesses of factory farms, I believe it is essential at all times to be fair, be accurate, and not amplify allegations which may be unsubstantiated—not least because amplifying an unfounded or premature allegation tends to erode the credibility of the critic.

As of the moment, about two weeks into formal medical forensic investigation, no one knows just what the source of the mutant H1N1 virus first discovered in the Vera Cruz region of Mexico might have been.

Much attention has been given to the case of five-year-old Edgar Hernandez, of the La Gloria hamlet in Perote, near the Granjas Carroll factory pig farm. Hernandez—who survived—is the earliest victim of the mutant H1N1 virus from whom a sample was preserved. La Gloria residents blamed Granjas Carroll for an outbreak of illness in February and March 2009. Officially attributed to biting flies, the illness produced flu-like symptoms.

. May 1, 2009 at 10:20 am

Aporkalypse now! Essential H1N1 “don’t call it swine flu” reading
by Ethicurean @ 10:40 pm on 29 April 2009.

If you’re right, you’re a hero; if you’re wrong, you’re an Internet arsonist: Praising blogs for goosing mainstream media (aka MSM) to investigate whether industrial hog farms might be the swine flu outbreak’s “ground zero,” this article credits FoE Tom Philpott at Grist to be the first to blog the possible connection. But since so far there seems to be no direct link, bloggers get spanked for being on the wrong side of asking tough questions vs. jumping to conclusions. (Columbia Journalism Review) Related: Longtime science journalist (and vegan!) Merritt Clifton also says the evidence just isn’t there yet, and premature finger-pointing ain’t helpful. (Grist)

. May 1, 2009 at 11:23 am

‘New Scientist’: Swine flu stems from virus that evolved in U.S.

n a pair of articles in New Scientist, Debora MacKenzie links the swine flu virus now spreading across the globe to large-scale pork-raising operations in the United States.

In the first article, titled “Swine flu: the predictable pandemic?,” MacKenzie writes that the “virus has been a serious pandemic threat for years, New Scientist can reveal—but research into its potential has been neglected compared with other kinds of flu.” She writes that the strain now in the headlines has its origins in an earlier outbreak in the United States a decade ago:

CDC: swine flu strain has genetic roots in U.S.A.

In an interview with Science Magazine, the CDC’s chief virologist, Ruben Donis’ essentially confirmed the reading of the current swine flu strain made by New Scientist: that it evolved from a strain that cropped up in U.S. hog farms in 1998. Both New Scientist and Donis emphasize that what we’re talking about is a swine flu—in direct contradiction of the pork industry’s party line. In an interview with me today, David Warner, director of communications at the National Pork Producers Council, repeatedly attributed the outbreak to “human flu, not swine flu.” He acknowledged that new strain had swine and avian components, but insisted that the human components dominated; and he denied outright that the hog industry had anything to do with it. So that’s the pork industry’s take. Here’s the assessment of CDC’s Donis, as portrayed in this Science interview.

Jumping to conclusions in health matters may have adverse side effects

The past week, the Netiverse has erupted with stories linking the Granjas Carroll confined animal feeding operations (CAFOs) near La Gloria, Vera Cruz, Mexico, with the outbreak of a strain of H1N1 influenza, commonly called “swine flu,” that has triggered concerns about possible flu pandemic reminiscent of the one that claimed tens of millions of lives between 1918 and 1920. Outlets such as Grist, Huffington Post, and Daily Kos have contributed to the eruption, as have some members of the old-line print and broadcast media, but I find much of the reportage at this point troubling.

. May 4, 2009 at 2:03 pm

The Path of a Pandemic
How one virus spread from pigs and birds to humans around the globe. And why microbes like the H1N1 flu have become a growing threat.

Last year researchers from Iowa State University in Ames warned that pigs located in industrial-scale farms were being subjected to influenza infections from farm poultry, wild birds and their human handlers. Writing in The Journal of Infectious Diseases, Eileen Thacker and Bruce Janke said, “As a result of the constantly changing genetic makeup of individual influenza viruses in pigs, the U.S. swine industry is continually scrambling to respond to the influenza viruses circulating within individual production systems.”

Something was changing. Pigs notoriously eat just about anything thrown their way, and rub up against each other frequently, readily passing infections within herds. Their stomachs are remarkably tolerant environs for microbes, which since ancient times have caused illness in humans who dined on raw or undercooked pork. Investigation of the 1918 influenza pandemic, which is now estimated to have killed up to 100 million people worldwide in 18 months, revealed that the viral culprit was a type H1N1 human flu that had infected pigs, and then circulated back to humans.

. May 4, 2009 at 2:17 pm

“This virus has been evolving for a long time, no doubt aided in its transformation by the ecology of industrial-scale pig farming in North America. Some scientists say there are genetic elements in the virus that date back to an Indiana pig farm in 1987. In that sense, it is similar to the “bird flu,” or H5N1, which surfaced in wild migratory water birds in southern China some time in the early 1990s and infected people in Hong Kong in 1997. As that virus has evolved over the past 12 years, it has taken advantage of large poultry farms, and major bird-migration centers, to spread rapidly and absorb new genetic material along the way. In 2005, as H5N1 spread to Siberia and Europe, the United Nations and the Bush administration mobilized cash, scientific expertise and the needed infrastructure to find and contain outbreaks, primarily by slaughtering infected chicken flocks.

A wiser set of pig-related actions would turn to the strange ecology we have created to feed meat to our massive human population. It is a strange world wherein billions of animals are concentrated into tiny spaces, breeding stock is flown to production sites all over the world and poorly paid migrant workers are exposed to infected animals. And it’s going to get much worse, as the world’s once poor populations of India and China enter the middle class. Back in 1980 the per capita meat consumption in China was about 44 pounds a year: it now tops 110 pounds. In 1983 the world consumed 152 million tons of meat a year. By 1997 consumption was up to 233 million tons. And the United Nations Food and Agriculture Organization estimates that by 2020 world consumption could top 386 million tons of pork, chicken, beef and farmed fish.

This is the ecology that, in the cases of pigs and chickens, is breeding influenza. It is an ecology that promotes viral evolution. And if we don’t do something about it, this ecology will one day spawn a severe pandemic that will dwarf that of 1918.”

. May 4, 2009 at 2:26 pm

Yes, it’s the CAFOs
Now is not the time for timidity

Posted 12:30 PM on 1 May 2009
by Tom Laskawy

I agree with the calls for some amount of caution in the search for a smoking gun in the swine flu pandemic. There’s always the danger of over-reaching and turning your target into an object of sympathy. But really, the science IS behind us on this one. The head virologist of the CDC has indeed identified the core strain of this outbreak as one that arose in a North Carolina CAFO. Meanwhile, another voice, this time Johann Hari of the London Independent (via HuffPo) convincingly touts the idea that our desire for cheap meat is a cause of the current crisis. He very elegantly describes how factory farms manufacture potent viruses along with their cheap meat

For his part, Smithfield CEO Pope in his interview doubted that “they’ll ever find the source of this” outbreak. And given that his company controls access to the facility at the center of the pandemic, it’s possible that he’s knows what he’s talking about. He reported that Smithfield has given samples from pigs at the Veracruz facility to a Mexican lab for analysis—samples chosen by Smithfield, not by independent experts. We shouldn’t then be surprised at the ultimate absence of a smoking gun, but neither should we demand one. We know more than enough to assert that it’s time for the public to learn what those of us in the sustainable world have understood for a long time—CAFOs are public health hazards of the highest order. And it’s also time that the public started to openly question why CAFOs and their owners are able to so brazenly flout environmental law—even laws written specifically to regulate their operations. When you look at the totality of the evidence, I don’t think it’s fair to say that WE’RE the ones who’ve over-reached.

. May 4, 2009 at 3:33 pm

Pork industry in panic as pigs catch the flu

PATRICK WHITE

From Monday’s Globe and Mail

May 4, 2009 at 7:00 AM EDT

WINNIPEG — The influenza outbreak has so far spared Canadian lives, but it is laying waste to the country’s struggling pork industry, drawing comparisons to the crippling blow mad-cow disease delivered to beef producers in 2003.

“We’re heading for a wreck,” said Simon Goodwin, a pig farmer in Alberta, where a herd infected with the new influenza AH1N1 strain was recently quarantined. “We’ve already seen 20 dollars knocked off our price, and that was before we heard about it spreading to hogs in Alberta.”

The province quarantined 2,200 pigs on a central Alberta farm after Canadian Food Inspection Agency officials confirmed that a farm-worker infected the animals with influenza A H1N1.

Anon May 4, 2009 at 7:19 pm
Milan May 4, 2009 at 8:54 pm

Now that Newsweek has printed it, I don’t feel as though it is too speculative for my blog.

Milan May 8, 2009 at 11:24 am

On the May 6th episode of The Colbert Report, author Laurie Garrett also alluded to the connections between swine flu and the “unnatural ecosystems” that have been created through contemporary agricultural techniques.

. May 11, 2009 at 11:38 am

Uncomfortable facts about the swine flu outbreak

Don’t associate U.S. pork with the swine flu outbreak—you can’t catch it through pork. Plus, no pigs on U.S. CAFOs are infected with it.

That’s message the industry and the USDA are straining to get across, anyway. Except … you can catch swine flu from pork, according to the World Health Organization. Here is the Reuters:

“Meat from pigs infected with the new H1N1 virus shouldn’t be used for human consumption, the World Health Organisation cautioned on Wednesday, adding it was drawing up guidelines to protect workers handling pigs.”

The article continues: “[V]eterinary experts say it’s impossible to know whether U.S. pigs are free of the new virus, which was detected over the weekend in a Canadian hog herd. Farmers aren’t required to report flu outbreaks in their pigs to authorities, and the collection of the 500 samples [assembled nationwide from livestock vets] wasn’t designed to detect a low level of a new virus in U.S. swine, of which there are about 65 million head.”

. May 15, 2009 at 10:34 am

A U.S. Hog Giant Transforms Eastern Europe

By DOREEN CARVAJAL and STEPHEN CASTLE
Published: May 5, 2009

But Smithfield found it hard to overcome fallout from the swine fever outbreak that struck Cenei. At the time, hog corpses lay in heaps, and residents remember chaotic efforts to shoot and burn them. That particular strain affects only hogs, but scientists have found elements of swine viruses — one from Europe or Asia, the other from North America — in the genetic code of the new influenza A(H1N1) virus.

Smithfield contends that “it is impossible to know” why the pigs got sick, while noting a breakdown in the supply of government-supplied swine flu vaccines. But several officials on both sides of the debate believe that Smithfield was overwhelmed by its own industrial machine and its ever multiplying pigs.

“Thousands of piglets were born,” Mr. Seculici, the architect, said. “There was no place to put them because the new farms weren’t finished. Nobody admits this, but this was the cause of swine flu. They were forced to improvise.”

Smithfield acknowledges that it placed young pigs on farms under construction, but insists that doing so had no impact on health.

“It was done too fast; that caused a lot of problems,” Mr. Taubman, the former U.S. ambassador, said.

. June 19, 2009 at 12:57 pm

The origin of swine flu
Putting the pieces together

May 28th 2009 | NEW YORK
From The Economist print edition
A better understanding of how the new strain of influenza arose

YOU are now officially permitted to blame the pigs. When a strain of influenza with pandemic potential struck in April, it was generally referred to as “swine flu” because it seemed similar to an existing group of strains, known as A/H1N1, which are commonly found in pigs. But when it became clear that the new bug was being spread by people, not porkers, the pig-breeding industry complained that it was being unfairly maligned. It also became apparent that the new virus contains bits and pieces derived from avian and human strains of influenza, as well as porcine ones, further muddying its origins.

A new study, however, suggests pigs really were to blame. Several dozen researchers, led by Rebecca Garten of America’s Centres for Disease Control and Prevention (CDC), sequenced full or partial genomes of 76 samples of the new virus, which has afflicted almost 13,000 people around the world so far. In a paper published in Science, they confirm that the closest genetic relatives of the new virus are swine-flu strains from both North America and Eurasia. The virus is made of eight gene segments of known provenance but which have not previously been seen in this combination. The genetic material in them is indeed a hotchpotch derived from avian, human and swine sources, but all eight segments come most recently from pigs.

On the positive side, the researchers discovered that the antigens (proteins that provoke an immune response) found in different samples have remained similar to each other. That, according to Derek Smith of Cambridge University, one of the paper’s authors, may make it easier to design a vaccine against the new virus. The World Health Organisation and a number of European governments are now talking to manufacturers about expediting the development of such a vaccine and, on May 22nd, American officials announced a $1 billion scheme with the same goal.

. June 30, 2009 at 10:25 am

Swine flu ‘shows drug resistance’

Experts have reported the first case of swine flu that is resistant to tamiflu – the main drug being used to fight the pandemic.

Roche Holding AG confirmed a patient with H1N1 influenza in Denmark showed resistance to the antiviral drug.

David Reddy, company executive, said it was not unexpected given that common seasonal flu could do the same.

The news comes as a nine-year-old girl has become the third to die in the UK with swine flu.

It is understood from her doctors at Birmingham Children’s Hospital that she had underlying health conditions. It is not yet known whether swine flu contributed to her death.

. July 10, 2009 at 12:27 pm

Concern over Ebola virus in pigs

A form of Ebola virus has been detected in pigs for the first time, raising concerns it could mutate and pose a new risk to humans.

Ebola-Reston virus (REBOV) has only previously been seen in monkeys and humans – and has not caused illness.

But researchers are concerned that pigs might provide a melting pot where the virus could mutate into something more menacing for humans.

. September 4, 2009 at 2:50 pm

STRATFOR sources involved in examining the strain have also suggested that the initial analysis of the swine flu was in fact in error, and that the swine flu may have originated during a 1998 outbreak in a pig farm in North Carolina. This information reopens the question of what killed the individuals whose deaths were attributed to swine flu.

. September 14, 2009 at 11:07 am

A(H1N1): Just Another Flu
September 14, 2009

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.

. September 15, 2009 at 3:30 pm

Swine flu
Expert says swine flu ‘hid’ for decade

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.”

. October 29, 2009 at 10:02 am

Swine flu roots traced to Spanish flu
Last Updated: Friday, May 1, 2009 | 5:17 PM ET

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.

. October 29, 2009 at 11:11 am

Six months after the outbreak, who’s investigating the CAFO-swine flu link?

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.

. November 8, 2009 at 10:02 pm

For swine flu, forget origins and start thinking about practices

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.

. November 16, 2009 at 5:08 pm

Time for the mainstream media to face the factory farm-swine flu link

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.

. November 17, 2009 at 2:50 pm

“The USDA is the federal agency tasked with ensuring that practices on farms, including factory animal farms, are safe. But it’s also the agency that exists to promote U.S. agricultural interests. In other words, the USDA has an inherent conflict around overseeing conditions on factory-style farms. For example, training a cold eye on the systemic safety hazards of factory farming isn’t likely to do much to promote the pork industry.

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.”

. July 2, 2010 at 2:13 pm

“As part of a long-running research project (beefed up since last year’s outbreak), a group at the University of Hong Kong has been monitoring the viruses of pigs slaughtered in the territory’s main abattoir. Malik Peiris and his colleagues have found strong evidence that the A/H1N1 virus afflicting humans is indeed recombining in pigs. They saw the mingling of A/H1N1 with two other types of swine influenza virus. These were the North American triple-reassortant viruses and the Eurasian avian-like swine viruses. They did not, however, observe reassortment with human seasonal influenza viruses, something they had worried might happen.

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.

Peer reviewed science October 7, 2011 at 6:17 pm

Analyses of historical data from the devastating influenza pandemic of 1918 have facilitated our understanding and preparations for controlling contemporary outbreaks. Fraser et al. accessed previously unpublished data from the fall of 1918, gathered during a household survey of over 7000 Maryland households conducted by Wade Hampton Frost, who led the U.S. Public Health Service’s investigations into the Spanish flu. Frost made a mathematical model of disease transmission, which Fraser et al. have expanded on. The most important parameter in epidemic control is transmissibility, and the new analysis shows that rates of transmission within households were actually quite low and very variable. It appears that not only were roughly a fifth of the population immune before the fall wave of infection, but also that there appeared to have been very few asymptomatic infections. These revelations show that influenza is consistently only moderately transmissible and thus always potentially controllable, provided that the measures and tools available to us now remain available.

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

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

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