A Virus by Any Other Name: Lessons from an Outbreak (so far…)


photo: CDC

A week has passed since the World Health Organization convened its first emergency meeting to deal with menacing new flu virus thought to have sickened thousands and killed dozens of young Mexican men. New cases continue to tally up around the world (15 countries so far) and the virus is  spreading person-to-person. The outbreak has been ranked at an unprecedented level 5 (out of 6 ) on the WHO’s pandemic scale. But for now, at least, it appears the world has dodged a bullet. Most cases are non-lethal, if not exactly mild. This is not 1918 Spanish flu redux. Yet. And if it does mutate into something more dangerous, we now have viral “seed stock” and a battalion of scientists working around the clock on a vaccine.


So what has been learned by this apparent near-miss?

The most important take-away may just be what a near miss it has been. Factory farms – aka Confined Area Feeding Operations, aka CAFOs – have been royally “outed” as a major threat to global public health. And thanks to the web (Twitter in particular), it is not going to be easy for special interests to duck hard questions and discredit sources.

Five years ago, an enterprising journalist might have written an investigative piece on CAFOs for a major newspaper that might have caused a stir for moment or two, won some awards and then been filed in the  paper’s “morgue” (news-speak for library), only to be discovered a few years later by the next enterprising journalist. Or maybe the story would be written for a hip rock’n’roll magazine (“Boss Hog” / Rolling Stone).

There has been no shortage of well-researched articles, books, television news exposes, radio segments and documentaries on CAFOs over the last 20 years. But it has taken the web to unleash the power of the aggregate. Seen individually, these stories alarm. Seen together, their collective roar may finally manage to turn outrage into action.



Over the last week, articles in web publications The Huffington Post and Grist were among the first to connect the epidemiological dots pointing to a CAFO in Veracruz, Mexico as the probable of an outbreak of flu in a nearby town that sickened 1,800 people in early April.  Others, including this blog (“Follow the Pigs”) were on the trail as well, with content linked to research papers and reports – something not possible in the Age of Paper.

Obscure studies on swine viruses  – the kind of wonky detail usually of interest only to a handful of veterinarians –  were passed around the web as smoking gun evidence. Veratect, a private health & hazard surveillance company, published  a flu outbreak time line that included an entry explicitly flagging the outbreak in Veracruz as early as April 6 (10 days before the Mexican authorities alerted the Pan American Health Organization, and nearly 3 weeks before the WHO’s first meeting).

Even the genome of the virus itself was published online, a triumph of open source research for the greater good. There, for all to see, analyze and debate were eight tiny genetic segments of inconvenient truth: The virus was almost identical to a strain circulating in American pig farms for at least a decade. This was not a man-made virus, but was a man-mediated one. CAFOs clearly had played a pivotal role amplifying and spreading the disease, giving a swine virus plenty of opportunity to transform into a human threat.

A human outbreak wasn’t a matter of if or even when, but where.



There were plenty of warnings (Pew Commission on Industrial Animal Production report, “Multiple lineages of antigenically and genetically diverse influenza A virus co-circulate in the United States swine population” & “Swine Influenza Viruses: A North American Perspective”).

Yet despite the certainty of its genetic identity, the strain has been officially rechristened by the CDC and the WHO as  “H1N1” in a bold effort to quell a backlash against the pork industry. Good luck with that. H5N1 is still known bird flu or avian influenza, despite what poultry producers may prefer.

Not only will this re-branding effort fail, but it also obscures a connection of real value to public health: Flu viruses mix and match genetic components and jump species.

Even if it turned out this new tweaked human-friendly swine strain didn’t cause clinical illness in pigs (and it does), it is important to understand the connections in order to identify systemic vulnerabilities (CAFOs).

In the era of “One Health,” a surveillance approach that focuses on links between human, animal, plant and environmental health, it may be time to redefine zoonoses: Instead thinking of them as animal diseases that jump to humans, it may be more productive to see them as diseases that affect multiple species, including humans. Germ-jumping is a two-way street with human pathogens  jumping into other species. It’s not “us” versus “animals” but all of us animals versus germs.

“If you wait for the first human index case, you’ve lost critical time,” according to veterinary epidemiologist Tracey McNamara whom I interviewed after the West Nile outbreak a few years ago. McNamara played a key role making the link between dead crows and sick people and spearheaded using crows as an early warning for the virus.



twittervariationAs the week wore on, articles, studies and blog posts were flagged, linked, tweeted and retweeted on Twitter –  a torrent of information that quickly began to appear in stories produced by traditional media outlets.

Twitter’s value was not in its #swineflu message stream, which was was littered with gossip, misinformation and noise, but in streams in from individuals and news and health organizations:

@veratect, @microbeworld, @aetiology @nprhealth @bloodandmilk @wired @cdcemergency @trackernews (among others) Yet even the #swineflu stream provided a good sense of public concern.

Twitter fractured, inverted, pixelated and reconstructed the entire news cycle (ironically, not unlike a re-assorted flu virus). One example: Hours before the WHO officially announced it would raise the pandemic level to 5, Reuters put up a bulletin that promptly raced around the twitterverse. By the time officials gathered for news conference, it was old news.



Journalists chased after one another down dusty rutted roads to ground zero, the small town of La Gloria, a five-hour drive from Mexico City. There they met a four year-old with the dubious distinction of being earliest known victim of H1N1 swine flu, then trucked over to the nearby CAFO, Granjas Carroll, a subsidiary of American agro-giant Smithfield Foods, for a quick tour.

In report after report, the residents of La Gloria stuck to their story:

  • The CAFO had been a stinking health hazard since it opened
  • A swarm of flies from the Granjas Carroll’s hog waste pond invaded the town in  March / early April
  • Soon after half the town – about 1,800 people – became ill with what appeared to be flu
  • Granjas Carroll had been cleaned up for the press

They had been told by Mexican health officials they had a bacterial illness. One of the few samples saved and sent abroad for testing proved otherwise. Score one of the locals.

photo: Encyclopedia of Life, Phil Myers, Museum of Zoology, University of Michigan

photo: Encyclopedia of Life, Phil Myers, Museum of Zoology, University of Michigan

But can flies spread flu? There hasn’t been much research, though it’s not entirely out of the range of possibility. (Detection and isolation of highly pathogenic H5N1 avian influenza A viruses from blow flies collected in the vicinity of an infected poultry farm in Kyoto, Japan, 2004)

As for Granjas Carroll, a definitive link will probably never be made. It is simply too easy to lose the evidence. According the Smithfield website, Grajas processes 950,000 hogs annually, or about 80,000 per month. It takes between 5 and 6 months to raise a piglet to bacon-ready. I have been puzzling about the math, but clearly the turnover is ferociously rapid. Infected pigs, including those that might have had subclinical infections, could have easily been lost in the shuffle, or dumped into a waste pond to be feasted upon by flies.

It is important to note that swine flu, which is endemic in much of the United States and Mexico, is not a reportable disease, but seen more as a nuisance for farmers because it affects productivity and profits. Sick animals don’t fatten up as fast. Federal inspectors, already stretched to the limit, aren’t focused on it. Inspections, especially at such vast operations, are largely paperwork. Most likely it is a staffer rather than a government veterinarian that selects which animals to test, how many to test and who does the lab analysis. It would be surprising if blood samples were kept. And, finally, given the variety of strains that can circulate in a single herd, the effectiveness of vaccination has itself become question.

Wired.com’s Brendon Keim interviewed Columbia University epidemiologist / pathologist Ian Lipkin,  a member the WHO’s surveillance network: “We haven’t found evidence of infected pigs. But even if we never find that smoking pig, we can surmise that this is probably where it came from.”

CAFOs are where public health, environmental  health, food policy and global trade intersect. More and better regulations are urgently needed. Let’s make the most of this wake up call. The next time we probably won’t be so lucky.


more reading:

Pork industry is blurring the science of swine flu, Debora Mackenzie, New Scientist

Exclusive Interview: CDC Head Virus Sleuth, Science Insider, AAAS

Corridors of Power: Fidel Miramon? (photos of Granjas Carroll waste ponds – original in Spanish – cannot independently verify authenticity)

Interview with Ilaria Capua, founder of GISAID flu database, SEED magazine (print & video)

Poisoned Waters, PBS/Frontline (2-hour documentary on the destruction of the Chesapeake Bay and Puget Sound watersheds, includes section on chicken CAFOs)

7 Responses

  1. Hi, Excellent post, some really useful environmental information here and well worth knowing about.


  2. […] A Virus by Any Other Name: Lessons from an Outbreak (so far…) (TrackerBlog) […]

  3. Very nice, I sure will be coming back more often. I bookmarked your site also, thank you.

  4. Great read, had to re-read it a few times so I could process everything, but you seem to know what your talking about when it comes to animals!

  5. I really loved that post.I will be reading a lot more of this blog.But

  6. First-rate website. You have earned a recent fan. Please keep up the nice posts and I look forward to more of your fascinating updates.

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