New light on our common African history

The results suggest that all modern humans can trace their origin to a population that lived near the border between South Africa and Namibia – although Tishkoff stresses that these people may have moved into the area from elsewhere. As expected, the study also places the exit point for humanity's great "out of Africa" migration near to the Red Sea.

http://www.newscientist.com/article/dn17057-huge-gene-study-shines-new-light-on-african-history.html

The horror that is Smithfield ~ Rolling stone

Smithfield Foods actually faces a more difficult task than transmogrifying the populations of America's thirty-two largest cities into edible packages of meat. Hogs produce three times more excrement than human beings do. The 500,000 pigs at a single Smithfield subsidiary in Utah generate more fecal matter each year than the 1.5 million inhabitants of Manhattan. The best estimates put Smithfield's total waste discharge at 26 million tons a year. That would fill four Yankee Stadiums. Even when divided among the many small pig production units that surround the company's slaughterhouses, that is not a containable amount.

Smithfield estimates that its total sales will reach $11.4 billion this year. So prodigious is its fecal waste, however, that if the company treated its effluvia as big-city governments do -- even if it came marginally close to that standard -- it would lose money. So many of its contractors allow great volumes of waste to run out of their slope-floored barns and sit blithely in the open, untreated, where the elements break it down and gravity pulls it into groundwater and river systems. Although the company proclaims a culture of environmental responsibility, ostentatious pollution is a linchpin of Smithfield's business model.

A lot of pig shit is one thing; a lot of highly toxic pig shit is another. The excrement of Smithfield hogs is hardly even pig shit: On a continuum of pollutants, it is probably closer to radioactive waste than to organic manure. The reason it is so toxic is Smithfield's efficiency. The company produces 6 billion pounds of packaged pork each year. That's a remarkable achievement, a prolificacy unimagined only two decades ago, and the only way to do it is to raise pigs in astonishing, unprecedented concentrations.

Smithfield's pigs live by the hundreds or thousands in warehouse-like barns, in rows of wall-to-wall pens. Sows are artificially inseminated and fed and delivered of their piglets in cages so small they cannot turn around. Forty fully grown 250-pound male hogs often occupy a pen the size of a tiny apartment. They trample each other to death. There is no sunlight, straw, fresh air or earth. The floors are slatted to allow excrement to fall into a catchment pit under the pens, but many things besides excrement can wind up in the pits: afterbirths, piglets accidentally crushed by their mothers, old batteries, broken bottles of insecticide, antibiotic syringes, stillborn pigs -- anything small enough to fit through the foot-wide pipes that drain the pits. The pipes remain closed until enough sewage accumulates in the pits to create good expulsion pressure; then the pipes are opened and everything bursts out into a large holding pond.

The temperature inside hog houses is often hotter than ninety degrees. The air, saturated almost to the point of precipitation with gases from shit and chemicals, can be lethal to the pigs. Enormous exhaust fans run twenty-four hours a day. The ventilation systems function like the ventilators of terminal patients: If they break down for any length of time, pigs start dying.

From Smithfield's point of view, the problem with this lifestyle is immunological. Taken together, the immobility, poisonous air and terror of confinement badly damage the pigs' immune systems. They become susceptible to infection, and in such dense quarters microbes or parasites or fungi, once established in one pig, will rush spritelike through the whole population. Accordingly, factory pigs are infused with a huge range of antibiotics and vaccines, and are doused with insecticides. Without these compounds -- oxytetracycline, draxxin, ceftiofur, tiamulin -- diseases would likely kill them. Thus factory-farm pigs remain in a state of dying until they're slaughtered. When a pig nearly ready to be slaughtered grows ill, workers sometimes shoot it up with as many drugs as necessary to get it to the slaughterhouse under its own power. As long as the pig remains ambulatory, it can be legally killed and sold as meat.

The drugs Smithfield administers to its pigs, of course, exit its hog houses in pig shit. Industrial pig waste also contains a host of other toxic substances: ammonia, methane, hydrogen sulfide, carbon monoxide, cyanide, phosphorous, nitrates and heavy metals. In addition, the waste nurses more than 100 microbial pathogens that can cause illness in humans, including salmonella, cryptosporidium, streptocolli and girardia. Each gram of hog shit can contain as much as 100 million fecal coliform bacteria.

Smithfield's holding ponds -- the company calls them lagoons -- cover as much as 120,000 square feet. The area around a single slaughterhouse can contain hundreds of lagoons, some of which run thirty feet deep. The liquid in them is not brown. The interactions between the bacteria and blood and afterbirths and stillborn piglets and urine and excrement and chemicals and drugs turn the lagoons pink.

More at rolling stone

Economic Stress and swine flu..

Some researchers speculate that in 1918 immune systems were weakened by malnourishment and the stresses of life. The lower socioeconomic groups of Mexico had been very stressed by a collapse in the oil price and hence economic activity generally, the US recession in contruction, which has lead to vastly decreased remittances from family members working in the US.

CDC officials expect to see more severe cases in the U.S. as well - and as better epidemiological work is done in Mexico, we'll probably hear about more mild cases there too.

The true severity of the H1N1 swine flu virus is an open question. The 1918 Spanish flu pandemic began with a fairly mild wave of infections in the spring, but the virus returned a few months later in a far more virulent form. That could happen with the current swine flu as well. "It's quite possible for this virus to evolve," said Fukuda. "When viruses evolve, clearly they can become more dangerous to people."

Advice ignored: 65m hogs are concentrated in 65,000 facilities.

Six years ago, Science dedicated a major story to evidence that "after years of stability, the North American swine flu virus has jumped onto an evolutionary fasttrack".

Since its identification during the Great Depression, H1N1 swine flu had only drifted slightly from its original genome. Then in 1998 a highly pathogenic strain began to decimate sows on a farm in North Carolina and new, more virulent versions began to appear almost yearly, including a variant of H1N1 that contained the internal genes of H3N2 (the other type-A flu circulating among humans).

Researchers interviewed by Science worried that one of these hybrids might become a human flu (both the 1957 and 1968 pandemics are believed to have originated from the mixing of bird and human viruses inside pigs), and urged the creation of an official surveillance system for swine flu: an admonition, of course, that went unheeded in a Washington prepared to throw away billions on bioterrorism fantasies.

But 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.


Last year a commission convened by the Pew Research Center issued a report on "industrial farm animal production" that underscored the acute danger that "the continual cycling of viruses … in large herds or flocks [will] increase opportunities for the generation of novel virus through mutation or recombinant events that could result in more efficient human to human transmission." The commission also warned that promiscuous antibiotic use in hog factories (cheaper than humane environments) was sponsoring the rise of resistant staph infections, while sewage spills were producing outbreaks of E coli and pfiesteria (the protozoan that has killed 1bn fish in Carolina estuaries and made ill dozens of fishermen).

Any amelioration of this new pathogen ecology would have to confront the monstrous power of livestock conglomerates such as Smithfield Farms (pork and beef) and Tyson (chickens). The commission reported systemic obstruction of their investigation by corporations, including blatant threats to withhold funding from cooperative researchers .

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.

This is not to say that a smoking gun will never be found: there is already gossip in the Mexican press about an influenza epicentre around a huge Smithfield subsidiary in Veracruz state. But what matters more (especially given the continued threat of H5N1) is the larger configuration: the WHO's failed pandemic strategy, the further decline of world public health, the stranglehold of big pharma over lifeline medicines, and the planetary catastrophe of industrialised and ecologically unhinged livestock production.

http://www.guardian.co.uk/commentisfree/2009/apr/27/swine-flu-mexico-health

Two little pigs cooked up disaster ~ Swine Flu

according to wired...

The deadly H1N1 influenza virus that’s fueling fears of a global pandemic appears to be a hybrid of two common pig flu strains, scientists who have studied the disease told Wired.com Tuesday. Earlier reports called it a combination of pig, human and avian influenza strains.

The findings may resolve some uncertainty about the nature of the virus, but much is still unknown about its origins and effects.

“This is what we call a reassortment between two currently circulating pig flu viruses,” said Andrew Rambaut, a University of Edinborough viral geneticist. “Why it’s emerged in humans is anyone’s guess. It hasn’t been seen before in pigs as far as I know.”

Rambaut analyzed the gene sequences of viral samples taken from two infected California children. The samples were collected by the Centers for Disease Control and Prevention, and made available to researchers through an international database of flu genomes.

His conclusions were echoed by Eddie Holmes, a virus evolution specialist at the University of Pennsylvania, and Steven Salzberg, a University of Maryland bioinformaticist. Both have looked at the CDC-provided sequences. The CDC could not be reached for comment, but a document released to scientists and obtained by Wired.com affirms their analysis.

Researchers believe the samples from California represent the same viral strain as one that is believed to have killed as many as 150 of an estimated 1,600 hospitalized Mexicans, and caused hundreds more infections worldwide, including at least 64 in the United States. However, as samples from Mexico have not yet been sequenced, the similarity is not conclusive.

The two strains whose genes are found in the California samples belong to influenza families known generally as North American and Eurasian pig flu. The former was first described in the 1930s, and the latter in 1979. The Eurasian strain is generally found in Europe and Asia, rather than North America.

Neither of the strains have ever proven contagious in humans. One of the genes inherited from the Eurasian strain has reportedly never been seen in humans. It codes for the neuraminidase enzyme — the N1 in H1N1 — which controls the expansion of the virus from infected cells.

“The new neuraminidase gene that came in from Eurasian swine is one we’ve never before seen circulating in humans,” said Rambaut. “That’s one of the reasons it’s spreading rapidly. Very few people will have any immunity to this particular combination, which is what gives the concern that this will be a pandemic rather than just a normal seasonal flu outbreak. It remains to be seen how much and to what extent there is existing immunity.”

In medical terms, the genetic origins of the virus may not matter. Whether it come solely from pigs rather than a mix of pigs, birds and humans doesn’t change its immunological novelty.

However, understanding the origins could eventually help scientists determine how the virus evolved and where it originally emerged.

The earliest cases occurred in the town of La Gloria in the Mexican state of Veracruz, not far from a large and notoriously unsanitary hog farm operated by Granjas Carroll, a subsidiary of giant American food company Smithfield Foods.

Vercruz residents and some journalists have alleged that the virus could have evolved in the farm’s pigs, then passed into humans through water or insects tainted by infected waste. Many researchers, including the authors of a report issued last year by the Pew Commission on Industrial Farm Animal Production, have warned that unsanitary conditions at industrial hog farms could prove a breeding ground for new forms of influenza.

The World Health Organization has sent inspectors to the Granjas Carroll farm. The results of the investigation have not been announced. Smithfield issued a press release on Saturday stating 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.” The company declined further comment, though CEO Larry Pope told USA Today that “(The term) swine flu is a misnomer.”

Rambaut, Holmes and Salzberg declined to speculate on whether the new H1N1 virus evolved on a hog farm or specifically in the Granjas Carroll facility.

However, it seems likely that pigs were the original host.

“That’s a logical conclusion,” said Salzberger. “It was probably two different pigs, or one who got co-infected from others. The two strains mixed, and now you have a brand-new strain.”

“Presumably somewhere there was a pig infected with both forms. We don’t know where or when. It could have been circulating in this form for a while,” said Rambaut.

What comes next is anyone’s guess.

“Influenza virus mutates remarkably rapidly so there is no doubt that the virus will mutate and evolve in humans,” said Holmes. “Quite what this evolution will result in is difficult to tell.”

http://tinyurl.com/d8jf4w

Swine Infuenza Q and A from TED ~ Nathan Wolfe, Q&A, TED2009

.

SARS, avian flu, swine flu ... what's going on here? Why are we suddenly seeing so many more outbreaks of viruses from animals?

Viruses have always passed from humans to animals. In fact, the vast majority of human diseases have animal origins. But the human population is different from what it once was. For most of our history, we lived in geographically disparate populations. So viruses could enter from animals into humans, spread locally and go extinct. But the human population has gone through a connectivity explosion. All humans on the planet are now connected to each other spatially and temporally in a way that's unprecedented in the history of vertebrate biology. Humans -- as well as our domestic animals and wild animals we trade -- move around the planet at biological warp speed. This provides new opportunities for viruses that would have gone extinct locally to have the population density fuel they need to establish themselves and spread globally.

We've created a "perfect storm" for viruses. And we'll continue to see -- as we have in the past few years -- a whole range of new animal diseases as outbreaks in human populations. But we have to stop being surprised by them. Right now, global public health is like cardiology in the '50s -- just waiting for the heart attack, without understanding why they occur or the many ways to monitor for them, detect them early and ultimately prevent them. Swine flu is not an anomaly. We know that swine flu -- like the vast majority of new outbreaks -- comes from animals. We should be monitoring those animals and the humans that come into contact with them, so we can catch these viruses early, before they infect major cities and spread throughout the world.

Can we stop swine flu? Or is it too late?
If you catch one of these outbreaks early on, there may be the potential to do what we call containment, where you limit the outbreak to a particular site. But the reality is: By the time swine flu got on the radar screen of global public health, it had already spread. It was already in the States, it was in Mexico, it was in New Zealand. By the time it reaches that point, you've lost the ability to contain it. There are ways to decrease the spread of the pandemic, but by that point, it can't be contained. (Editor's note: See Larry Brilliant's 2006 TEDTalk for more on the importance of early containment.)

The more fundamental question is: How do we prevent these pandemics from occurring? There are commonalities among all the pandemics that occur, and we can learn from them. One commonality is that they all come from animals. And the other commonality is that we wait too long.

At the Global Viral Forecasting Initiative, our approach is to take it a step back. If we can contain and monitor animal viruses at an earlier stage -- when they're first entering human populations, preferably before they've had a chance to become human-adapted, certainly before they've had a chance to spread -- we can head off pandemics altogether.

Swine flu may or may not end up being an important human pandemic. But it's a perfect illustration of the need for a paradigm shift in the way we approach global disease control.

In your TEDTalk, you lay out plans for monitoring humans who have close contact with animals in African jungles and Asian "wet markets." Should you be monitoring pig farms as well?

Absolutely. What we do is all of the above. We monitor people with contact with wild animals as well as domestic animals. Chickens, ducks, pigs, monkeys ... wherever people have contact with animals, that's where we want to be, so we can catch potential pandemics at the moment that they're born.

The good news is: For a variety of reasons, the percentage of the human population that's in direct contact with animals is decreasing. So that gives us the potential to put a substantive percentage of that population into regular monitoring. Maybe we won't catch everything, but we can create a much more substantive safety net for capturing these things before they go international or global.


READ MORE: Nathan Wolfe talks about why swine flu victims are dying in Mexico but not yet in the US; how swine flu is a "cosmopolitan virus"; and more ...

Your Global Viral Forecasting Initiative is expanding worldwide, but mainly in Asia and Africa. If you were in Mexico, how might things have gone differently?

In this case, we would have hoped to catch and contain swine flu when there were just dozens -- instead of hundreds or thousands -- of cases in Mexico, and before it spread globally.

GVFI's objective is to monitor the portal of entry for new diseases into human populations -- that means looking at the point at which humans and animals interface. We work with people who have high exposure to animals throughout the world, whether that means exposure to domestic animals -- as with farm workers -- or wild animals, as with people who hunt bushmeat in Africa or people who work in live animal markets in Asia. The minute we see new viruses that are entering into humans, we make this information available for the public health community, so we can develop drugs and diagnostics and potentially vaccines based on them.

When we see new diseases spreading in local communities, we monitor them very closely. If we were working in Mexico -- and we were doing our jobs correctly -- we would have caught this thing, perhaps in rural villages, before it made it to a site like Mexico City, and before it went international.

How do we understand the difference between the cases reported in Mexico, where many have died, and those in the US, which seem very mild?

There is a striking anomoly between what appears to be a very low rate of mortality and illness among the American cases and what appears, on the surface, to be a higher rate of illness among the Mexican cases. It could, of course, be the result of a difference in the viruses, although that doesn't necessarily appear to be the case. It could be a difference in host populations, although again, that's difficult to explain.

One possibility is that because we've looked more carefully for cases in the States, we're more likely to see individuals who are mildly ill. We might find that if we looked more comprehensively in Mexico, we'd see the same number of people who were very ill -- because they're easy to find -- and a much larger number of people who were mildly ill. That would reduce the actual rate of mortality to a much lower number, and that may be more compatible with what we would see if the number increased in the American epidemic.

As the number of cases climb worldwide, many people are comparing this swine flu outbreak to the 1918 flu pandemic. Is that an apt comparison?

Well, they both represent novel introductions of influenza into human populations that were capable of spreading substantively. The 1918 flu was notable in the sense that it spread comprehensively, globally, and it had a very high rate of mortality -- affecting not only the very old or very young (who have weak immune systems) but also people in the prime of their lives, who are overcome by their body's own immune response.

Whether or not this happens with swine flu remains to be seen. Initially, it does not appear to have the level of deadliness that the 1918 flu had.

I love bacon. Am I at risk?

Go ahead and have that BLT. It's not a problem. You can't get swine flu from eating pork. You'd have to have close contact with a living, breathing, infected pig to get this virus -- or rather, in order to have contracted the original pig virus. The interesting and important thing about this "pig flu" is that it's now spreading from human to human. It's become a human virus.

So people should take the usual precautions: Stay away from individuals who are sick. Wash your hands frequently. And the less you touch your face, nose and eyes, the better.

Take us back a step or two: How did swine flu enter into the human population?

Swine flu has been known since at least the early part of the 20th century, since the 1930s. It was originally a virus of bird origin -- all influenza viruses were originally bird viruses -- and it probably spread to humans before it was in pigs.

Now, we still haven't received definitive information on the underlying genetics of this particular virus. But initial reports suggest that it may be what's known as a "mosaic virus," which includes components of swine influenzas, bird influenzas and human influenzas. A cosmopolitan virus like that wouldn't be unprecedented. (Editor's Note: see Joe DeRisi's 2006 TEDTalk for more on state-of-the-art virus detection.)

But in any case, this is a virus that appears to come from pigs, and pigs in close proximity spread the flu in much the same way that humans do -- coughing, sneezing, and so on. The virus probably initially entered into human populations through people who work with livestock.

Is swine flu here to stay?

Whether this particular virus will sustain itself and become a permanent part of the human landscape is unclear, but that's certainly what we're watching for. As it is, the virus may just disappear because of the weather; summers aren't good for flu viruses.

So this heat wave is working in our favor?

It might be. The virus has had a good start, from the flu perspective, considering that this is really the end of the season. But the unseasonably hot weather may bode poorly for this virus' potential to establish itself definitively and cause a pandemic. Had this happened in September or October, it would be much more concerning.

Having said that, it's not impossible that a virus like this might "go into hiding" -- in the southern hemisphere or the tropics -- and might come to light again next year. So there will be a lot of discussion about expanding the fall flu vaccine to try to control it next cycle.

Is it really possible for us to prevent future outbreaks like this?

Yes, I believe it is. We spend tons of money trying to predict complex phenomena like tsunamis, hurricanes, earthquakes. There's no reason to believe that a pandemic is harder to predict than a tsunami. And we'd be foolish not to include forecasting and prevention as part of our overall portfolio to fight these pandemics.

Swine flu and Industrial scale pig farms ~ western owned

The boy’s hometown, La Gloria, is also close to a pig farm that raises almost 1 million animals a year. The facility, Granjas Carroll de Mexico, is partly owned by Smithfield Foods, a Virginia-based US company and the world’s largest producer and processor of pork products. Residents of La Gloria have long complained about the clouds of flies that are drawn the so-called “manure lagoons” created by such mega-farms, known in the agriculture business as Confined Animal Feeding Operations (CAFOs).
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It is now known that there was a widespread outbreak of a powerful respiratory disease in the La Gloria area earlier this month, with some of the town’s residents falling ill in February. Health workers soon intervened, sealing off the town and spraying chemicals to kill the flies that were reportedly swarming through people’s homes.

A spokeswoman for Smithfield, Keira Ullrich, said that the company had found no clinical signs or symptoms of the presence of swine influenza in its swine herd or its employees working at its joint ventures anywhere in Mexico. Meanwhile, Mexico’s National Organisation of Pig Production and Producers released its own statement, saying: “We deny completely that the influenza virus affecting Mexico originated in pigs because it has been scientifically demonstrated that this is not possible.”

According reports gathered on the website of James Wilson, a founding member of the Biosurveillance Indication and Warning Analysis Community (BIWAC), about 60 per cent of La Gloria’s 3,000-strong population have sought medical assistance since February.

“Residents claimed that three pediatric cases, all under two years of age, died from the outbreak,” wrote Mr Wilson. “However, officials stated that there was no direct link between the pediatric deaths and the outbreak; they said the three fatal cases were isolated and not related to each other.”

The case of the four-year-old boy was announced yesterday by Mexico’s Health Minister, Jose Angel Cordova, at a press conference that was briefly interrupted by an earthquake. “We are at the most critical moment of the epidemic. The number of cases will keep rising so we have to reinforce preventive measures,” he said, adding that in addition to the 149 deaths another 2,000 had been hospitalised with “grave pneumonia”, although at least half of that number had since made a full recovery.