Bird Flu Book

“If you get a [H5 or H7] virus into a high-density poultry operation and give it a period of time, generally a year or so, then you turn that virus into a highly virulent virus. That’s what always happens….”2005 Canada’s National Manager of Disease Control within the Food Inspection Agency seems to agree: “Just passing the virus to 3,000 or 4,000 chickens is enough to change a harmless virus into something more pathogenic.”5006 “It is high-density chicken farming that gives rise to highly-virulent influenza viruses,” Brown concluded. “That’s pretty clear.”2007

The Netherlands outbreak showed not only that intensive chicken farms may brew a virus capable of human-to-human transmission, but that such a strain can arise in an advanced industrialized country with modern, high-tech poultry facilities.2020

We can learn from past mistakes. In the early 1970s, for example, the U.S. corn industry developed “Tcms” corn, a highly profitable strain adapted for large-scale farming. Only after 85% of the nation’s seed corn acreage was covered with the new variety did the industry realize that the strain also happened to be particularly susceptible to a rare form of leaf blight fungus that then wiped out areas of the U.S. corn belt.1932

Biodiversity is biosecurity. Even the most virulent of diseases typically do not kill all infected individuals, in part due to natural inborn genetic variability. In the wild, natural selection takes advantage of this variation to pass disease-resistant qualities to the next generation.1937 The diversity in nature tends to ensure that some individuals will survive whatever comes along. Artificial selection for production qualities undermines Mother Nature in two ways, by inbreeding unnaturally elevated egg production and fleshiness over fitness, as well as by reducing the genetic diversity that can act as resistance insurance against present and unforeseen threats of disease.1938

That’s why we’ve been so concerned about pigs. Ducks have the 2,3 linkages, humans have the 2,6 linkages, and pigs have both. So, in a pig, the duck virus could theoretically accustom itself to our receptors and burst throughout the human population.1586 Unfortunately for the human race, researchers recently discovered that chickens have human 2,6 receptors in their lungs as well.1587

Just a single point mutation may change a virus that binds duck 2,3 receptors to a virus that binds human 2,6 receptors.1594 The researchers who resurrected the 1918 virus found that the receptor binding site on the virus differed from the binding site of its presumed avian precursor by just one or two tiny amino acid substitutions, presumably all it needed to go human.

In nature, the influenza virus has existed for millions of years as a harmless intestinal waterborne infection of waterfowl, particularly ducks.1510 The duck doesn’t get sick, because the virus doesn’t need to make the duck sick to spread. In fact, it may be in the virus’s best interest for the bird not to get sick so as to spread farther. Dead ducks don’t fly.

“Humans have altered the natural ecosystems of birds through captivity, domestication, industrial agriculture, and nontraditional raising practices. This has created new niches for AI [avian influenza] viruses….”1537

In aquatic birds, the virus is and has been in total evolutionary stasis.1542 But, when thrown into a new environment, it quickly starts accumulating mutations to try to adapt to the new host.1543 The virus must mutate or die.1544 “Unless it mutates,” said one renowned flu researcher, “and unless a new mutant is selected, it’s going to disappear.”1545 Thankfully for the virus, mutating is what influenza does best.1546

The hemagglutinin spike of H5 and H7 viruses can mutate over time to be activated by enzymes in any organ in the body, allowing the virus to go on a rampage and essentially liquefy the bird from the inside—the “flubola” phenomenon of highly pathogenic avian influenza.1549

If a virus kills the host too quickly, there is less opportunity to spread in both time and space. Just as dead ducks don’t fly, dead rabbits don’t hop. Unless farmers could cram rabbits by the thousands into some kind of bunny barn, viral mutants with diminished lethality may have an overall advantage since the host may stay alive longer and have more occasion to pass on the virus. This is a risky strategy for the virus—if it becomes too weak, the hosts’ defenses may quash it completely. Natural selection mediates this evolutionary process, choosing over time the virus with the perfect balance of lethality and contagion.1558

Chickens and ducks, geese and quail are crammed into small plastic cages stacked as much as five high in these live animal “wet” markets. Distressed birds defecate on those below them.1353 Feathers and feces are everywhere.1354 So are blood and intestines.1355 According to the World Health Organization, the birds are often slaughtered on the spot, “normally with very little regard for hygiene.”1356 “The activities of humans have affected the evolution of influenza,”

“And birds under stress are much more prone to disease.”1383

The sialic acid receptors lining the intestines of ducks have what are called alpha-2,3 linkages, whereas human lungs have sialic acid receptors with alpha-2,6 linkages. Influenza strains tend only to bind effectively with one type of receptor or the other. This difference in receptor compatibility helps form a species barrier, keeping the bird strains in the birds and the human strains in the humans.1286

in August 1998, a barking cough resounded throughout a North Carolina pig farm in which all the thousands of breeding sows fell ill. An aggressive H3N2 virus was discovered, the type of influenza that had been circulating in humans since 1968. Not only was this highly unusual—only a single strain of human virus had ever previously been isolated from an American pig population—but upon sequencing of the viral genome, researchers found that it was not just a double reassortment (a hybrid of human and pig virus, for example) but a never-before-described1291 triple reassortment, a hybrid of three viruses—a human virus, a pig virus, and a bird virus.

the primary route of swine flu transmission is thought to be the same as human flu—via droplets or aerosols of infected nasal secretions1303

Analyzing the genome of H5N1, scientists now suspect that the 1997 outbreak arose when an H5 goose virus combined with an N1 duck virus with quail acting as the mixing vessel (another species “raised under battery conditions”1253 ). The virus then jumped from quail to chickens and then from chickens to humans.1254



In 2001, in what seems to be a separate emergence, that same H5 goose virus combined with an N1 duck virus in a duck, then jumped to chickens directly, bypassing the quail.1255 In both cases, the H5 virus first isolated from a farmed domestic goose population in Guangdong province was found,1256 surprisingly, to be already partially adapted to mammals.1257 Scientists speculate that this could have been a result of the virus acclimating to a pig, especially, perhaps, given Asia’s unique fish-farming technique.1258

The influenza virus found naturally and harmlessly in ducks’ intestines are excreted in the water. The chickens may drink the virus-laden water. The pigs then eat the virus-laden chicken feces. The ducks then drink the pond water contaminated by the virus-laden pig excrement and the cycle can continue.

Because of its extreme mutation rate, influenza is a perpetually emerging disease. Anthony Fauci, the NIH’s pandemic planning czar, calls it “the mother of all emerging infections.”1249

The changes in the digestive tracts of cattle fattened in feedlots with energy-dense grain to marble the flesh with saturated fat (instead of natural cattle foodstuffs like hay) has been blamed for the emergence of E. coli O157:H7. Grain-fed beef may be more tender, but grass-fed beef may be safer.1184

Factory farms are considered such breeding grounds for disease that much of the animals’ metabolic energy is spent just staying alive under such filthy, crowded, stressful conditions;1188 normal physiological processes like growth are put on the back burner.1189

The majority of the antibiotics produced in the world go not to human medicine but to prophylactic usage on the farm.1194 This may generate antibiotic resistance.

there was a tremendous environmental pressure on the virus to mutate resistance to the antiviral

microbiologists are aware of, and understand, the weight of evidence linking the subtherapeutic use of antibiotics with the emergence of resistant bacteria.

The poultry industry blames the dramatic rise in antibiotic-resistant bacteria on the overprescription of antibiotics by doctors.1215 While doctors undoubtedly play a role, according to the CDC, more and more evidence is accumulating that livestock overuse is particularly worrisome.1216

Science editor-in-chief Dr. Kennedy, who served as commissioner of the U.S. Food and Drug Administration, describes the antibiotic debate as a “struggle between good science and strong politics.” When meat production interests pressured Congress to shelve an FDA proposal to limit the practice, Kennedy concluded: “Science lost.”2193

The reality is that these birds exist under such grossly unsanitary conditions, cramped together in their own waste, that the industry feels forced to lace their water supply with antibiotics. “Present production is concentrated in high-volume, crowded, stressful environments, made possible in part by the routine use of antibacterials in feed,”

bacteria seem to be evolving resistance faster than our ability to create new antibiotics. “It takes us 17 years to develop an antibiotic,” explains a CDC medical historian. “But a bacterium can develop resistance virtually in minutes.

farm practice is the continued feeding of slaughterhouse waste, blood, and excrement to livestock to save on feed costs.1074

The livestock industry has experimented with feeding newspaper, cardboard, cement dust, and sewer sludge to farm animals.1076

In modern corporate agribusiness, protein concentrates (or “meat and bone meal,” euphemistic descriptions of “trimmings that originate on the killing floor, inedible parts and organs, cleaned entrails, fetuses…”1080 ) are fed to dairy cows to increase milk production,1081 as well as to most other livestock.1082

Unfortunately, the United States still feeds some of these potentially risky tissues to people, pigs, pets, poultry, and fish.1102 Then pig remains can be fed back to cattle.1103 Cattle remains are still fed to chickens, and poultry litter (the mixture of excrement, spilled feed, dirt, feathers, and other debris that is scooped from the floors of broiler sheds1104 ) is fed back to cows.1105

The American Protein Corporation is the largest spray-dryer of blood in the world1141 and advertises blood products that can even be fed “through the drinking water” to calves and pigs.1142

yet the U.S. government still allows dairy farmers to feed calves gallons of a mixture of concentrated cow blood and fat collected at the slaughterhouse.1148

According to the executive editor of Meat Processing magazine, “Nearly every food consumers buy in supermarkets and order in restaurants can be eaten with certainty for its safety—except for meat and poultry products.”1013

the overwhelming majority of the 9 billion chickens raised each year are stocked in densities between 10 and 20 birds per square yard,1016 ,1017 unable even to stretch their wings.1018 Under this avian carpet is a fecal carpet of filth most of the birds spend their lives upon.1019

Combined with the stress associated with overcrowding and poor water quality, it is not hard to imagine how the factory farming methods associated with the so-called “Blue Revolution” expansion of fish farming in the 1980s1023 resulted in the emergence of another zoonotic disease.1024

Medical researchers at the University of Minnesota published a clue to the mystery in the April 2005 issue of the Journal of Infectious Disease. Taking more than 1,000 food samples from multiple retail markets, they found evidence of fecal contamination in 69% of the pork and beef and 92% of the poultry samples as evidenced by E. coli contamination. More surprising was that more than 80% of the E. coli they recovered from beef, pork, and poultry were resistant to one or more antibiotics, and greater than half of the samples of poultry bacteria “were resistant to >5 drugs!”

Veterinarian and academician David Waltner-Toews writes in his book Food, Sex, and Salmonella, “The most serious problems [with foodborne disease] invariably come back to the willingness of pureblooded capitalists to take risks with other people’s lives.”1064

Campylobacter is a spiral-shaped poultry bacteria1053 that corkscrews its way into the lining of the intestine “with a speed that cannot be matched by other bacteria.”1054 Just as H. pylori bacteria has been linked to stomach cancer, Campylobacter, according to a 2004 report in the New England Journal of Medicine, may trigger cancer as well, a rare lymphoma of the intestines.1055 Campylobacter, not even proven to cause human illness until the 1970s,1056 is now the suspected cause of up to 25% of cases of irritable bowel syndrome1057 and is currently the number-one bacterial cause of food poisoning, sickening millions of Americans every year.1058

In the United States, farm animals produce more than one billion tons of manure each year—the weight of 10,000 Nimitz-class aircraft carriers.974 That is one huge load of crap. Each steer can produce 75 pounds of manure a day, turning feedlots into wading pools of waste.975

Treatment may be given to sows for metritis, mastitis, and for diseases such as erysipelas and leptospirosis. In most indoor herds antibiotic treatment starts soon after birth. Piglets will receive drugs for enteritis and for respiratory disease. From weaning (usually three weeks) all piglets are gathered, mixed and then reared to finishing weights. Weaners usually develop post-weaning diarrhea caused by E. coli which occurs on day 3 post-weaning…. Post-weaning diarrhea is quickly followed by a range of other diseases. Glasser’s Disease (haemophilus parasuis) occurs at 4 weeks, pleuropneumonia at 6–8 weeks, proliferative enteropathy from 6 weeks and spirochaetal diarrhea and colitis at any time from 6 weeks onward…. At 8 weeks the pigs are termed growers and moved to another house. Here they will develop enzootic pneumonia, streptococcal meningitis (Streptococcus suis), and, possibly, swine dysentery. Respiratory disease may cause problems until slaughter.979

The USDA cites a loss of genetic diversity in herds and flocks.988 A former chief of the Special Pathogens Branch of the CDC explains: “Intensive agricultural methods often mean that a single, genetically homogeneous species is raised in a limited area, creating a perfect target for emerging diseases, which proliferate happily among a large number of like animals in close proximity.”989

With billions of feathered and curly-tailed test-tubes for viruses to incubate and mutate within, a WHO official described the last few decades as “the most ambitious short-term experiment in evolution in the history of the world.”995

Raising pigs is not new in Malaysia, but intensive industrial production is. The Leong Seng Nam farm, where the epidemic broke out, confined more than 30,000 pigs. The Nipah virus, like all contagious respiratory diseases, is a density-dependent pathogen,925 requiring a certain threshold density of susceptible individuals to spread, persist, and erupt from within a population.926

The USDA explains that this bacteria can exist as a harmless component of a pig’s normal bacterial flora, but stress due to factors like crowding and poor ventilation can drop the animal’s defenses long enough for the bacteria to become invasive and cause disease.937

Even industry groups like the American Association of Swine Veterinarians blame “[e]merging livestock production systems, particularly where they involve increased intensification” as a main reason why zoonotic diseases are of increasing concern. These intensive systems, in addition to their high population density, “may also generate pathogen build-ups or impair the capacity of animals to withstand infectious agents.”949

Increasing consumer demand for animal products worldwide over the past few decades has led to a global explosion in massive animal agriculture operations which have come to play a key role in the Third Age of emerging human disease.950

Given that “highly crowded” animals are reared in “extreme proximity” in the United States, one infected animal could quickly expose thousands of others.887

Herds that have been subjected to such modifications—which have included everything from sterilization programs to dehorning, branding, and hormone injections—have typically suffered higher stress levels that have lowered the animals’ natural tolerance to disease from contagious organisms and increased the viral and bacterial “volumes” that they normally shed in the event of an infection.888

“Transport of livestock is undoubtedly the most stressful and injurious stage in the chain of operations between farm and slaughterhouse,” leading to significant “loss of production.”866 This stress impairs immune function, increasing the animals’ susceptibility to any diseases they might experience on their prolonged, often overcrowded journeys.867

“All considered,” wrote two chief wildlife veterinarians in the Council on Foreign Relations journal Foreign Affairs, “at least a billion direct and indirect contacts among wildlife, humans, and domestic animals result from the handling of wildlife and the wildlife trade annually.”842

Growing populations and increasing demands for wildlife meat exceed local supplies of these animals.859 This has resulted in an enormous (and largely illegal) transboundary trade of wildlife and the setting up of intensive captive production farms in which wild animals are raised under poor sanitation in unnatural stocking densities. These animals are then packed together into markets for sale. All of these factors favor the spread and emergence of mutant strains of pathogens capable of infecting hunters, farmers, and shoppers.860

Animals sold live guarantee freshness in the minds of consumers, but in all their “freshness,” the animals cough and defecate over one another, spewing potential pathogens throughout the market wet with blood and urine.862 These viral swap meets are blamed for the transformation of a class of viruses, previously known for causing the common cold, into a killer.863

Having finally sequenced the genome of the chimpanzee, though, scientists realize we may share more than 95% of our DNA with our fellow great apes.818 “Darwin wasn’t just provocative in saying that we descend from the apes—he didn’t go far enough,” one primatologist said. “We are apes in every way….”819 By cannibalizing our fellow primates, we are exposing ourselves to pathogens particularly fine-tuned to human primate physiology.

Developers chopped America’s woods into subdivisions, scaring away the foxes and bobcats who had previously kept mouse populations in check. Animal ecologists recover some seven times more infected ticks from 1- and 2-acre woodlots than lots of 10 to 15 acres. The pioneer in this area concluded, “You’re more likely to get Lyme disease in Scarsdale than the Catskills.”810

“Mostly these days,” wrote one prominent medical microbiologist, “it is man’s intrusion on the natural environment which is the all-important key to emerging viruses.”803

In the accompanying Lancet editorial, we are reminded that zoonotic cross-species infections are “among the most important public health threats facing humanity.”830

Australia’s National Centre for Epidemiology and Population Health says we shouldn’t be surprised by the recent explosion in zoonotic disease given recent environmental changes. “We need to think ecologically,” he said. “These viruses are trying to evolve.”785 Just as plants and animals in the wild try to adapt to new environments to spread their species, viruses also expand to exploit any newly exposed niches. “Show me almost any new infectious disease,” said the executive director of the Consortium of Conservation Medicine, “and I’ll show you an environmental change brought about by humans that either caused or exacerbated it.”786

Two centuries ago, Edward Jenner, the founder of modern vaccines, proposed that the “deviation of man from the state in which he was originally placed by nature seems to have proved him a prolific source of diseases.”788 This observation dates back to the 2^nd century, when Plutarch argued that new classes of diseases followed profound changes in the way we live.789 The same can be said for animals. “Something is not right,” reflects Professor Shortridge. “Human population has exploded, we are impinging on the realms of the animals more and more, taking their habitats for ourselves, forcing animals into ever more artificial environments and existences.”790

According to the World Health Organization’s coordinator for zoonoses control, “The chief risk factor for emerging zoonotic diseases is environmental degradation by humans….”791 This includes degradation wrought by global climate change, deforestation, and, as described by the WHO, “industrialization and intensification of the animal production sector.”792

Medical historians have long conjectured that the reason there were so many plagues in Eurasia was that “crowd” diseases required large, densely-populated cities, unlike the presumed small tribal bands of the Americas. But that presumption turned out to be wrong. "New world" cities like Tenochtitlan were among the most populous in the world.775