Swine Flu News

Readers might have wondered why Effect Measure has held the number one spot in my "Blogs I'm Reading now" list. I started reading Effect Measure, an epidemiologists' blog, when I was interested in avian flu and backyard chickens. Mainstream news outlets were desperately trying to take an evolving science story and fit it into the "beginning, middle and end" story formula, preferably with a gripping headline that would get us tuning in again tomorrow and the next day. Effect Measure's editors were engaging in a more collaborative investigation that was much more interesting and to which I, as a backyard chicken keeper, could occasionally contribute some practical observations.

Now, with the swine flu news getting similar treatment, I recommend Effect Measure to readers who want up to date news and science without the premature conclusions. I'm also stocking up on Lysol spray, decongestants, garlic, and chicken soup.

More on what people do with chickens

This is the Denizli Horozu rooster of Turkey, a breed that has been bred for its long crow. I had no idea this sort of bird existed until I saw it on YouTube, and even then I thought at first that it was a joke.

But, as the Turkish Ministry of Culture tells us in this oddly translated page, the roosters of the city of Denizli are a local treasure, providing a sense of place from dawn's first crow.

The sound of Denizli roosters are classified according to the tone and clearness. According to sound tones they are divided into 3 groups: İNCE, DAVUDİ, KALIN SES. Davudi (bass) voice is between high pitched and deep voice and is the only sound close to deep voice. According to clearness, they are divided into 4 groups, namely: SAD VOICE, SHRILL VOICE, WAVY VOICE (FUNNY VOICE).

Crowing of Denizli roosters is performed upon use of all abilities. Crowing is divided into 4 groups depending on body position during crowing, which are LION CROWING, WOLF CROWING, HERO CROWING, PUS CROWING.

A good Denizli Rooster must have: alive apearance, long and strong legs and neck, wide and deep chest, sharp and sloped toward head tail. The same features are true for the chicken. The crowing period of Denizli Roosters in the first year must be 20 to 25 seconds.

The article contains a refutation of rumours that Denizli roosters are a result of crossbreeding with Albanian birds and a local homily,

Each rooster crows at its own place,
But Denizli Rooster crows everywhere.

These people are passionate about their local breed of chicken!

Humans and chickens have evolved together since prehistory, with many interesting local variants. I have felt an urgency about publicizing these variants since I read in 2006 about a plan to fight avian flu by replacing the world's infinite variety of chicken breeds with a new genetically-modified flu resistant strain. The idea starts out innocent enough, but it is the sort of cultural misunderstanding that starts wars.

It seems crazy, but I really think I can promote peace by raising awareness of the world's peoples' chicken practices.......

Microchips on the Farm

I've been watching the growing controversy about the microchip tracking of farm animals for about six months. This week it made national news in a NYTimes article:

A federal effort to quickly pinpoint and contain outbreaks of disease among livestock is coming under attack on farms, in Internet chat rooms and at livestock markets, ranches and feed shops across the nation.

Although the effort, the National Animal Identification System, intended to trace a sick animal to the property it came from within 48 hours, is still in early, voluntary stages, the United States Department of Agriculture has had to retreat from a proposal to make it mandatory. Officials now say that further participation will result from financial incentives and market pressure.

I'm glad that the feds are backing off the program, which I suspect was propelled in part by microchip manufacturers looking for new markets. (There has also been a similar push to implant US servicemen with microchips). Once again, we see policy makers who have very little knowledge of the various ways in which people interact with animals.

When I get day-old chicks, they cost about $1.25 each, shipped in the US Mail in lots of 25. They are remarkably hardy, but I still expect to lose two or three in those first few days. (We have to carefully remove them from the shipping box one at a time and dip each one's beak in the water to teach them how to drink, else they'll die of thirst.) According to the proposed policy, I would pay an additional three dollars per chick to buy them each a microchip, plus whatever it cost to get the microchip implanted. When a bird died, I would have to report the death and somehow scan the microchip. When we took birds to the fair, or sold them, it would require a permit. When I have a broody hen who raised her own chicks I would have to get them implanted, if I could find out where she was hiding them.

I suspect that more regulations, imposed by a federal bureaucracy that can't afford to do the job right, will burden the good farmers and be flaunted by the few who don't give a hoot. Why bother to keep your fences mended if all of your cows can be located by GPS when they stray?

Profit margins in agriculture are not that great, and it's not clear that small farms will be able to absorb the new costs of this program. The microchip program is being promoted as a remedy for concerns like avian flu and mad cow disease, that are arguably the result of the globalization of our food chain. We need small local farms now more than ever.

Avian Flu and Intellectual Property

Data hoarding continues to impede avian flu research. While many samples of the virus have been collected and genetically sequenced, the researchers, labs and nations involved have been reluctant to make this information public.

Everyone hopes to be the first to win fame and fortune as the developer of the first avian flu vaccine, the patent-holder on the next flu drug, or even the genetic engineers of the flu-resistant chicken.

The chicken engineers are thinking big. Just look at this quote from the UK Times:

Even if the technique works, it will be several years before it can be used to stock farms and it also faces important regulatory hurdles and a battle to win over public opinion. If these obstacles are overcome and farmers are willing to adopt GM chickens, the entire world stock could be replaced fairly quickly.

Once we have regulatory approval, we believe it will only take between four and five years to breed enough chickens to replace the entire world population, Professor Tiley said. Developing flu-resistant chickens has clear benefits for human health and animal welfare, as we wouldn't have to slaughter chickens around the world. Chickens provide a link between the wild bird population, where avian influenza thrives, and humans, where new pandemic strains can emerge. Removing that bridge will dramatically reduce the risk posed by avian viruses.

Wow. Replacing the world's mind-boggling diversity of chicken breeds with a few genetically-engineered breeds.

One of our favorite pastimes this time of year is catalog shopping for chicken breeds. We get the catalog from Murray McMurray Hatcheries and weigh the strengths and weaknesses of various breeds. Some are bred for egg laying, some are bred for meat, some are old fashioned "dual purpose" birds. Some are known for temperment, important if you have a small yard and close neighbors. Some have retained "broodiness", the instinct to set on eggs and raise chicks that has been discouraged in lines bred strictly for egg laying. There are fancy breeds, blue egg layers, Polish crested chickens, and feather footed cochins.

So many chickens! Some breeds are foragers, ready to go out in the world and scratch for their dinner. Some are bred to just hang around and pump out eggs. Some are smart enough to roost in the trees at night. Some have had the sense bred out of them; they just huddle on the ground and wait to be eaten.

Each breed is the result of generations of breeding. I suspect the smarter, thriftier birds are the result of breeding that spans human generations, not poultry generations. There are countless more varieties of chickens, a different variety living in each little corner of the world, bred for centuries to best suit the microclimate and needs of the people who live there.

This is the old-fashioned method of genetic engineering: selective breeding and cross breeding to secure the traits that are favored. In good times, you might breed for a fancy tail. In bad times you might breed for survival in famine or resistance to the latest disease.

Now, confident that the only answer is in gene splicing, we are depopulating the countysides of their locally-bred chickens, in a losing battle to contain the virus. The disease is devastating to flocks; the birds look fine one day and the next morning 80 to 90% are dead. One wonders if the clue to flu resistance in poultry lies in that small sliver of surviving birds, the ones that are being culled with the rest. Or maybe it lies with the flock next door that appeared untouched by the disease but was culled anyway.

The first images of avian flu showed us armloads of chickens, held upside down by their feet, on the way to incineration. As someone who has catalog shopped chicken breeds, I wanted to shout: "Wait! What kind of chicken is that? Show me again, right side up! What a cool bird!"

But it was gone. Not just from my TV screen, but probably from the face of the earth.

Some people's intellectual property lies in their lab. Some people's intellectual property scratches and clucks out in the yard. How odd that we allow lab-base intellectual property to be hoarded, to the detriment of mankind, while barnyard-based intellectual property is tossed on the burn-pile?

Avian Flu Hits Europe

The progress of avian flu across Europe gives us a picture of how the disease might look in our area.

It was mute swans that were the sentinels. Reports of dead swans came in rapid succession from first Greece, Italy, Slovenia, Bulgaria. Tests showed that they were positive for H5N1. A few days later they were finding dead swans in Austria, France, and finally Ireland. Dead swans were the first sign, probably because they are more susceptible and because they are easy to spot when the corpses wash ashore. These are mute swans, the same species that live in our lakes and rivers here in Leelanau. Still, it was notable how quickly the disease seemed to spread, even thought it is still early for the big migration season.

Avian flu has also been spreading in both Nigeria and India. Indian authorities have been notably coy about giving the world details about the situation there. In Nigeria, BBC news reports that publicity about the disease has sparked a rush to sell poultry, overwhelming the authorities' feeble attempts to contain the disease.

Today the NY Times reports that a large turkey farm in eastern France has suffered an infection. It is the first time the disease has been found in farm animals in the EU. It was a large farm, housing over 11,000 turkeys. Events have unfolded with blinding speed for this family:

Meanwhile, Daniel Clair, the owner of the turkey farm where the flu was confirmed, told the newspaper Le Parisien that he thought the virus was carried on bales of straw that he had put into his indoor pens after his turkeys had been treated for diarrhea.

A local veterinarian, Claude Lessus, who told Le Figaro that he had prescribed antibiotics for the turkeys, said Mr. Clair collected seven big bales of straw with his tractor, adding, "This could be the means by which the animals became
infected."

On Wednesday night, his turkeys were fine, he said. But on Thursday morning, he found 400 dead birds in his flock, and others that were sick. It was, he said, "a thing so thunderous, I immediately understood."

Mr. Clair's remaining turkeys were slaughtered, even before the final determination was announced after 1 a.m. Saturday.

Mr. Clair, his wife and their 8-year-old son are being treated with Tamiflu, an antiviral drug, and have been quarantined in their home. He said he had been told to notify the authorities if they became ill. An 11-year-old daughter, who was not at home when authorities intervened, has not been allowed to return.

A security zone of two miles and a surveillance zone of five miles has been created around the farm, French officials said. The police are disinfecting the farm, where other animals are also raised, as well as the wheels of vehicles that had traveled near the area.

Mr. Clair said that he wanted all necessary precautions to be taken, but he confessed he felt a bit like a pariah. The policeman delivering the flu medicine refused to come up to his house, but left the drug on the road, he said; his mail is not being delivered.

"I have begun to worry," Mr. Clair said. "We have started to run out of food."

It is still frustrating to note how much is not known about this disease. Before now, I have been thinking that we would get some warning that the disease was in the area before it actually hit our barnyards. Poor Mr. Claire's experience was much more sudden.

And the disease is spreading far faster than our understanding of the basic mechanisms of the disease. Yesterday's Effect Measure discussed the lack of a consistent pattern of connectons between the human victims of the disease and the birds. There are too many cases of human victims who had no known contact with birds. And when there is contact, researchers have not been able to find identical viruses in the birds and the people. There is speculation that there may be a connecting vector, another species that carries the virus from bird to humans. (Cats?)

So many questions and not enough research going on. Or the research is being ramped up way late. (This is why it is important, in good times, to keep funding research on seemingly silly questions. You never know when you might suddenly need to know about the migration patterns of ducks or the mutation rates of seemingly benign viruses. And if you have extra people trained and working as researchers, you can easily divert their expertise in an emergency.) We don't know how the virus travels, whether it moves mostly with wild birds or with domestic poultry moved by people. We don't know how it infects people; many people have been exposed to sick birds with no apparent effect, yet some people have gotten sick with no apparent exposure to sick birds. We are sadly lacking in any sort of large scale testing of humans in infection areas to determine how many people carry the antibodies to the disease, indicating that they had an infection with no symptoms.

Ducks seem to be good at carrying the virus without getting sick. I haven't heard any talk of the disease in songbirds, so I guess the bird feeders are still OK. Will we be worried about swimming in the lake with the ducks this summer, or about letting the kids chase seagulls on the beach?

I have chickens die from time to time. One will start to look peaked, standing in one place with her head scrunched down in her shoulder, staring off at nothing. A few mornings later I go out to the barn and find her dead. I used to try to nurse sick ones, but it generally isn't worth the trouble. I have never had birds die as fast as Mr. Claire's turkeys, and never more than one at a time.

The thought of having my family quarantined because of the chickens puts a new spin on things. I now have 15 chickens, including the nasty rooster and Harry Houdini. The hens are over two years old and are past their egg laying prime. I put off slaughtering the whole flock last fall, in part because I feared that the avian flu might make it hard to get replacement birds. (I also had no room in the freezer.) As I watched events unfold I plotted ways to get the flock out of the barn this spring and into a coop that I could more easily sterilize or even burn down if needed. Now I'm thinking I will slaughter them all after the spring egg season, or sooner if we start finding infected dead swans in the US.

Read the next avian flu post here.

The pace of avian flu news picked up over the weekend as three children from one family in Turkey died of the disease and a fourth is ill. At least 30 people have been hospitalized; it is unknown how many of them will test positive for avian flu.

This is a larger than usual cluster and the first human infection outside of Asia. Turkey, of course, borders Iraq, an area devastated by war and populated by US soldiers who are coming and going all the time.

I'm checking the news at Effect Measure.

Avian Flu and the Home Flock

From an interview with the Center for Disease Control:

Q: We keep a small flock of chickens. Should we get rid of them?

A: No.

Keeping chickens is a sort of window to the wider world. The everyday chores of caring for poultry is something that humans have been doing in similar fashion for most of recorded time. It is also something that is done, with little variation, almost everywhere that people live.

It was hard to stop thinking about those first bird flu reports from Asia. I saw fleeting images of beautiful birds on the evening news as they told of killing all poultry in whole provinces. At first I wondered how many interesting breeds of chickens were going extinct.

Then I worried about the households that owned those birds. The Food and Agriculture Organization of the United Nations tells us that one-quarter of the world's poor keep livestock and that livestock is often the "only means of asset accumulation and risk diversification that can prevent a slide into abject poverty by rural poor in marginal areas." Poultry is traditionally the livestock of choice for women because the animals are smaller and more manageable, and they don't require a long trek to pasture. If culling chickens was impoverishing households, these were likely to be the households headed by women. It was particularly hard to imagine impoverishing more women in Thailand, which has an active prostitution industry, and where AIDS is already entrenched. I wondered if culling chickens to prevent a potential bird flu epidemic was really preferable to leaving women and children with no economic alternatives except the sex trade and the very real AIDS epidemic.

For a while, watching the avian flu news was like watching two raindrops make their way down a windowpane. The virus would eventually make its way to my neighborhood, but would it be spread by humans or birds? When the tsunami hit Southeast Asia, the chicken farmer in me started to relax. It seemed inevitable that all of those people crowded into refugee camps would be the opportunity the virus needed to start spreading through the human population.

But it didn't happen that way. Now the nightly news tells us that the virus has been found in Turkey, then Romania, then London. The matter-of-fact explanation is that the virus is spread by the migration of "wild birds".

Bird lovers are, naturally, alarmed by this talk, especially when authorities start proposing to kill wild birds and drain wetlands. Seattle Audubon published a nice page on the implications for bird watchers and policy-makers. They note that songbirds are not known carriers of the virus and that keeping feeders in one's backyard is not a health risk. (Birds can spread other diseases to each other at backyard feeders, so it is a good idea to disinfect them periodically with bleach.)

Living the Scientific Life lays the blame for SE Asia's poultry epidemic on farming methods, not wild bird:

Bird flu is typically carried in the intestines of wild birds. These avian carriers often remain healthy but shed the virus in their feces, especially when they are under stress, thus transmitting it to other birds and also becoming ill themselves. In 1997, this bird flu virus roared onto the epidemiological scene by decimating poultry markets in Hong Kong and stunning health officials around the world by killing six people in that city. However, after extensive testing, scientists realized that this supposedly new virus had actually been identified decades earlier: It is a variant of the H5N1 virus that was first isolated in 1961 from terns in South Africa.

It is not known how this particular virus managed to disperse away from South Africa, but scientists suspect that it sequestered itself inside the intestines of migratory wild birds and hitchhiked around the world, as is typical for flu viruses. But this virus did not pose an international health problem until it reached eastern Asia, where huge concentrations of domestic poultry are found. Thus, combined with the effects of widespread poverty, particularly with its resulting overcrowding, poor hygiene and inadequate nutrition, H5N1 found itself in the ideal environment to enhance its lethality and transmissibility while also being presented with numerous opportunities to jump the species barrier into humans and other animal species.

I'm frustrated by the lack of hard science in the news reports about bird flu. (You can't understand viral diseases without understanding evolution, and if we're afraid to evolutionvoultion in school, what do you think is going to happen to our understanding of diseases like influenza and West Nile virus and AIDS?) The news reports repeat the same "facts" over and over again without asking the qualifying questions that might help us make sense of the situation. The avian flu situation is a dramatic picture of how science works; data is gathered, theories are posed, the next round of data either supports or disproves the current theories. The news media wants to make this all into a neatly packaged cause-effect-cure scenario, when no such scenario exists.

A population addicted to CSI-style dramas might just appreciate the science thriller of avian flu research, except that the tools and funds that real scientists have at their disposal grossly inferior to the glamorous world of TV crime labs. A January 2005 article in Nature, Vietnam's War on Flu, details the opportunity for studying human exposure to the virus in the countryside of Vietnam:

Vietnam's economy may be growing rapidly, but the vast majority of its people are still small-scale farmers who share their living space with chickens and ducks. "The hinterland of Vietnam is, for all practical purposes, one huge free-roaming farm," says Anton Rychener, who heads the Hanoi office of the UN Food and Agriculture Organization (FAO). This, experts agree, provides the ideal breeding ground for deadly strains of flu, which are likely to emerge when viruses pass between different species of livestock and people, and exchange genetic material in the process.

Yet, the few epidemiologists working in Vietnam complained that the rest of the world is interested, not in doing public health research in Vietnam, but in collecting samples and then high-tailing it back to their first-world labs. Many people have been exposed to avian flu in Vietnam, but only a small percentage appear to have gotten sick. It would be very interesting to check both populations (human and poultry) for avian flu antibodies in an attempt to answer some very basic questions: Are only a few poultry infected, or have most poultry been exposed? Are birds that are kept in less stressful conditions more likely to resist infection? Are people simply not getting infected or are they having very mild symptoms? If they aren't getting infected, why not? Is the virus just not good at infecting humans, or have the humans gotten an immunity from somewhere?

One of the researchers in the Nature article noted that most of the people who died from avian flu were young. He wondered if the elders had acquired immunity from some previous wave of poultry flu. I read accounts of the Spanish flu epidemic that my grandparents lived through, and once again, it was the young people in the prime of life that seemed most susceptible. The theory is that the disease killed by overactivating the immune system, thus people with the most healthy immune systems were the most vulnerable. Yet, the similarities between the two situations are interesting. Humpoultry pountry have been living in close contact for so long (yes, evolving together) that it is inevitable that the two species would occasionally swap viruses. Will it turn out that contact with poultry results in a immunity (or even a partial immunity)against the next wave of flu virus?

In the last few days, President Bush has announced a new avian flu initiative. The epidemiologists at Effect Measure are glad to see avian flu getting attention and funding, but they note that the US has been systematically dismantling our public health infrastructure since the Reagan administration. The worry that, even if we can catch up from years of failing to fund basic research, we may lack the networks that will be needed to distribute vaccine or flu drugs, or even to effectively monitor the progress of an epidemic. In the end, any funding of public health initiatives is an improvement over the "less government is always better" philosophy.

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So what does this mean to those of us who keep backyard poultry? The CDC's one-syllable answer, top of this page, to the only reporter who thought to ask the question, seems comical at best. Most of the information on poultry disease is aimed at farms with large indoor flocks. I found little information appropriate to a home flock situation; APHIS Tips on Biosecurity came as close as anything. They advocate housing birds away from foot traffic, quarantining new birds, disinfecting food and water equipment.

I will never be able to keep my chickens away from all contact with wild birds, but it seems that the wild birds I really have to worry about are ducks, geese, wild turkeys, and seagulls. It makes sense to dedicate a pair of boots for working around the chickens, and then avoid wearing that footwear to the piers, beaches, or golf courses where there is likely to be wild bird poop. My dirt floor barn, although it is great for keeping birds warm in winter and protected from predators, cannot be thoroughly disinfected. I may keep a much smaller flock next summer and house them in a structure that can either be cleaned or burned. I anticipate that at some point we will no longer be able to ship live poultry though the mail, so I am thinking about how to get along with that nasty rooster of mine, and how to encourage my hens to brood eggs next spring. I am culling hens this fall, keeping a handful of Partridge Rocks and Black Australorps as they have always been sturdy and healthy breeds. I need to make my whole setup leaner and more flexible, so I can change my methods as the situation unfolds.

The situation will unfold, as real science does, as a series of observations, guesses, experiments, and then more observations and guesses. All backyard poultry farmers are hands-on scientists, watching our birds, trying new methods, discarding what flops and refining what works, but always observing. We need to extend that home-grown pragmatism and demand that our tax dollars be spent on real science, where the theories spring from the observations, instead of visa versa.

Cornell Ornithology

Thought about Knowledge for Development

The image at the top of the page is from The Red Jungle Fowl, posted by HS Wong of Kuala Lumpur. The Red Jungle Fowl (gallus gallus) is the original chicken, from which all domestic chicken breeds are descended.

The next avian flu post