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Home  > Avian Flu

Avian Influenza in Free-Range and Organic Poultry Production

September 2006
Contact Terrell Spencer for more information, 800-346-9140

Free-range chickens ~


Free-range and organic poultry producers raise a specialty product. Birds are provided with outdoor access, natural or organic feed, and routine antibiotics are avoided. Many producers believe outdoor access maximizes welfare by offering a healthy environment for poultry due to the ample space, sunlight, and fresh air. Many operations are independent and small-scale. This publication provides information on avian influenza as it pertains to this type of specialty poultry production.

Avian influenza (AI) is a respiratory disease of birds and is caused by a virus. It is similar to human influenza and is spread by coughing, sneezing, and touching infected surfaces. Avian influenza can infect a wide variety of birds, including chickens, turkeys, ducks, and geese. Wild waterfowl (ducks, geese, shorebirds) tend to be more resistant and are, in fact, reservoirs or carriers of the disease.

Influenza viruses are categorized according to type. Type A can infect humans, birds, pigs, and other animals, but wild birds are its natural hosts (U.S. Department of Health & Human Services, 2006). (The low-pathogenic influenza types B and C usually infect only humans and are not addressed in this bulletin.) Type A influenza viruses are further classified by hemagluttinin (H) and neuraminidase (N) proteins, of which there are many combinations. A few A subtypes commonly circulate among humans (e.g., H1N1, H1N2, and H3N2), but the subtypes prefaced by H5 and H7 are of greater concern because they infect both birds and people. Avian influenza viruses are further categorized by the ability to cause disease in birds: low-pathogenic avian influenza (LPAI) or high-pathogenic avian influenza (HPAI).

The Asian strain H5N1 HPAI is of concern not only because it is highly lethal to birds, but because it has also infected humans, although not easily. Human infection has mainly occurred in Asian regions where people live in close proximity with poultry. The evidence suggests that only significant exposure to sick birds causes the disease in humans. A concern is that H5N1 HPAI will mutate and transmit more effectively from poultry to humans and even human-to-human. Mortality in humans with H5N1 influenza is about 50 percent. A human health pandemic occurs when a pathogen is highly infectious and people have little resistance.

The H5N1 HPAI has spread from Asia to Russia to Europe and to some African countries. See for a map of its spread. At the time of this writing, Asian H5N1 HPAI has not been detected in North America.

The U.S. has seen mild outbreaks of LPAI and even the more severe HPAI that causes high mortality in birds, but HPAI is rare. Only three known outbreaks have occurred in the U.S.: 1924, 1983, and 2004. No human illness was associated with these outbreaks. ( U.S. Department of Agriculture, 2006) Although LPAI causes little disease in poultry, it must be controlled, since it can mutate into a more highly pathogenic form.


The source of the AI virus raises questions. Is AI spread by wild birds or by human activity? Is it spread by small-scale production systems and live markets or is it due to large-scale poultry? The conventional school of thought holds that wild waterfowl brought HPAI to domestic poultry. An alternative school of thought is that large-scale domestic poultry is part of the problem and could be spreading the disease to wild birds.

Wild waterfowl can be asymptomatic carriers of low pathogenic avian influenza, and their long migrations can spread the disease. In some countries outdoor poultry are banned because of concerns that wild birds help spread the disease. In the U.S., the live poultry market is also considered a reservoir of LPAI (USDA, 2006). Fighting cocks are also a concern because infected birds may be smuggled into the country. Fighting cocks travel through human activity and the birds might spread the disease where they are gathered for fights.

Alternative theories about the source of the high pathogenic Asian avian flu (H5N1 HPAI) are summarized below:

  • Fowl Play: The Poultry Industry's Central Role in the Bird Flu, a publication by the nonprofit organization GRAIN, asserts that wild birds and small free-range flocks are unfairly blamed for the spread of AI. According to the article, AI is spread through commercial pathways, not migratory flyways, and by the use of poultry litter on land or as a feed for fish. The authors contend that low-density and genetic diversity among small flocks keep viral loads low, and small numbers of birds cannot generate enough virus for the mutation process to occur. With a low density of birds, a pathogen that has mutated to a highly pathogenic form dies out quickly because it kills all its hosts. High-density environments, on the other hand, provide conditions that allow mutation from low a pathogenic form to high pathogenic form. Because of the large number of birds, the virus can move quickly from bird to bird (GRAIN, 2006).

  • Dead Birds Don't Fly is a publication by the sustainable agriculture organization, Institute for Agriculture and Trade Policy. The role of migratory waterfowl in spreading H5N1 HPAI is not completely clear (Hillesheim, 2006). The authors maintain that the spread of H5N1 HPAI has been mainly through human activity, and the jump of the virus to western China, Russia, Turkey, and France seemingly implicates migratory waterfowl because no direct human activity is apparent. However, H5N1 HPAI has not followed well-known migratory patterns. According to Dead Birds Don't Fly, H5N1 HPAI kills wild waterfowl as well as domestic poultry, so wild waterfowl could not spread the virus. The publication speculates that wild waterfowl were infected by domestic poultry.

  • According to an article in the magazine People and Livestock, genetically similar birds used in commercial production may be responsible for HPAI becoming a problem. Conventional birds have a poor immune system, whereas local birds have more resistance to AI because it is endemic in the region (Köhler-Rollefson and Mathias, 2006). According to the publication, only hardy, local breeds should be used in areas that traditionally have AI to prevent the virus from mutating to a dangerous form.


Transmission of the virus occurs by non-infected birds in direct contact with infected birds or their droppings, or by contaminated equipment, clothes, and shoes.

AI is spread primarily by direct contact between healthy and infected birds and by indirect contact with contaminated equipment and materials. The virus is excreted from infected birds through feces and secretions from the nose, mouth, and eyes. Contact with infected fecal material is the most common means of bird-to-bird transmission. Wild ducks often introduce LPAI into domestic flocks raised on range or in open flight pens through fecal contamination. Within a poultry house, transfer of the HPAI virus between birds can also occur via airborne secretions. The spread of avian influenza between poultry premises almost always follows the movement of infected people and equipment. AI also can be found on the outer surfaces of egg shells. Movement of eggs is a potential means of AI transmission. Airborne transmission of virus from farm to farm is highly unlikely under usual circumstances. HPAI viruses can survive for long periods at lower temperatures. The incubation period for AI ranges from 3-7 days depending on the isolate, dose, species, and age. (USDA, 2006)

The virus tends to be fragile after the host is gone and usually disintegrates after a few hours. (Soil Association, 2006) However, the AI virus can remain viable up to 30 days on a surface (Knepley, 2006) and, in water, the virus can survive up to 90 days. (Pendleton, 2006)

Preparedness and Prevention

In general, preventative practices should be used to prevent disease in poultry flocks. Organic poultry producers do not give their birds synthetic drugs and, therefore, focus on reducing stress in order to improve the birds' immune system. Low stocking density, good ventilation, and good nutrition reduce stress, and many free-range and organic producers believe that outdoor access is important for a healthy environment. However, even low stress and a good immune system is no match for the Asian H5N1 HPAI, and biosecurity is needed to help prevent it.

If you are a producer, it is important to keep your birds in good condition, to keep your birds protected, and to control what comes onto your farm. Biosecurity practices help prevent not only AI but other diseases as well.

  • Start with clean birds. The National Poultry Improvement Program (NPIP) certifies that breeding flocks and hatcheries are clean of certain diseases. Make sure your hatchery is NPIP-certified. If you take your birds to shows, keep them separated for two weeks after you return home to make sure they don't get sick. Handle or feed your quarantined birds last.

  • Use footbaths with disinfectant before entering poultry house. Chlorine and iodine disinfectants are allowed in U.S. organic production. If a footbath is not realistic, use a spray, disposable booties, or footwear that is only used in the poultry area. Wash your hands before and after handling your birds.

  • Use all-in, all-out management. If you depopulate at the end of a flock, you can reduce pathogens, because some pathogens die when there is no host.

  • Do not mix ages or species. Older birds can carry disease while showing no sign of disease and infect young birds. Likewise, domestic ducks and geese can carry diseases that infect chickens.

  • Reduce contact with wild waterfowl. Birds with outdoor access should not share areas with wild ducks, geese, or shorebirds. Being close to wetlands or flyways is a risk factor. See for a map of North American waterfowl flyways. Make sure free-range areas do not have attractions for wild waterfowl, such as a pond, which may become contaminated with wild waterfowl droppings. Use self-feeders that dispense grains or pellets on demand instead of open feeders (see for examples). You may consider covering the feed area with netting or keeping all feeders and waterers inside the poultry house. In extreme situations, be prepared to cover your entire yard with netting or to enclose your birds under roofed cover if necessary.

  • Clean and disinfect. Clean objects of dirt or manure before disinfecting them or the disinfectant will not work. Porous surfaces like wood and cardboard are hard to disinfect; plastic surfaces are easier. Sunlight is a good drying agent and disinfectant. Sanitize water lines (vinegar and other organic acids and hydrogen peroxide are allowed in organic production).

  • Limit access to poultry houses. Discourage unnecessary visitors; make sure visitors have not been around other poultry or birds in the past 24 hours.

  • Spray tires and undercarriage of delivery vehicles with disinfectant. Gas trucks, vendors, etc. may visit other poultry farms and their tires should be sprayed before entering your property.

The USDA has a "Biosecurity for the Birds" campaign and Web site ( that is useful for small producers. Your biosecurity is even more important if you are in a high-poultry-producing area, because of the high number of birds that could potentially be affected. According to Dr. Paul Kepley of the Pennsylvania Department of Agriculture, "Is this the time to get out of the poultry business? The answer is no. It is time to rethink your biosecurity plan."

An avian veterinarian is very useful in helping to develop a biosecurity plan, as well as a health management plan. If you do not have a vet, refer to the list of state diagnostic laboratories at for assistance or call your State Veterinarian.

Monitoring, Surveillance and Testing

The USDA has a National Highly Pathogenic Avian Influenza (HPAI) Response Plan to respond to HPAI. It is in draft form at the current time and a summary is available at the USDA APHIS (Animal and Plant Health Inspection Service) Web site ( Its domestic prevention and surveillance plan focuses on wild bird and domestic bird surveillance and educational programs for backyard producers.

Wild birds. APHIS' Wildlife Services and U.S. Fish and Wildlife are leading efforts to detect HPAI in wild birds in North American flyways, especially in Alaska where migratory birds from Asia spend summers. The surveillance includes "the investigation of wild bird deaths or sickness; the sampling of live-captured and hunter-harvested birds; the use of sentinel species; and environmental sampling." (USDA, 2006)

Domestic birds. APHIS' National Poultry Improvement Program (NPIP) is a voluntary federal-state-industry cooperative program. Historically, NPIP tested to ensure that birds do not have pullorum or typhoid, diseases that decimated flocks in the past. However, it now also includes tests for other diseases and can confer an "AI Clean" status on flocks that participate in AI testing. Its program has focused on breeding flocks and hatcheries, but it is expanding programs to include broiler, turkey, and egg layer operations (for flocks greater than 25,000 birds). See NPIP Web site ( for information on testing programs. The poultry industry voluntarily tests each commercial flock for AI.

On a smaller scale, APHIS has developed a monitoring program for the live bird market. The live poultry market is of special concern in regard to AI. Most live poultry markets are located in major cities on the East coast, where live birds are sold and slaughtered on-site in small processing facilities. Customers are mainly from ethnic groups that prefer older birds, a particular feather color, or gender. Birds for the live market come from multiple sources and sometimes are returned to the farm if not sold at the market, potentially bringing disease back with them. LPAI has historically been widespread in the live market.

The NPIP program has provisions for waterfowl, exhibition (hobby) poultry, and game bird breeding flocks, largely due to the leadership efforts of these specialty groups. In some states, exhibition poultry producers must test birds for AI before showing. For "AI Clean," in specialty flocks, generally 30 birds in a flock are tested every 90 days.

Small commercial poultry producers, including free-range and organic, have an opportunity to get involved in routine testing, especially since most states have increased funding to handle the AI threat. To help prevent disease, develop a preventive program for biosecurity. Benefits of testing include being aware of disease in a flock and having opportunity to eliminate it. In some states, being involved in a federal testing program can provide additional indemnity if the flock needs to be destroyed. Disease-free status can be used as a marketing tool. See the link on the NPIP Web site ( on "How to become a participant." State contacts for NPIP are listed.

Training schools are held by states each year to train and certify testers in pullorum testing, and AI testing may be added to the training. AI sampling of live birds includes a tracheal swab or a cloacal swab. AI samples must be sent to a certified laboratory (see NPIP list of labs) for the actual test to be run. Some state labs do not charge small flocks for testing. Producers interested in becoming trained to collect samples should contact their state department of agriculture.

Organizing is crucial for small commercial poultry producers in the face of a threat like AI. Consider joining a national organization like the American Pastured Poultry Producers Association (; some states have local organizations. It is important for the voices of free-range and organic poultry producers to be heard in government.

Surveillance methods will continue to improve. In June 2006, the USDA draft response received criticism from an audit by the USDA Inspector General that the extent of surveillance in each state is not clear; there is not sufficient surveillance of all types of poultry, including commercial, backyard, ducks, geese, etc, and that the federal government relies too heavily on states and testing varies from state to state. See for the audit report. The USDA is working to improve national AI testing systems.

Whether or not producers test for AI, they should learn the signs of disease. Signs include "lack of energy and appetite; decreased egg production; soft-shelled or misshapen eggs; swelling; purple discoloration of comb, wattles, or legs; nasal discharge; coughing, sneezing; lack of coordination; and diarrhea." (USDA, 2006) Large numbers of mortality should always be reported. Call the USDA Veterinary Services toll-free at 1-866-536-7593 to report sick birds.

Response and Eradication

In the event of an HPAI outbreak in the U.S., the USDA APHIS is the lead responder. U.S. policy is usually a rapid response to eradicate disease by destroying infected flocks.

A summary of the draft USDA response plan to HPAI is available on the Internet. The response involves the following components:

  • Quarantine. A quarantine will be imposed on the farm and surrounding area and movement controlled. Premises are defined as infected, contact, suspect, or at-risk.

  • Appraisal and compensation. If there is a question about the value of birds (unique, specialty, exotic, purebred), a special expert appraiser is consulted. Some small breeders have very valuable birds. Eggs and feed may be included in the appraisal.

  • Euthanasia. Gassing is the most common method of mass euthanasia on poultry farms. The World Animal Health Organization (OIE) has written Guidelines for Killing of Animals for Disease Control Purposes (, which recommends methods of euthanasia. Animal welfare groups are very concerned that the most humane form of euthanasia be used.

  • Disposal. Carcasses will be disposed of in a timely, safe, and environmentally acceptable way and options include incineration, burial, and composting. Usually on-site disposal is preferred, and composting in-house may be considered.

  • Cleaning and disinfection. It is important to first clean houses and equipment because disinfection is more effective on a clean surface. Once manure and litter is removed, air blowers and vacuums can remove dust and cobwebs. The house should be washed with high pressure water with a detergent.

  • Biosecurity. Biosecurity measures may include controlling the movement of other livestock such as cattle.

  • Vaccination. A vaccination program to control infectious disease is an undertaking that involves complex decision-making, usually at a governmental level.

  • Wildlife management. Wildlife may need to be controlled because they can be involved in the transmission of poultry disease.

Elm Farm Research Center, an organic research center in the UK, published a report called Vaccination Nation (Woodward, 2006) that encourages a vaccination program on the part of the UK government for organic and outdoor flocks. The center maintains that vaccines are crucial to sustainable disease control. According to the report, isolation and slaughter are out-dated methods of control. The report addresses the concern that vaccines can mask the effect of the disease and make halting its spread more difficult. It states that tests are available to differentiate between naturally infected birds and vaccinated birds (DIVA technology). Preventative use of vaccination may become more prevalent as more countries accept meat from vaccinated birds and if AI becomes endemic in wild birds.

If HPAI is detected in the U.S., it is possible that outdoor poultry will be banned temporarily. In many European countries where H5N1 HPAI has been detected, outdoor access is not permitted, especially during wild waterfowl migration periods. Sustainable agriculture proponents are concerned that outdoor flocks will be unfairly targeted.

Protecting People

The welfare of people who care for poultry should be protected. They should be encouraged to stay up to date on annual influenza vaccines. Duo-infection with both human influenza and avian influenza could help the virus mutate to a form more able to infect humans. Small producers who process on-farm should be aware that when birds are slaughtered, fine particles of blood, feces, and body fluids can spray in the air. Gloves and masks are helpful.

In the event of an outbreak, workers who help destroy and dispose of flocks must be protected. Gloves, masks or respirators, and protective clothing are needed.

Producers can help educate consumers that avian influenza is not a food safety issue. Currently H5N1 HPAI is not in the U.S., but if an infected bird were to enter the food supply, cooking the meat to 165°F destroys pathogens. Consumers will not get avian influenza from properly cooked poultry meat. The conventional poultry industry is making a strenuous effort to reassure consumers by testing each flock for AI.

In the event of an outbreak of AI, it will be important to convey to the public that this does not mean an outbreak of a human pandemic.

Basic hygiene is important to reduce spreading any influenza and includes washing hands before eating or touching the face, and covering the mouth when sneezing or coughing.

Sustainable agriculture and consumer watch groups have concerns about the mass depopulation of millions of poultry and humane euthanasia methods. These groups are also concerned about social issues such as ensuring that contract poultry growers are reimbursed for destroyed birds, as well as the impact on plant workers who may have reduced work opportunities if flocks are not going to slaughter. Small, independent processors may go out of business.

Because there are many types of AI, this will be a long term issue with which producers must deal. All poultry sectors, including conventional, hobby, and small commercial, should unite for prevention and public education.


At the time of this writing, H5N1 HPAI is not currently in the U.S. Poultry producers should use biosecurity practices to prevent disease. U.S. free-range and organic poultry producers have the opportunity to get involved in routine disease testing.

Additional Resources

Extension Poultry Specialists at universities are resources, along with State Veterinarians. State NPIP contacts are also a resource. USDA APHIS is a resource on a national level.

Many resources are on the internet rather than in printed copy because of the changing nature of AI incidents. If you are reading this publication and do not have access to the internet, please contact ATTRA at 800-346-9140 for hard copies of the resources mentioned.

Poultry Producer Resources:

  • A meeting in April 2006 focused on AI from a "pastured poultry" perspective in Pennsylvania. Participants include Penn State University, PA Department of Agriculture, APHIS, and small poultry producers. See for videos of the talks.

  • The Soil Association is a UK organization for organic and sustainable agriculture. See for AI information.

  • The poultry industry has the following Web site. Avian Influenza: Protecting Flocks, Protecting People

  • Council for Agricultural Science and Technology

Educational Resources:

Government Resources:

International resources:


GRAIN. 2006. Fowl Play: The Poultry Industry's Central Role in the Bird Flu Crisis. Barcelona, Spain.

Hillesheim, Lindsey. 2006. Dead Birds Don't Fly. Institute for Agriculture and Trade Policy, Minneapolis, MN. 16 p.

Knepley, Paul. 2006. Pastured Poultry Producer Avian Influenza Workshop. April 18, Harrisburg, PA.

Köhler-Rollefson, Ilse and Evelyn Mathias. 2006. Industrial poultry monocultures cultivate avian flu. People and Livestock. Issue 4. p. 1-2.

Pendleton, Eva Wallner. 2006. Pastured Poultry Producer Avian Influenza Workshop. April 18, Harrisburg, PA.

Soil Association. 2006.

USDA. 2006. Draft Summary of the National Highly Pathogenic Avian Influenza (HPAI) Response Plan. USDA, APHIS, Veterinary Services, Emergency Management. Washington, DC. 72 p.

U.S. Department of Health & Human Services . 2006.

Woodward, Lawrence. 2006. Vaccination Nation. Elm Farm Research Center, Berkshire, UK. 12 p.


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This page was last updated on: December 13, 2014