Avian Flu Basics

Most flu strains that affect people ultimately come from mixtures of strains that were once more prevalent in birds. When a new strain of influenza, dubbed H5N1, which is highly lethal to poultry, started showing up in people in 1997, flu experts around the world grew alarmed. The threat of a severe pandemic caused by H5N1 triggered many of the preparedness plans that came into effect since the outbreak of H1N1 swine flu in the spring of 2009.

This section provides a quick overview of avian influenza, from scientific basics to a summary of the H5N1 case to treatment and prevention options to outbreak control efforts.

On this page...
Avian Influenza Overview:
  Birds: a major reservoir »
  Clinical characteristics »
  H5N1 »
  Detection »
  Treatment »
  Vaccines »
  Prevention »
  Outbreak control »
Special focus: Understanding pathogenicity
  Low pathogenic avian influenza (LPAI) »
  Highly pathogenic avian influenza (HPAI) »

Avian Influenza Overview:

Birds: a major reservoir

Avian influenza is caused by influenza A subtypes that infect many domestic and wild bird species. Species include chickens, turkeys, ducks, domestic geese, quail, pheasants, partridges, parrots, gulls, shore and seabirds, eagles, and others.

Influenza A subtypes are classified by antigenic properties of hemaglutinin (H) and neuraminidase (N).1

All known subtypes of influenza A can be found in birds.
These subtypes contain one of 16 different H antigens (H1 to H16), and one of nine different N antigens (N1 to N9).
Frequent mutations of H and N result in influenza variants that are described by host of origin (if other than human), site of isolation, strain number, year of isolation, and H and N types.
An example for a duck virus: A/Teal/HK/W312/97 (H6N1).

Wild aquatic birds serve as the major reservoir for influenza A viruses. Many wild birds carry the virus with no apparent disease. Domestic birds develop disease when they contact wild birds or swim or feed in areas frequented by wild birds. Humans can also be infected with bird viruses.

Clinical characteristics

Clinically, infections in birds can range from asymptomatic to rapidly fatal disease. The incubation period is between 3 and 7 days.

Clinical signs vary depending on disease severity and can include edema of the head and neck, ruffled feathers with severe depression, excessive thirst, watery diarrhea, reduced egg production, and sudden death.

Four avian influenza viruses known to have caused human infections are H5N1, H7N3, H7N7, and H9N2.2 Experts are concerned that infection of humans with influenza viruses from other animal or birds can produce more virulent viruses to which humans have no natural immunity.

H5N1 infection in humans appears as severe pneumonia. The condition often progresses to acute respiratory distress syndrome (ARDS). The incubation period is thought to be 2 to 5 days, but can be as long as 9 days.


H5N1 has caused a panzootic (the animal equivalent of a pandemic) (glossary) among domestic poultry and other birds in Europe, Africa, the Middle East, and Asia. People affected have mostly been those who have had interactions with domestic poultry.

H5N1 is of concern for human health because the virus has:

caused the greatest number of deaths from avian flu viruses (the fatality rate among reported cases is 59 percent).
crossed the species barrier at least three times since 1997.
infected other mammals including cats, leopards, tigers, civets (a wild Asian cat), and dogs.
developed all but one of the characteristics needed to start another pandemic; H5N1 currently lacks only the ability to spread efficiently and sustainably among humans.

WHO has officially recognized 442 human cases of H5N1, with 262 deaths3 since 2003.4 Most infections have been among people who have had direct contact with poultry, for example through slaughtering, plucking, or preparing diseased birds, handling infected poultry that appear well, or consuming raw or undercooked poultry.

H5N1 was originally classified into one of 3 clades (groups of related viruses); clade 2 had 7 subtypes. H5N1 strains have been genetically reclassified into 10 clades (0 to 9) as part of a WHO unified nomenclature system based on viral sequence relatedness.5


Avian influenza can be identified in samples taken from dead birds (internal organs, cloacal or throat swabs) and from live birds (throat or cloacal swabs).

Virus can be detected with serologic tests for viral antigens or viral antibodies and with molecular methods (reverse transcriptase-polymerase chain reaction [RT-PCR]) for viral nucleic acids.

Newer tests that are being developed can detect viral antigens or nucleic acids more quickly than current tests (15 minutes to hours versus hours to days, depending on the method).


No treatment exists for H5N1 in birds.

Humans can be treated with oseltamivir (Tamiflu) and zanamivir (Relenza), although some resistance to oseltamivir has recently been reported. Amantadine or rimantadine (admantanes) have been used but drug resistance has occurred. Clade 1 viruses and most clade 2 viruses from Indonesia are completely resistant to adamantanes; clade 2 viruses from Eurasia and Africa are still susceptible.


Two vaccines are available for birds. Both must be injected. Several newer vaccines are under development. Vaccines may be used as an additional method for controlling outbreaks among birds.

Human vaccines against H5N1 are being developed, partly out of concern for the risk of an H5N1-derived pandemic strain. One recombinant H5N1 has been produced from the A/Egypt/2321-NAMRu3/2007 strain and is available for distribution.6


FAO (Food and Agriculture Organization of the United Nations) and WHO officials have outlined methods for preventing avian influenza among animals that include educational efforts for small-scale farmers, segregation of animal species, incentives for farmers to report suspected cases, and vaccination of flocks.

Outbreak control

FAO steps for controlling an outbreak of HPAI7 include:

Restriction of movement of birds and products potentially containing virus. This includes identifying zones of infection and controlling movement of birds from those areas.
Destruction of infected birds and those at-risk birds from infected flocks (the preferred method). Birds should be dispatched quickly after detection, and carcasses and animal products properly disposed of.
Vaccination of flocks may be used as an adjunct measure in some instances.

Experts note that mass culling of birds may have severe economic impacts for local and regional economies and on food supplies in poor areas.

Special focus: understanding pathogenicity

Many wild bird species carry influenza viruses without apparent signs of disease. Other bird species, including domestic poultry (such as chickens and turkeys), however, contract influenza in two different forms. One form is common and mild (low pathogenic), while the other is rare and highly lethal (high pathogenic).8

Low pathogenic avian influenza (LPAI)

These viruses are less virulent and cause mild or no illness, but can serve as the progenitors of highly pathogenic viruses.

H9 strains are only LPAI, but some strains may have both HPAI and LPAI strains.
The signs of illness are mild and may range from ruffled feathers, reduced egg production, or mild respiratory effects to no clinical signs.
Human infections with LPAI have involved H5, H7, and H9 strains.
Because LPAI strains rarely cause apparent illnesses, some researchers suggest that LPAI infections may have been underestimated.9
Evidence suggests that H9N2 viruses can evolve and reassort extensively (see section 2.2 viral reassortment), a finding that may allow the viruses to adapt for more efficient transmission among mammals, including humans.

Highly pathogenic avian influenza (HPAI)

HPAI forms are less common than low pathogenic forms, but HPAI is difficult to miss.

These viruses are highly virulent. Mortality rates among birds in infected flocks approach 100% within 48 hours.
Clinical signs include severe depression with ruffled feathers, edema of the head and neck, swollen combs and wattles, watery diarrhea, and sudden death.
In addition to affecting the respiratory tract, HPAI also invades multiple organs and tissues to cause massive internal hemorrhage. Because of the massive internal hemorrhage observed, the disease is often referred to as “chicken Ebola.”
All highly pathogenic strains identified to date have involved H5 and H7 subtypes.10

Four avian influenza viruses known to have caused human infections are H5N1, H7N3, N7N7, and H9N2.11 The avian influenza viruses that contributed to the origin of the pandemics of 1957 and 1968 were LPAI viruses of chicken and domestic poultry.

Recent concern has focused on H5N1, because of the potentially high fatality rate among people who are infected. The H5N1 avian virus replicates efficiently in infected people, but has not yet adapted to efficient human-to-human transmission.


  1. World Health Organization, Avian influenza (“bird flu”), February 2006.

  2. Ibid.

  3. World Health Organization, Availability of a recombinant H5N1 vaccine virus, May 2009.

  4. Ibid.

  5. World Health Organization, Continuing progress towards a unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses, March 2009.

  6. World Health Organization, Availability of a recombinant H5N1 vaccine virus, May 2009.

  7. Food and Agriculture Organization of the United Nations, World Organisation for Animal Health, World Health Organization, The global strategy for the progressive control of H5N1 highly pathogenic avian influenza (HPAI), revised March 2007.

  8. World Health Organization, February 2006, op. cit.

  9. Hongquan Wan, Erin M. Sorrel, Haichen Song, et al. “Replication and transmission of H9N2 influenza viruses in ferrets: evaluation of pandemic potential,” PLoS ONE 3 (August 2008): 1-13.

  10. World Health Organization, February 2006, op. cit.

  11. Ibid.

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