- For the current concern about the transmission of an avian flu to humans see Transmission and infection of H5N1.
Avian flu (also "bird flu", "avian influenza", "bird influenza"), means "flu from viruses adapted to birds", but is sometimes mistakenly used to refer to both other flu subsets (such as H5N1 flu) or the viruses that cause them (such as H5N1).      
"Bird flu" is a phrase similar to "Pig flu", "Dog flu", "Horse flu", or "Human flu" in that it refers to an illness caused by any of many different strains of flu viruses such that the strain in question has adapted to the host. "Avian flu" differs in being named after an entire vertebrate class with 8,80010,200 species. All known avian flu viruses belong to the species of virus called Influenza A virus. All subtypes (but not all strains of all subtypes) of Influenza A virus are adapted to birds, which is why for many purposes avian flu virus is the Influenza A virus (note that the "A" does not stand for "avian").
Adaptation is sometimes partial or multiple so a flu virus strain can be partially adapted to a species or adapted to more than one species. Flu pandemic viruses are human adapted and also bird adapted. Being adapted to one species does not mean another species can not catch it; nor does it mean it can not adapt to another species.
Genetic factors in distinguishing between "human flu viruses" and "avian flu viruses" include:
- PB2: (RNA polymerase): Amino acid (or residue) position 627 in the PB2 protein encoded by the PB2 RNA gene. Until H5N1, all known avian influenza viruses had a Glu at position 627, while all human influenza viruses had a lysine.
- HA: (hemagglutinin): Avian influenza HA bind alpha 2-3 sialic acid receptors while human influenza HA bind alpha 2-6 sialic acid receptors. Swine influenza viruses have the ability to bind both types of sialic acid receptors.
The HA changes have not yet occurred in any sequenced H5N1 virus - even ones from humans that died from it and the PB2 changes don't stop it from being a flu virus adapted to birds (the definition of "avian flu virus").
Pandemic flu viruses have some avian flu virus genes and usually some human flu virus genes. Both the H2N2 and H3N2 pandemic strains contained genes from avian influenza viruses. The new subtypes arose in pigs coinfected with avian and human viruses and were soon transferred to humans. Swine were considered the original "intermediate host" for influenza, because they supported reassortment of divergent subtypes. However, other hosts appear capable of similar coinfection (e.g., many poultry species), and direct transmission of avian viruses to humans is possible. The Spanish flu virus strain may have been transmitted directly from birds to humans. 
In spite of their pandemic connection, avian flu viruses are noninfectious for most species. When they are infectious they are usually asymptomatic, so the carrier does not have any disease from it. Thus while infected with an avian flu virus, the animal doesn't have a "flu". Typically, when illness (called "flu") from an avian flu virus does occur, it is the result of an avian flu virus strain adapted to one species spreading to another species (usually from one bird species to another bird species). So far as is known, the most common result of this is an illness so minor as to be not worth noticing (and thus little studied). But with the domestication of chickens and turkeys, humans have created species subtypes (domesticated poultry) that can catch an avian flu virus adapted to waterfowl and have it rapidly mutate into a form that kills in days over 90% of an entire flock and spread to other flocks and kill 90% of them and can only be stopped by killing every domestic bird in the area. Until H5N1 infected humans in the 1990s, this was all that was considered important about avian flu (outside of the poultry industry). Since then, avian flu viruses have been intensively studied; resulting in changes in what is believed about flu pandemics, changes in poultry farming, changes in flu vaccination research, and changes in flu pandemic planning.
H5N1 has evolved into a flu virus strain that inflects more species than any previously known flu virus strain, is deadlier than any previously known flu virus strain, and continues to evolve becoming both more widespread and more deadly causing the world's number one expert on avian flu to publish an article titled "The world is teetering on the edge of a pandemic that could kill a large fraction of the human population" in American Scientist. He called for adequate resources to fight what he sees as a major world threat to possibly billions of lives. Since the article was written, the world community has spent billions of dollars fighting this threat with limited success. It is a race between an exceptionally fast mutating virus and modern scientific research capabilities, with the winner of the race still in doubt.
- Source WHO Confirmed Human Cases of H5N1
- "[T]he incidence of human cases peaked, in each of the three years in which cases have occurred, during the period roughly corresponding to winter and spring in the northern hemisphere. If this pattern continues, an upsurge in cases could be anticipated starting in late 2006 or early 2007." Avian influenza epidemiology of human H5N1 cases reported to WHO
- The regression curve for deaths is y = a + ek x, and is shown extended through the end of November, 2006.
As of 2006, "avian flu" is being commonly used to refer to infection from a particular subtype of Influenza A virus, H5N1, which can cause severe illness in humans who are infected. Currently, this strain is transmitted by contact with infected birds, and has been transmitted from one person to another only in a few cases. H5N1 flu is therefore not pandemic now and is not currently capable of causing a pandemic. Only if H5N1 mutates into a form that can be readily transmitted from one person to another could it cause a pandemic.
Illustrative examples of correct usage
WHO pandemic phases
In technical contexts, correct usage of terms is necessary because precise distinctions are the essence of the communication.
- "Avian influenza strains are those well adapted to birds" 
- "An outbreak of influenza A (H5N1), also known as 'avian flu' or 'bird flu,' has been reported in several countries throughout Asia." 
- "Avian influenza virus usually refers to influenza A viruses found chiefly in birds, but infections can occur in humans."
- "Of the few avian influenza viruses that have crossed the species barrier to infect humans, H5N1 has caused the largest number of cases of severe disease and death in humans. Unlike normal seasonal influenza, where infection causes only mild respiratory symptoms in most people, the disease caused by H5N1 follows an unusually aggressive clinical course, with rapid deterioration and high fatality." Seasonal influenza is human flu.
- "avian influenza HA bind alpha 2-3 sialic acid receptors while human influenza HA bind alpha 2-6 sialic acid receptors. Swine influenza viruses have the ability to bind both types of sialic acid receptors." 
- Sometimes a virus contains both avian adapted genes and human adapted genes. Both the H2N2 and H3N2 pandemic strains contained avian flu virus RNA segments. "While the pandemic human influenza viruses of 1957 (H2N2) and 1968 (H3N2) clearly arose through reassortment between human and avian viruses, the influenza virus causing the 'Spanish flu' in 1918 appears to be entirely derived from an avian source (Belshe 2005)." 
Illustrative examples of imprecise usage
In nontechnical contexts, imprecise usage of terms is typical when discussing complex things.
- "A 1,000 square mile quarantine zone to combat an outbreak of bird flu was lifted in Scotland today - despite the spread of a similar disease south of the border." Here "bird flu" is used to mean "Asian lineage HPAI A(H5N1) flu" (which is a bird flu) and contrasted with flu from an avian adapted strain of H7N3 (which is also a bird flu).
- Timeline data on avian flu
- Timeline data on avian flu can be found at the article on the causative agent species called Influenza A virus.
- Timeline data on the global spread of the strain that is the current pandemic concern (called Asian lineage HPAI A(H5N1)) can be found at Global spread of H5N1.
- Timeline data on creation of a flu vaccine for H5N1 can be found at H5N1 clinical trials.
- Subtypes of the causative agent species of avian flu include
- Information concerning research about it can be found at
Sources and notes
- ^ a b "Avian influenza strains are those well adapted to birds"EUROPEAN CENTRE FOR DISEASE PREVENTION AND CONTROL.
- ^ a b Chapter Two : Avian Influenza by Timm C. Harder and Ortrud Werner from excellent free on-line Book called Influenza Report 2006 which is a medical textbook that provides a comprehensive overview of epidemic and pandemic influenza.
- ^ Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Nature magazine presents a summary of what has been discovered in the Influenza Genome Sequencing Project.
- ^ Full HTML text of Avian Influenza A (H5N1) Infection in Humans by The Writing Committee of the World Health Organization (WHO) Consultation on Human Influenza A/H5 in the September 29, 2005 New England Journal of Medicine
- ^ The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005) Full text of online book by INSTITUTE OF MEDICINE OF THE NATIONAL ACADEMIES
- ^ Here is the tree showing evolution by antigenic drift since 2002 that created dozens of highly pathogenic varieties of the Z genotype of avian flu virus H5N1, some of which are increasingly adapted to mammals.
- ^ Evolutionary characterization of the six internal genes of H5N1 human influenza A virus
- ^ Chapter Two : Avian Influenza by Timm C. Harder and Ortrud Werner from excellent free on-line Book called Influenza Report 2006 which is a medical textbook that provides a comprehensive overview of epidemic and pandemic influenza.
- ^ Webster, R. G. and Walker, E. J. (2003). "The world is teetering on the edge of a pandemic that could kill a large fraction of the human population". American Scientist 91 (2): 122. DOI:10.1511/2003.2.122.
- ^ OSHA
- ^ CDC Avian Influenza (Bird Flu)
- ^ WHO Avian influenza frequently asked questions
- ^ Greninger Paper (PDF)
- ^ News Avian flu quarantine zone lifted published May 1, 2006.
- Official - international
World Health Organization
- The United Nation's World Health Organization's Avian Flu Facts Sheet for 2006
- Epidemic and Pandemic Alert and Response Guide to WHO's H5N1 pages
- Avian Influenza Resources (updated) - tracks human cases and deaths
- National Influenza Pandemic Plans
- WHO Collaborating Centres and Reference Laboratories Centers, names, locations, and phone numbers
- FAO Avian Influenza portal Information resources, animations, videos, photos
- WHO World Health Organization
- OIE World Organisation for Animal Health - tracks animal cases and deaths
- Official - United States
- PandemicFlu.Gov U.S. Government's avian flu information site
- USAID U.S. Agency for International Development - Avian Influenza Response
- CDC Centers for Disease Control - responsible agency for avian influenza in humans in US - Facts About Avian Influenza (Bird Flu) and Avian Influenza A (H5N1) Virus
- USGS - NWHC National Wildlife Health Center - responsible agency for avian influenza in animals in US
- HHS U.S. Department of Health & Human Services - Pandemic Influenza Plan
- Official - United Kingdom
- Exotic Animal Disease Generic Contingency Plan DEFRA generic contingency plan for controlling and eradicating an outbreak of an exotic animal disease. PDF hosted by BBC (a government entity).
- UK Influenza Pandemic Contingency Plan NHS (a government entity). Contingency planning for an influenza pandemic. PDF hosted by BBC
- Influenza Report 2006 Online book. Research level quality information. Highly recommended.
- Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Nature magazine presents a summary of what has been discovered in the Influenza Genome Sequencing Project.
- Links and descriptions to abstracts and full texts This bibliography of avian influenza publications was complied through the cooperative effort of the USGS National Wildlife Health Center and the Wildlife Disease Information Node.
- Search for research publications about H5N1: Entez PubMed
- Latest publications on H5N1
- Full HTML text of Avian Influenza A (H5N1) Infection in Humans by The Writing Committee of the World Health Organization (WHO) Consultation on Human Influenza A/H5 in the September 29, 2005 New England Journal of Medicine
- Evolutionary "Tree of Life" for H5N1:
- Here is the phylogenetic tree of the influenza virus hemagglutinin gene segment. Amino acid changes in three lineages (bird, pig, human) of the influenza virus hemagglutinin protein segment HA1.
- Here is the tree showing the evolution by reassortment of H5N1 from 1999 to 2004 that created the Z genotype in 2002.
- Here is the tree showing evolution by antigenic drift since 2002 that created dozens of highly pathogenic varieties of the Z genotype of avian flu virus H5N1, some of which are increasingly adapted to mammals.
- WHO (PDF} contains latest Evolutionary "Tree of Life" for H5N1 article Antigenic and genetic characteristics of H5N1 viruses and candidate H5N1 vaccine viruses developed for potential use as pre-pandemic vaccines published August 18, 2006
- Evolutionary characterization of the six internal genes of H5N1 human influenza A virus
- Genome database Page links to the complete sequence of the Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) genome.
- General information
- Avian influenza disease and control strategies site sponsored by Intervet International
- CIDRAP-Avian Flu
- Nature Magazine focus on the global spread of H5N1
- Bird Flu Fears: Is There a Better Way to Develop Drugs? (Center for Economic and Policy Research) October 2005 (PDF)
- Q&A: What is Bird Flu and Who's At Risk?
- Nature Magazine: Avian flu special: The flu pandemic: were we ready!? - Fictional account of flu epidemic from Nature magazine
- The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005) - Online book by Board on Global Health (BGH) from the Institute of Medicine of The National Academies
- Flu Wiki
- FAO's map of overlapping flyways for migratory waterfowl worldwide
- Google Earth updated maps of avian flu spread in poultry and humans
- Department of Health and Human Services Pandemic Planning Update A Report from Secretary Michael O. Leavitt March 13, 2006This report outlines how the 3.3 billon dollar funding is being used to help achieve HHSs five primary objectives around Pandemic Response.
- WHO Avian influenza resource (updated)
- CDC Facts About Avian Influenza (Bird Flu) and Avian Influenza A (H5N1) Virus
- FAO information on Avian Influenza - Latest news, Disease Card, Maps, Animations
- Avian Influenza (Bird Flu): Agricultural and Wildlife Considerations
Woodrow Wilson International Center for Scholars
(text and video)
- Emerging Pandemic: Costs and Consequences of an Avian Influenza Outbreak
- Critical Dialogues on Avian InfluenzaBringing Together the Public Health, Animal Health, and Wildlife Management Communities
- The Avian Flu Challenge in Southeast Asia: the Potential of Public-Private Partnerships
- Blauer's Bird Flu and H5N1 News Overview using Reuters and Yahoo News
- Current status (Google news of "H5N1")
- Bird Flu news updates
- Bird Flu News Focus from SciDev.Net, regularly updated with the latest news stories