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| {{Taxobox
| | #redirect [[Influenza]] |
| | name = [[Orthomyxoviridae]]
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| | image = Influenza A - late passage.jpg
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| | image_width = 175px
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| | image_description = Source: Dr. Erskine Palmer, [[Centers for Disease Control and Prevention|CDC]]
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| | image_caption = [[Electron micrograph]] of Influenza A viruses
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| | virus_group = v
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| | familia = '''''Orthomyxoviridae'''''
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| | subdivision_ranks = Genera
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| | subdivision = ''[[Influenzavirus A]]''<br>
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| ''[[Influenzavirus B]]''<br>
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| ''[[Influenzavirus C]]''<br>
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| ''[[Isavirus]]''<br>
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| ''[[Thogotovirus]]
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| }}
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| {{CMG}}
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| __NOTOC__
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| ==Overview==
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| {{Flu}}{{H5N1}}
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| '''Influenzavirus A''' is a [[genus]] of the [[Orthomyxoviridae]] family of [[virus]]es. Influenzavirus A includes only one [[species]]: ''Influenza A virus'' which causes [[influenza]] in [[bird]]s and some [[mammal]]s. Strains of all subtypes of influenza A virus have been isolated from wild birds, although disease is uncommon. Some [[isolates]] of influenza A virus cause severe disease both in domestic poultry and, rarely, in [[human]]s.<ref> [http://www.who.int/mediacentre/factsheets/avian_influenza/en/ WHO] Avian influenza (" bird flu") - Fact sheet</ref> Occasionally viruses are transmitted from wild aquatic birds to domestic poultry and this may cause an outbreak or give rise to human influenza [[pandemic]]s.<ref name=sobrino6>{{cite book |chapterurl=http://www.horizonpress.com/avir|author=Klenk et al|year=2008|chapter=Avian Influenza: Molecular Mechanisms of Pathogenesis and Host Range|title=Animal Viruses: Molecular Biology|publisher=Caister Academic Press|id=[http://www.horizonpress.com/avir ISBN 978-1-904455-22-6]}}</ref> <ref name=Kawaoka>{{cite book | author = Kawaoka Y (editor). | title = Influenza Virology: Current Topics | publisher = Caister Academic Press | year = 2006 | url=http://www.horizonpress.com/flu | id = [http://www.horizonpress.com/flu ISBN 978-1-904455-06-6 ]}}</ref>
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| ==Variants and subtypes==
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| Variants are identified and named according to the isolate that they are like and thus are presumed to share lineage (example [[Fujian flu]] virus like); according to their typical host (example [[Human flu]] virus); according to their subtype (example [[H3N2]]); and according to their deadliness (example LP). So a [[flu]] from a virus similar to the isolate A/Fujian/411/2002(H3N2) is called Fujian flu, human flu, and H3N2 flu.
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| Variants are sometimes named according to the species (host) the strain is endemic in or adapted to. The main variants named using this convention are:
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| * [[Avian influenza|Bird flu]]
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| * [[Human flu|Human Flu]]
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| * [[Swine flu|Swine Flu]]
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| * [[Horse flu|Horse Flu]]
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| * [[Dog flu|Dog Flu]]
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| Avian variants have also sometimes been named according to their deadliness in poultry, especially chickens:
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| * Low Pathogenic Avian Influenza (LPAI)
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| * Highly Pathogenic Avian Influenza (HPAI), also called: deadly flu or death flu
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| The Influenza A virus subtypes are labeled according to an H number (for [[hemagglutinin]]) and an N number (for [[neuraminidase]]). Each subtype virus has [[mutate]]d into a variety of strains with differing [[pathogenic]] profiles; some pathogenic to one species but not others, some pathogenic to multiple species. Most known strains are extinct strains. For example, the annual flu subtype [[H3N2]] no longer contains the strain that caused the [[Hong Kong Flu]].
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| Influenza A [[virus]]es are negative sense, single-stranded, segmented [[RNA virus]]es. "There are 16 different HA [[antigen]]s (H1 to H16) and nine different NA [[antigen]]s (N1 to N9) for influenza A. Until recently, 15 HA types had been recognized, but a new type (H16) was isolated from [[black-headed gull]]s caught in [[Sweden]] and the [[Netherlands]] in [[1999]] and reported in the literature in [[2005]]." <ref>[http://id_center.apic.org/cidrap/content/influenza/panflu/biofacts/panflu.html CIDRAP - Center for Infectious Disease Research And Policy] Pandemic Influenza Overview</ref>
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| == Annual flu ==
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| {{main|Flu season}}
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| The annual flu (also called "[[flu season|seasonal flu]]" or "[[human flu]]")
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| in the U.S. "results in approximately 36,000 deaths and more than 200,000 hospitalizations each year. In addition to this human toll, influenza is annually responsible for a total cost of over $10 billion in the U.S." <ref>[http://www.whitehouse.gov/homeland/pandemic-influenza.html whitehouse.gov] National Strategy for Pandemic Influenza - Introduction - "Although remarkable advances have been made in science and medicine during the past century, we are constantly reminded that we live in a universe of microbes - viruses, bacteria, protozoa and fungi that are forever changing and adapting themselves to the human host and the defenses that humans create. Influenza viruses are notable for their resilience and adaptability. While science has been able to develop highly effective vaccines and treatments for many infectious diseases that threaten public health, acquiring these tools is an ongoing challenge with the influenza virus. Changes in the genetic makeup of the virus require us to develop new vaccines on an annual basis and forecast which strains are likely to predominate. As a result, and despite annual vaccinations, the U.S. faces a burden of influenza that results in approximately 36,000 deaths and more than 200,000 hospitalizations each year. In addition to this human toll, influenza is annually responsible for a total cost of over $10 billion in the U.S. A pandemic, or worldwide outbreak of a new influenza virus, could dwarf this impact by overwhelming our health and medical capabilities, potentially resulting in hundreds of thousands of deaths, millions of hospitalizations, and hundreds of billions of dollars in direct and indirect costs. This Strategy will guide our preparedness and response activities to mitigate that impact."</ref>.
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| The annually updated trivalent [[influenza vaccine]] consists of [[hemagglutinin]] (HA) surface glycoprotein components from influenza [[H3N2]], [[H1N1]], and [[Influenzavirus B|B influenza]] viruses. <ref>[http://www.cdc.gov/ncidod/EID/vol11no08/05-0302.htm CDC] Centers for Disease Control and Prevention - Research Article - ''Influenza A (H3N2) Outbreak, Nepal'' - "The 2003–2004 influenza season was severe in terms of its impact on illness because of widespread circulation of antigenically distinct influenza A (H3N2) Fujian-like viruses. These viruses first appeared late during the 2002–2003 influenza season and continued to persist as the dominant circulating strain throughout the subsequent 2003–2004 influenza season, replacing the A/Panama/2007/99-like H3N2 viruses (1). Of the 172 H3N2 viruses genetically characterized by the Department of Defense in 2003–2004, only 1 isolate (from Thailand) belonged to the A/Panama-like lineage. In February 2003, the World Health Organization (WHO) changed the H3N2 component for the 2004–2005 influenza vaccine to afford protection against the widespread emergence of Fujian-like viruses (2). The annually updated trivalent vaccine consists of hemagglutinin (HA) surface glycoprotein components from influenza H3N2, H1N1, and B viruses."</ref>
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| The dominant strain in [[January 2006]] is [[H3N2]]. Measured resistance to the standard antiviral drugs [[amantadine]] and [[rimantadine]] in [[H3N2]] has increased from 1% in [[1994]] to 12% in [[2003]] to 91% in [[2005]].
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| "[C]ontemporary [[human]] [[H3N2]] influenza viruses are now [[endemic (epidemiology)|endemic]] in [[pig]]s in southern [[China]] and can [[reassortment|reassort]] with avian [[H5N1]] viruses in this intermediate host." <ref>[http://www.nap.edu/books/0309095042/html/126.html NAP Books] National Academies Press - Books - "The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)" - page 126 - "H5N1 virus is now endemic in poultry in Asia (Table 2-1) and has gained an entrenched ecological niche from which to present a long-term pandemic threat to humans. At present, these viruses are poorly transmitted from poultry to humans, and there is no conclusive evidence of human-to-human transmission. However, continued, extensive exposure of the human population to H5N1 viruses increases the likelihood that the viruses will acquire the necessary characteristics for efficient human-to-human transmission through genetic mutation or reassortment with a prevailing human influenza A virus. Furthermore, contemporary human [[H3N2]] influenza viruses are now endemic in pigs in southern China (Peiris et al., 2001) and can reassort with avian [[H5N1]] viruses in this 'intermediate host.' Therefore, it is imperative that outbreaks of H5N1 disease in poultry in Asia are rapidly and sustainably controlled. The seasonality of the disease in poultry, together with the control measures already implemented, are likely to reduce temporarily the frequency of H5N1 influenza outbreaks and the probability of human infection."</ref>
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| ==Genetics==
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| "The physical structure of all influenza A viruses is similar. The virions or virus particles are enveloped and can be either spherical or filamentous in form. In clinical isolates that have undergone limited passages in eggs or tissue culture, there are more filamentous than spherical particles, whereas passaged laboratory strains consist mainly of spherical virions."<ref> [http://www.clinicalservicesjournal.com/print.asp?id=872 Clinical Services Journal] article ''Avian influenza issues analysed'' published March 2006</ref>
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| The Influenza A virus genome is contained on eight single (non-paired) RNA strands that code for eleven proteins (HA, NA, NP, M1, M2, NS1, NEP, PA, PB1, PB1-F2, PB2). The segmented nature of the genome allows for the exchange of entire genes between different viral [[strain (biology)|strains]] during cellular cohabitation. The eight RNA segments are:
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| *HA encodes [[hemagglutinin]] (about 500 molecules of [[hemagglutinin]] are needed to make one [[virion]]) "The extent of infection into host organism is determined by HA. Influenza viruses bud from the apical surface of polarized epithelial cells (e.g. bronchial epithelial cells) into lumen of lungs and are therefore usually pneumotropic. The reason is that HA is cleaved by tryptase clara which is restricted to lungs. However HAs of H5 and H7 pantropic avian viruses subtypes can be cleaved by furin and subtilisin-type enzymes, allowing the virus to grow in other organs than lungs." <ref>[http://www.expasy.org/uniprot/P09345 UniProtKB/Swiss-Prot entry P09345] Complete sequence of a cDNA clone of the hemagglutinin gene of influenza A/Chicken/Scotland/59 (H5N1) virus: comparison with contemporary North American and European strains.</ref>
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| *NA encodes [[neuraminidase]] (about 100 molecules of [[neuraminidase]] are needed to make one [[virion]]).
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| *NP encodes [[nucleoprotein]].
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| *M encodes two [[matrix protein]]s (the [[M1 protein|M1]] and the [[M2 protein|M2]]) by using different [[reading frame]]s from the same RNA segment (about 3000 matrix protein molecules are needed to make one [[virion]]).
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| *NS encodes two distinct non-structural proteins (NS1 and NEP) by using different reading frames from the same RNA segment.
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| *PA encodes an [[RNA polymerase]].
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| *PB1 encodes an [[RNA polymerase]] and PB1-F2 protein (induces [[apoptosis]]) by using different reading frames from the same RNA segment.
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| *PB2 encodes an [[RNA polymerase]].
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| The genome segments have common terminal sequences, and the ends of the RNA strands are partially [[complementarity (molecular biology)|complementary]], allowing them to bond to each other by [[hydrogen bond]]s. After transcription from negative-sense to [[positive-sense RNA]] the +RNA strands get the cellular [[5' cap]] added by cap snatching, which involves the viral protein NS1 binding to the cellular pre-mRNAs. The cap is then cleaved from the cellular pre-mRNA using a second viral protein, PB2. The short [[oligo]] cap is then added to the influenza +RNA strands, allowing its processing as [[messenger RNA]] by [[ribosome]]s. The +RNA strands also serve for synthesis of -RNA strands for new virions.
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| The [[RNA]] synthesis and its assembly with the nucleoprotein takes place in the [[cell nucleus]], the synthesis of proteins takes place in the [[cytoplasm]]. The assembled virion cores leave the nucleus and migrate towards the [[cell membrane]], with patches of viral [[transmembrane protein]]s (hemagglutinin, neuraminidase and M2 proteins) and an underlying layer of the M1 protein, and [[budding|bud]] through these patches, releasing finished enveloped [[virus]]es into the [[extracellular fluid]].
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| ==In nonhumans==
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| :''See [[H5N1]] for the current [[epizootic]] (an [[epidemic]] in nonhumans) and panzootic (a disease affecting animals of many species especially over a wide area) of H5N1 influenza''
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| Wild [[fowl]] act as natural [[asymptomatic carrier]]s of Influenza A viruses. Prior to the current [[H5N1]] epizootic, strains of Influenza A virus had been demonstrated to be transmitted from wild fowl to only [[bird]]s, [[pig]]s, [[horse]]s, [[Pinniped|seal]]s, [[whale]]s and [[human]]s; and only between humans and pigs and between humans and domestic fowl; and not other pathways such as domestic fowl to horse. <ref>[http://www.nap.edu/books/0309095042/html/30.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 30</ref>
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| Wild aquatic birds are the natural hosts for a large variety of [[influenza]] A viruses. Occasionally viruses are transmitted from these birds to other species and may then cause devastating outbreaks in domestic poultry or give rise to human influenza [[pandemic]]s.<ref name=sobrino6>{{cite book |chapterurl=http://www.horizonpress.com/avir|author=Klenk et al|year=2008|chapter=Avian Influenza: Molecular Mechanisms of Pathogenesis and Host Range|title=Animal Viruses: Molecular Biology|publisher=Caister Academic Press|id=[http://www.horizonpress.com/avir ISBN 978-1-904455-22-6]}}</ref> <ref name=Kawaoka>{{cite book | author = Kawaoka Y (editor). | title = Influenza Virology: Current Topics | publisher = Caister Academic Press | year = 2006 | url=http://www.horizonpress.com/flu | id = [http://www.horizonpress.com/flu ISBN 978-1-904455-06-6 ]}}</ref>
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| [[H5N1]] has been shown to be transmitted to tigers, leopards, and domestic cats that were fed uncooked domestic fowl (chickens) with the virus. [[H3N8]] viruses from [[horse]]s have crossed over and caused outbreaks in [[dog]]s. Laboratory mice have been infected successfully with a variety of avian flu genotypes. <ref>[http://www.nap.edu/books/0309095042/html/82.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 82 - "Interestingly, recombinant influenza viruses containing the 1918 HA and NA and up to three additional genes derived from the 1918 virus (the other genes being derived from the A/WSN/33 virus) were all highly virulent in mice (Tumpey et al., 2004). Furthermore, expression microarray analysis performed on whole lung tissue of mice infected with the 1918 HA/ NA recombinant showed increased upregulation of genes involved in apoptosis, tissue injury, and oxidative damage (Kash et al., 2004). These findings were unusual because the viruses with the 1918 genes had not been adapted to mice. The completion of the sequence of the entire genome of the 1918 virus and the reconstruction and characterization of viruses with 1918 genes under appropriate biosafety conditions will shed more light on these findings and should allow a definitive examination of this explanation. Antigenic analysis of recombinant viruses possessing the 1918 HA and NA by hemagglutination inhibition tests using ferret and chicken antisera suggested a close relationship with the A/swine/Iowa/30 virus and H1N1 viruses isolated in the 1930s (Tumpey et al., 2004), further supporting data of Shope from the 1930s (Shope, 1936). Interestingly, when mice were immunized with different [[H1N1]] virus strains, challenge studies using the 1918-like viruses revealed partial protection by this treatment, suggesting that current vaccination strategies are adequate against a 1918-like virus (Tumpey et al., 2004)."</ref>
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| Influenza A viruses spread in the air and in [[manure]] and survives longer in cold weather. It can also be transmitted by contaminated feed, water, equipment and clothing; however, there is no evidence that the virus can survive in well-cooked meat. Symptoms in animals vary, but virulent [[strain (biology)|strain]]s can cause death within a few days.
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| "Highly pathogenic avian influenza virus is on every top ten list available for potential agricultural bioweapon agents". <ref>[http://www.nap.edu/books/0309095042/html/285.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 285 - "As of October 2001, the potential for use of infectious agents, such as anthrax, as weapons has been firmly established. It has been suggested that attacks on a nation’s agriculture might be a preferred form of terrorism or economic disruption that would not have the attendant stigma of infecting and causing disease in humans. Highly pathogenic avian influenza virus is on every top ten list available for potential agricultural bioweapon agents, generally following foot and mouth disease virus and Newcastle disease virus at or near the top of the list. Rapid detection techniques for bioweapon agents are a critical need for the first-responder community, on a par with vaccine and antiviral development in preventing spread of disease."</ref>
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| Avian influenza viruses that the [[OIE]] and others test for in order to control poultry disease include: [[H5N1]], [[H7N2]], [[H1N7]], [[H7N3]], [[H13N6]], [[H5N9]], [[H11N6]], [[H3N8]], [[H9N2]], [[H5N2]], [[H4N8]], [[H10N7]], [[H2N2]], [[H8N4]], [[H14N5]], [[H6N5]], [[H12N5]] and others.
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| ;Known outbreaks of highly pathogenic flu in poultry 1959-2003<ref>[http://www.who.int/csr/don/2004_03_02/en/ WHO] Avian influenza A(H5N1)- update 31: Situation (poultry) in Asia: need for a long-term response, comparison with previous outbreaks - Known outbreaks of highly pathogenic flu in poultry 1959-2003. </ref>
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| {|class="wikitable" width=500
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| |-
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| !Year
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| !Area
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| !Affected
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| !Subtype
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| |-
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| | 1959
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| | Scotland
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| | chicken
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| | [[H5N1]]
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| |-
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| | 1963
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| | England
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| | turkey
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| | [[H7N3]]
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| |-
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| | 1966
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| | Ontario (Canada)
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| | turkey
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| | [[H5N9]]
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| |-
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| | 1976
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| | Victoria (Australia)
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| | chicken
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| | [[H7N7]]
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| |-
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| | 1979
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| | Germany
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| | chicken
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| | [[H7N7]]
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| |-
| |
| | 1979
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| | England
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| | turkey
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| | [[H7N7]]
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| |-
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| | 1983
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| | Pennsylvania (USA)*
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| | chicken,turkey
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| | [[H5N2]]
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| |-
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| | 1983
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| | Ireland
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| | turkey
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| | [[H5N8]]
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| |-
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| | 1985
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| | Victoria (Australia)
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| | chicken
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| | [[H7N7]]
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| |-
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| | 1991
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| | England
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| | turkey
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| | [[H5N1]]
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| |-
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| | 1992
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| | Victoria (Australia)
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| | chicken
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| | [[H7N3]]
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| |-
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| | 1994
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| | Queensland (Australia)
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| | chicken
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| | [[H7N3]]
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| |-
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| | 1994
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| | Mexico*
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| | chicken
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| | [[H5N2]]
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| |-
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| | 1994
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| | Pakistan*
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| | chicken
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| | [[H7N3]]
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| |-
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| | 1997
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| | New South Wales (Australia)
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| | chicken
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| | [[H7N4]]
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| |-
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| | 1997
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| | Hong Kong (China)*
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| | chicken
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| | [[H5N1]]
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| |-
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| | 1997
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| | Italy
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| | chicken
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| | [[H5N2]]
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| |-
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| | 1999
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| | Italy*
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| | turkey
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| | [[H7N1]]
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| |-
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| | 2002
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| | Hong Kong (China)
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| | chicken
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| | [[H5N1]]
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| |-
| |
| | 2002
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| | Chile
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| | chicken
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| | [[H7N3]]
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| |-
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| | 2003
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| | Netherlands*
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| | chicken
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| | [[H7N7]]
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| |-
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| | colspan=4 |
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| <small>'' *Outbreaks with significant spread to numerous farms, resulting in great economic losses. Most other outbreaks involved little or no spread from the initially infected farms.'' </small>
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| |}
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| [[1979]]: "More than 400 harbor seals, most of them immature, died along the New England coast between [[1979#December|December 1979]] and [[October 1980]] of acute pneumonia associated with influenza virus, A/Seal/Mass/1/180 ([[H7N7]])." <ref>[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7063847&query_hl=49 NCBI - NLM - NIH] National Center for Biotechnology Information (part of) U.S. National Library of Medicine (part of) National Institutes of Health (part of) US Government - Science. 1982 Feb 26;215(4536):1129-31. - ''Mass mortality of harbor seals: pneumonia associated with influenza A virus.'' - "More than 400 harbor seals, most of them immature, died along the New England coast between December 1979 and October 1980 of acute pneumonia associated with influenza virus, A/Seal/Mass/1/180 (H7N7). The virus has avian characteristics, replicates principally in mammals, and causes mild respiratory disease in experimentally infected seals. Concurrent infection with a previously undescribed mycoplasma or adverse environmental conditions may have triggered the epizootic. The similarities between this epizootic and other seal mortalities in the past suggest that these events may be linked by common biological and environmental factors." </ref>
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| [[1995]]: "[V]accinated birds can develop asymptomatic infections that allow virus to spread, mutate, and recombine (ProMED-mail, 2004j). Intensive surveillance is required to detect these “silent epidemics” in time to curtail them. In Mexico, for example, mass vaccination of chickens against epidemic H5N2 influenza in [[1995]] has had to continue in order to control a persistent and evolving virus (Lee et al., [[2004]])." <ref>[http://www.nap.edu/books/0309095042/html/15.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 15 - "Unlike most other affected countries, Indonesia also instituted mass vaccination of healthy domestic birds against H5N1, followed by routine vaccination (China has a similar policy; other Asian countries are considering it [ProMED-mail, 2004j]) (Soebandrio, 2004). This is a risky strategy, because vaccinated birds can develop asymptomatic infections that allow virus to spread, mutate, and recombine (ProMED-mail, 2004j). Intensive surveillance is required to detect these “silent epidemics” in time to curtail them. In Mexico, for example, mass vaccination of chickens against epidemic H5N2 influenza in 1995 has had to continue in order to control a persistent and evolving virus (Lee et al., 2004)."</ref>
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| [[1997]]: "Influenza A viruses normally seen in one species sometimes can cross over and cause illness in another species. For example, until [[1997]], only [[H1N1]] viruses circulated widely in the U.S. [[pig]] population. However, in [[1997]], [[H3N2]] viruses from humans were introduced into the pig population and caused widespread disease among pigs. Most recently, [[H3N8]] viruses from [[horse]]s have crossed over and caused outbreaks in [[dog]]s." <ref>[http://www.cdc.gov/flu/avian/gen-info/transmission.htm CDC] Centers for Disease Control and Prevention - ''Transmission of Influenza A Viruses Between Animals and People''</ref>
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| [[2000]]: "In [[California]], [[poultry]] producers kept their knowledge of a recent [[H6N2]] avian influenza outbreak to themselves due to their fear of public rejection of poultry products; meanwhile, the disease spread across the western United States and has since become endemic." <ref>[http://www.nap.edu/books/0309095042/html/27.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 27.</ref>
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| [[2003]]: In [[Netherlands]] [[H7N7]] influenza virus infection broke out in poultry on several farms. <ref>[http://news.bbc.co.uk/1/hi/programmes/panorama/4412932.stm BBC News] ''Early bird flu warning for Dutch'' - 6 November 2005 </ref>
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| [[2004]]: In [[North America]], the presence of avian influenza strain [[H7N3]] was confirmed at several [[poultry]] farms in [[British Columbia]] in [[February 2004]]. As of [[April 2004]], 18 farms had been quarantined to halt the spread of the virus. <ref>[http://www.cdc.gov/ncidod/EID/vol10no12/04-0961.htm CDC detailed analysis] ''Human Illness from Avian Influenza H7N3, British Columbia''</ref>
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| [[2005]]: Tens of millions of birds died of [[H5N1]] influenza and hundreds of millions of birds were culled to protect humans from [[H5N1]]. [[H5N1]] is endemic in birds in southeast Asia and represents a long term pandemic threat.
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| [[2006]]: [[H5N1]] spreads across the globe killing hundreds of millions of birds and over 100 people causing a significant [[H5N1 impact]] from both actual deaths and predicted possible deaths.
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| ;Swine flu
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| {{main|Swine Flu}}
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| :[[Swine flu]] (or "pig influenza") refers to a subset of [[Orthomyxoviridae]] that create [[influenza]] in [[pigs]] and are [[endemic (epidemiology)|endemic]] in pigs. The species of [[Orthomyxoviridae]] that can cause flu in pigs are Influenza A virus and [[Influenzavirus C|Influenza C virus]] but not all genotypes of these two species infect pigs. The known subtypes of Influenza A virus that create [[influenza]] in [[pigs]] and are [[endemic (epidemiology)|endemic]] in pigs are [[H1N1]], [[H1N2]], [[H3N1]] and [[H3N2]].
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| ;Horse flu
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| {{main|Horse flu}}
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| :[[Horse flu]] (or "Equine influenza") refers to varieties of Influenza A virus that affect horses. Horse 'flu viruses were only isolated in 1956. There are two main types of virus called equine-1 ([[H7N7]]) which commonly affects horse heart muscle and equine-2 ([[H3N8]]) which is usually more severe.
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| ;Dog flu
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| {{main|Dog flu}}
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| :[[Dog flu]] (or "canine influenza") refers to varieties of Influenza A virus that affect dogs. The equine influenza virus [[H3N8]] was found to infect and kill greyhound race dogs that had died from a respiratory illness at a Florida racetrack in [[January 2004]].
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| ;H3N8
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| {{main|H3N8}}
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| :[[H3N8]] is now endemic in birds, horses and dogs.
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| ==Human influenza virus==
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| "Human influenza virus" usually refers to those subtypes that spread widely among humans. [[H1N1]], [[H1N2]], and [[H3N2]] are the only known Influenza A virus subtypes currently circulating among humans. <ref>[http://www.cdc.gov/flu/avian/gen-info/facts.htm CDC] ''Key Facts About Avian Influenza (Bird Flu) and Avian Influenza A (H5N1) Virus''</ref>
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| Genetic factors in distinguishing between "[[human flu]] viruses" and "[[avian influenza]] viruses" include:
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| :'''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 [[Glutamic acid|Glu]] at position 627, while all human influenza viruses had a [[lysine]].
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| :'''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.
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| "About 52 key genetic changes distinguish avian influenza strains from those that spread easily among people, according to researchers in Taiwan, who analyzed the genes of more than 400 A type flu viruses."<ref> [http://www.bloomberg.com/apps/news?pid=20601086&sid=a6S3ZQwqZkS4&refer=latin_america Bloomberg News] article '' Scientists Move Closer to Understanding Flu Virus Evolution'' published August 28, 2006</ref> "How many mutations would make an avian virus capable of infecting humans efficiently, or how many mutations would render an influenza virus a pandemic strain, is difficult to predict. We have examined sequences from the 1918 strain, which is the only pandemic influenza virus that could be entirely derived from avian strains. Of the 52 species-associated positions, 16 have residues typical for human strains; the others remained as avian signatures. The result supports the hypothesis that the 1918 pandemic virus is more closely related to the avian influenza A virus than are other human influenza viruses."<ref> [http://www.cdc.gov/ncidod/EID/vol12no09/06-0276.htm CDC] Emerging Infectious Diseases Journal Volume 12, Number 9 – September 2006 - ''Genomic Signatures of Human versus Avian Influenza A Viruses article'' by Chen G-W, Chang S-C, Mok C-K, Lo Y-L, Kung Y-N, Huang J-H, et al. posted August 23, 2006</ref>
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| [[Human flu]] symptoms usually include
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| [[fever]], [[cough]], [[sore throat]], [[myalgia|muscle aches]], [[conjunctivitis]] and, in severe cases, severe breathing problems and [[pneumonia]] that may be fatal. The severity of the infection will depend to a large part on the state of the infected person's [[immune system]] and if the victim has been exposed to the strain before, and is therefore partially immune.
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| Highly pathogenic [[H5N1]] [[avian influenza]] in a human is far worse, killing 50% of humans that catch it. In one case, a boy with H5N1 experienced [[diarrhea]] followed rapidly by a [[coma]] without developing respiratory or flu-like symptoms. <ref>[http://content.nejm.org/cgi/content/short/352/7/686 New England Journal of Medicine] Volume 352:686-691 - February 17, 2005 - Number 7 - ''Fatal Avian Influenza A (H5N1) in a Child Presenting with Diarrhea Followed by Coma''</ref>
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| The Influenza A virus subtypes that have been confirmed in [[humans]], ordered by the number of known human pandemic deaths, are:
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| *[[H1N1]] caused "[[Spanish Flu]]"
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| *[[H2N2]] caused "Asian Flu"
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| *[[H3N2]] caused "Hong Kong Flu"
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| *[[H5N1]] is the world's major [[influenza pandemic]] threat
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| *[[H7N7]] has unusual [[zoonotic]] potential
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| *[[H1N2]] is currently endemic in humans and pigs
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| *[[H9N2]], [[H7N2]], [[H7N3]], [[H10N7]].
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| ;H1N1
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| {{main|H1N1}}
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| :[[H1N1]] is currently endemic in both human and pig populations. A variant of [[H1N1]] was responsible for the [[Spanish flu]] [[pandemic]] that killed some 50 million to 100 million people worldwide over about a year in [[1918]] and [[1919]]. <ref>[http://www.nap.edu/books/0309095042/html/7.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 7.</ref> Controversy arose in October, [[2005]], after the H1N1 [[genome]] was published in the journal, [[Science (journal)|''Science'']]. Many fear that this information could be used for [[bioterrorism]].
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| :"When he compared the [[Spanish flu|1918 virus]] with today's human flu viruses, Dr. Taubenberger noticed that it had alterations in just 25 to 30 of the virus's 4,400 amino acids. Those few changes turned a bird virus into a killer that could spread from person to person." <ref>[http://www.nytimes.com/2005/11/08/science/08flu.html?pagewanted=2 New York Times] Published: November 8, 2005 - ''Hazard in Hunt for New Flu: Looking for Bugs in All the Wrong Places''</ref>
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| ;H2N2
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| {{main|H2N2}}
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| :The [[Asian Flu]] was a [[pandemic]] outbreak of [[H2N2]] avian influenza that originated in [[China]] in [[1957]], spread worldwide that same year during which a [[influenza vaccine]] was developed, lasted until [[1958]] and caused between one and four million deaths.
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| ;H3N2
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| {{main|H3N2}}
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| :[[H3N2]] is currently endemic in both human and pig populations. It evolved from [[H2N2]] by [[antigenic shift]] and caused the [[Hong Kong Flu]] pandemic of 1968 and 1969 that killed up to 750,000. <ref>Detailed chart of its evolution [http://www.eletrica.ufsj.edu.br/~nepomuceno/references/epidemiology/ear_eal02.pdf here] at PDF called ''Ecology and Evolution of the Flu''</ref> "An early-onset, severe form of influenza A [[H3N2]] made headlines when it claimed the lives of several children in the United States in late [[2003]]." <ref>[http://www.nap.edu/books/0309095042/html/115.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 115 - "There is particular pressure to recognize and heed the lessons of past influenza pandemics in the shadow of the worrisome 2003–2004 flu season. An early-onset, severe form of influenza A [[H3N2]] made headlines when it claimed the lives of several children in the United States in late 2003. As a result, stronger than usual demand for annual flu inactivated vaccine outstripped the vaccine supply, of which 10 to 20 percent typically goes unused. Because statistics on pediatric flu deaths had not been collected previously, it is unknown if the 2003–2004 season witnessed a significant change in mortality patterns."</ref>
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| :The dominant strain of annual flu in [[January 2006]] is [[H3N2]]. Measured resistance to the standard antiviral drugs [[amantadine]] and [[rimantadine]] in H3N2 has increased from 1% in [[1994]] to 12% in [[2003]] to 91% in [[2005]]. <ref>[http://www.reason.com/rb/rb101905.shtml Reason] [http://www.nytimes.com/2006/01/15/health/15drugs.html New York Times] ''This Season's Flu Virus Is Resistant to 2 Standard Drugs'' By Altman Published: January 15, 2006 </ref>
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| :"[C]ontemporary human [[H3N2]] influenza viruses are now endemic in pigs in southern China and can reassort with avian [[H5N1]] viruses in this intermediate host." <ref>[http://www.nap.edu/books/0309095042/html/126.html NAP Books] National Academies Press Books - ''The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)'' - page 126</ref>
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| ;H5N1
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| {{main|H5N1}}
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| :[[H5N1]] is the world's major [[influenza pandemic]] threat.
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| ;H7N7
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| {{main|H7N7}}
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| :[[H7N7]] has unusual zoonotic potential. In [[2003]] in [[Netherlands]] 89 people were confirmed to have H7N7 influenza virus infection following an outbreak in poultry on several farms. One death was recorded.
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| ;H1N2
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| {{main|H1N2}}
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| :[[H1N2]] is currently endemic in both human and pig populations. The new [[H1N2]] strain appears to have resulted from the reassortment of the genes of the currently circulating influenza [[H1N1]] and [[H3N2]] subtypes. The [[hemagglutinin]] protein of the [[H1N2]] virus is similar to that of the currently circulating [[H1N1]] viruses and the [[neuraminidase]] protein is similar to that of the current [[H3N2]] viruses.
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| ;H9N2
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| {{main|H9N2}}
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| :Low pathogenic avian influenza A ([[H9N2]]) infection was confirmed in [[1999]], in [[China]] and [[Hong Kong]] in two children, and in [[2003]] in [[Hong Kong]] in one child. All three fully recovered. <ref>[http://www.cdc.gov/flu/avian/gen-info/avian-flu-humans.htm CDC] ''Avian Influenza Infection in Humans''</ref>
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| ;H7N2
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| {{main|H7N2}}
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| :One person in [[New York]] in [[2003]] and one person in [[Virginia]] in [[2002]] were found to have serologic evidence of infection with [[H7N2]]. Both fully recovered. <ref>[http://www.cdc.gov/flu/avian/gen-info/avian-flu-humans.htm CDC] ''Avian Influenza Infection in Humans''</ref>
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| ;H7N3
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| {{main|H7N3}}
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| :In [[North America]], the presence of avian influenza strain [[H7N3]] was confirmed at several poultry farms in [[British Columbia]] in [[February 2004]]. As of [[April 2004]], 18 farms had been quarantined to halt the spread of the virus. Two cases of humans with avian influenza have been confirmed in that region. "Symptoms included [[conjunctivitis]] and mild [[influenza]]-like illness." <ref>[http://www.cdc.gov/ncidod/EID/vol10no12/04-0961.htm CDC detailed analysis] ''Human Illness from Avian Influenza H7N3, British Columbia''</ref> Both fully recovered.
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| ;H10N7
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| {{main|H10N7}}
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| :In [[2004]] in [[Egypt]] [[H10N7]] is reported for the first time in humans. It caused illness in two infants in Egypt. One child’s father is a [[poultry]] merchant. <ref>[http://www3.niaid.nih.gov/news/focuson/flu/illustrations/timeline/timeline.htm niaid.nih.gov] Timeline of Human Flu Pandemics</ref>
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| ===Evolution===
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| :{{See also|Punctuated equilibrium}}
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| Taubenberger says:
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| :"All influenza A pandemics since [the [[Spanish flu]] pandemic], and indeed almost all cases of influenza A worldwide (excepting human infections from avian viruses such as [[H5N1]] and [[H7N7]]), have been caused by descendants of the 1918 virus, including "drifted" [[H1N1]] viruses and reassorted [[H2N2]] and [[H3N2]] viruses. The latter are composed of key genes from the 1918 virus, updated by subsequently incorporated [[avian influenza]] genes that code for novel surface proteins, making the 1918 virus indeed the "mother" of all [[pandemic]]s.<ref> [http://www.cdc.gov/ncidod/EID/vol12no01/05-0979.htm CDC] ARTICLE ''1918 Influenza: the Mother of All Pandemics'' by Jeffery K. Taubenberger published January 2006</ref>
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| Researchers from the [[National Institutes of Health]] used data from the [[Influenza Genome Sequencing Project]] and concluded that during the ten-year period examined most of the time the [[hemagglutinin]] gene in [[H3N2]] showed no significant excess of mutations in the antigenic regions while an increasing variety of strains accumulated. This resulted in one of the variants eventually achieving higher fitness, becoming dominant, and in a brief interval of rapid Darwinian [[evolution]] rapidly sweeping through the human population and eliminating most other variants.<ref> [http://www.sciencedaily.com/releases/2006/10/061026185115.htm Science Daily] article ''New Study Has Important Implications For Flu Surveillance'' published October 27, 2006</ref>
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| ==See also==
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| * [[Animal virology]]
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| * [[ACAM-FLU-A]]
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| ==Further reading==
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| ;Official sources
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| {{further|[[H5N1]]}}
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| *[http://www.cdc.gov/flu/avian Avian influenza] and [http://www.cdc.gov/flu/avian/gen-info/pandemics.htm Influenza Pandemics] from the [[Centers for Disease Control and Prevention]]
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| *[http://www.who.int/csr/disease/avian_influenza/avian_faqs/en Avian influenza] [[FAQ]] from the [[World Health Organization]]
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| *[http://www.fao.org/ag/againfo/subjects/en/health/diseases-cards/special_avian.html Avian influenza information] from the [[Food and Agriculture Organization]]
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| *[http://www.pandemicflu.gov U.S. Government's avian influenza information website]
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| *[http://www.ecdc.eu.int European Centre for Disease Prevention and Control] ([[ECDC]]) Stockholm, Sweden
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| ;General information
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| {{further|[[Flu]]}}
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| *[http://www.ndu.edu/ctnsp/Bird_flu.htm "The Bird Flu and You"] Full-color poster provided by the [[Center for Technology and National Security Policy]] at the [[National Defense University]], in collaboration with the [[National Security Health Policy Center]]
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| *[http://www.InfluenzaReport.com Influenza Report 2006] Online book. Research level quality information. Highly recommended.
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| *[http://www.nature.com/nature/focus/avianflu/index.html Special issue on avian flu] from ''[[Nature (journal)|Nature]]''
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| *[http://content.nejm.org/cgi/content/full/353/13/1374 Overview of H5N1] from ''[[New England Journal of Medicine]]''
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| *[http://digital.library.unt.edu/govdocs/crs/permalink/meta-crs-7927 Pandemic Influenza: Domestic Preparedness Efforts] Congressional Research Service Report on Pandemic Preparedness.
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| *[http://www.bbc.co.uk/health/conditions/birdflu1.shtml A guide to bird flu and its symptoms] from [[BBC]] Health
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| *[http://3dscience.com/Avian_Flu_Bird_Flu_License_Free_Images.asp A Variety of Avian Flu Images and Pictures]
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| *[http://www.nap.edu/books/0309095042/html/285.html Avian flu, bioterror, animals (page in an online book)] "Highly pathogenic avian influenza virus is on every top ten list available for potential agricultural bioweapon agents"
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| *[http://www.healthpolitics.com/archives.asp?previous=bird_flu&bhcp=1 'The Threat of Bird Flu': HealthPolitics.com]
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| *[http://www.infectioncontroltoday.com/articles/531feat1.html Is a Global Flu Pandemic Imminent?] from ''Infection Control Today''.
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| *[http://www.ninthday.com/bird_flu.htm Bird Flu is a Real Pandemic Threat to Humans] by Leonard Crane, author of [[Ninth Day of Creation]].
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| *[http://www.lib.uiowa.edu/hardin/md/birdflu.html Links to Bird Flu pictures (Hardin MD/Univ of Iowa)]
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| *[http://www.fluwikie.com/ Flu Wiki]
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| *[http://www.horizonpress.com/flu Influenza Virology: Current Topics ISBN 978-1-904455-06-6]
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| *[http://www.horizonpress.com/avir Animal Viruses: Molecular Biology ISBN 978-1-904455-22-6]
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| ;News
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| *[http://news.google.com/news?q=avian+OR+bird+flu+OR+influenza&hl=en&lr=&sa=N&tab=wn Current status (Google news of avian OR bird flu OR influenza)]
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| *[http://www.aboutflu.net/ Flu Breaking News] Avian flu, common symptom, influenza vaccine and flu shot and latest news
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| *[http://www.pandemic-news.info/pandemic.htm Global Pandemic News : 24×7 online news feeds on the threat of Bird Flu and a Global Pandemic]
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| ==References==
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| {{reflist|2}}
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| {{Influenza}}
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| [[Category:H5N1]]
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