Transmission and infection of H5N1

# Overview
Transmission and infection of H5N1 from infected avian sources to humans is a concern due to the global spread of H5N1 that constitutes a pandemic threat.
Infected birds pass on H5N1 through their saliva, nasal secretions, and faeces. Other birds may pick up the virus through direct contact with these excretions or when they have contact with surfaces contaminated with this material. Because migratory birds are among the carriers of the H5N1 virus it may spread to all parts of the world. Past outbreaks of avian flu have often originated in crowded conditions in southeast and east Asia, where humans, pigs, and poultry live in close quarters. In these conditions a virus is more likely to mutate into a form that more easily infects humans. A few isolated cases of suspected human to human transmission exist, with the latest such case in June 2006 (among members of a family in Sumatra). No pandemic strain of H5N1 has yet been found.
H5N1 vaccines for chickens exist and are sometimes used, although there are many difficulties, and it's difficult to decide whether it helps more or hurts more. H5N1 pre-pandemic vaccines exist in quantities sufficient to inoculate a few million people and might be useful for priming to "boost the immune response to a different H5N1 vaccine tailor-made years later to thwart an emerging pandemic". H5N1 pandemic vaccines and technologies to rapidly create them are in the H5N1 clinical trials stage but can not be verified as useful until after there exists a pandemic strain.

# Avian flu in birds
According to Avian Influenza by Timm C. Harder and Ortrud Werner:
The current method of prevention in animal populations is to destroy infected animals, as well as animals suspected of being infected.  In southeast Asia, millions of domestic birds have been slaughtered to prevent the spread of the virus.

## Poultry farming practices
There have been a number of farming practices that have changed in response to outbreaks of the H5N1 virus, including:
- vaccinating poultry against bird flu
- vaccinating poultry workers against human flu
- limiting travel in areas where H5N1 is found
- increasing farm hygiene
- reducing contact between livestock and wild birds
- reducing open-air wet markets
- limiting workers contact with cock fighting
- reducing purchases of live fowl
- improving veterinary vaccine availability and cost. 
For example, after nearly two years of using mainly culling to control the virus, the Vietnamese government in 2005 adopted a combination of mass poultry vaccination, disinfecting, culling, information campaigns and bans on live poultry in cities.

## Dealing with outbreaks
The majority of H5N1 flu cases have been reported in southeast and east Asia. Once an outbreak is detected, local authorities often order a mass slaughter of birds or animals affected. If this is done promptly, an outbreak of avian flu may be prevented. However, the United Nations (UN) World Health Organization (WHO) has expressed concern that not all countries are reporting outbreaks as completely as they should.  China, for example, is known to have initially denied past outbreaks of severe acute respiratory syndrome (SARS) and HIV, although there have been some signs of improvement regarding its openness in recent months, particularly with regard to H5N1.

## Use of vaccines
Dr. Robert Webster et al write
Webster speculates that substandard vaccines may be preventing the expression of the disease in the birds but not stopping them from carrying or transmitting the virus through feces, or the virus from mutating.
In order to protect their poultry from death from H5N1, China reportedly made a vaccine based on reverse genetics produced with H5N1 antigens, that Dr Wendy Barclay, a virologist at the University of Reading believes have generated up to six variations of H5N1. 

## Transmission
According to the United Nations FAO, wild water fowl likely plays a role in the avian influenza cycle and could be the initial source for AI viruses, which may be passed on through contact with resident water fowl or domestic poultry, particularly domestic ducks. A newly mutated virus could circulate within the domestic and possibly resident bird populations until HPAI arises. This new virus is pathogenic to poultry and possibly to the wild birds that it arose from.
Wild birds found to have been infected with HPAI were either sick or dead. This could possibly affect the ability of these birds to carry HPAI for long distances. However, the findings in Qinghai Lake-China, suggest that H5N1 viruses could possibly be transmitted between migratory birds. Additionally, the new outbreaks of HPAI in poultry and wild birds in Russia, Kazakhstan, Western China and Mongolia may indicate that migratory birds probably act as carriers for the transport of HPAI over longer distances. Short distance transmission between farms, villages or contaminated local water bodies is likewise a distinct possibility.
The AI virus has adapted to the environment in ways such as using water for survival and to spread, and creating a reservoir (ducks) strictly tied to water. The water in turn influences movement, social behavior and migration patterns of water bird species. It is therefore of great importance to know the ecological strategy of influenza virus as well, in order to fully understand this disease and to control outbreaks when they occur. Most research is needed concerning HPAI viruses in wild birds. For example, small birds like sparrows, starlings and pigeons can be infected with deadly H5N1 strains and they can carry the virus from chicken house to chicken house causing massive epidemics among the chickens.

# Avian flu in humans

## Human to human transmission
H5N1 infections in humans are generally attributed to bird to human transmission of the virus.  Until May 2006, the WHO estimate of the number of human to human transmission had been "two or three cases". On May 24, 2006, Dr. Julie L. Gerberding, director of the United States Centers for Disease Control and Prevention in Atlanta, estimated that there had been "at least three." On May 30, Maria Cheng, a WHO spokeswoman, said there were "probably about half a dozen," but that no one "has got a solid number." A few isolated cases of suspected human to human transmission exist. with the latest such case in June 2006 (among members of a family in Sumatra). No pandemic strain of H5N1 has yet been found. The key point is that, at present, "the virus is not spreading efficiently or sustainably among humans."
There is also concern, although no definitive proof, that other animals  particularly cats  may be able to act as a bridge between birds and humans. So far several cats have been confirmed to have died from H5N1 and the fact that cats have regular close contact with both birds and humans means monitoring of H5N1 in cats will need to continue.

## Prevention
The probability of a "humanized" form of H5N1 emerging through genetic recombination in the body of a human co-infected with H5N1 and another influenza virus type (a process called reassortment) could be reduced by influenza vaccination of those at risk for infection by H5N1. It is not clear at this point whether vaccine production and immunization could be stepped up sufficiently to meet this demand.  Additionally, vaccination of only humans would not address the possibility or reassortment in pigs, cats, or other mammal hosts.
If an outbreak of pandemic flu does occur, its spread might be slowed by increasing hygiene in aircraft, and by examining airline cabin air filters for presence of H5N1 virus.
The American Centers for Disease Control and Prevention advises travelers to areas of Asia where outbreaks of H5N1 have occurred to avoid poultry farms and animals in live food markets . Travelers should also avoid surfaces that appear to be contaminated by feces from any kind of animal, especially poultry.
There are several H5N1 vaccines for several of the avian H5N1 varieties. H5N1 continually mutates rendering them, so far for humans, of little use. While there can be some cross-protection against related flu strains, the best protection would be from a vaccine specifically produced for any future pandemic flu virus strain. Dr. Daniel Lucey, co-director of the Biohazardous Threats and Emerging Diseases graduate program at Georgetown University has made this point, "There is no H5N1 pandemic so there can be no pandemic vaccine."  However, "pre-pandemic vaccines" have been created; are being refined and tested; and do have some promise both in furthering research and preparedness for the next pandemic . Vaccine manufacturing companies are being encouraged to increase capacity so that if a pandemic vaccine is needed, facilities will be available for rapid production of large amounts of a vaccine specific to a new pandemic strain.
It is not likely that use of antiviral drugs could prevent the evolution of a pandemic flu virus. 

## Environmental survival
Avian flu virus can last indefinitely at a temperature dozens of degrees below freezing, as is found in the northern most areas that migratory birds frequent.
Heat kills H5N1 (i.e. inactivates the virus).
Influenza A viruses can survive:
- Over 30 days at 0C (32.0F) (over one month at freezing temperature)
- 6 days at 37C (98.6F) (one week at human body temperature)
- decades in permanently frozen lakes
- on hard non-porous surface such as plastic or stainless steel for 24-48 hours
- on clothes, paper and tissues for 8-12 hours
While cooking poultry to 70C (158F) kills the H5N1 virus, it is recommended to cook meat to 165F to kill all foodborne pathogens.
Inactivation of the virus also occurs under the following conditions:
- 30 minutes 60C (140.0F) (half hour at a temperature that causes first and second degree burns in humans in ten seconds)
- Acidic pH conditions
- Presence of oxidizing agents such as sodium dodecyl sulfate, lipid solvents, and B-propiolactone
- Exposure to disinfectants: formalin, iodine compounds 
Ordinary levels of chlorine in tap water kill H5N1 in public water systems.
To kill avian flu viruses, the "World Health Organization recommends that environmental surfaces be cleaned by the following:
- Disinfectants such as sodium hypochloride, 1% in-use dilution, 5% solution to be diluted 1:5 in clean water, for materials contaminated with blood and body fluids
- Bleaching powder seven grams per liter with 70% available chlorine for toilets and bathrooms
- 70% alcohol for smooth surfaces, tabletops, and other surfaces where bleach cannot be used"

## Symptoms
The human incubation period of avian influenza A (H5N1) is 2 to 17 days. Once infected, the virus can spread by cell-to-cell contact, bypassing receptors. So even if a strain is very hard to initially catch, once infected, it spreads rapidly within a body. For highly pathogenic H5N1 avian influenza in a human, "the time from the onset to presentation (median, 4 days) or to death (median, 9 to 10 days) has remained unchanged from 2003 through 2006."
Avian influenza HA bind alpha 2-3 sialic acid receptors while human influenza HA bind alpha 2-6 sialic acid receptors. Usually other differences also exist. There is as yet no human form of H5N1, so all humans who have caught it so far have caught avian H5N1.
Human flu symptoms usually include
fever, cough, sore throat, 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. No one knows if these or other symptoms will be the symptoms of a humanized H5N1 flu.
Highly pathogenic H5N1 avian influenza in a human appears to be far worse, killing over 50% of humans reported infected with the virus, although it is unknown how many cases (with milder symptoms) go unreported. In one case, a boy with H5N1 experienced diarrhea followed rapidly by a coma without developing respiratory or flu-like symptoms. 
As of February 2008, the "median age of patients with influenza A (H5N1) virus infection is approximately 18 years  The overall case fatality proportion is 61%  Handling of sick or dead poultry during the week before the onset of illness is the most commonly recognized risk factor  The primary pathologic process that causes death is fulminant viral pneumonia."
There have been studies of the levels of cytokines in humans infected by the H5N1 flu virus. Of particular concern is elevated levels of tumor necrosis factor-alpha (TNF), a protein that is associated with tissue destruction at sites of infection and increased production of other cytokines. Flu virus-induced increases in the level of cytokines is also associated with flu symptoms including fever, chills, vomiting and headache. Tissue damage associated with pathogenic flu virus infection can ultimately result in death . The inflammatory cascade triggered by H5N1 has been called a 'cytokine storm' by some, because of what seems to be a positive feedback process of damage to the body resulting from immune system stimulation. H5N1 type flu virus induces higher levels of cytokines than the more common flu virus types such as H1N1  Other important mechanisms also exist "in the acquisition of virulence in avian influenza viruses" according to the CDC.
The NS1 protein of the highly pathogenic avian H5N1 viruses circulating in poultry and waterfowl in Southeast Asia is currently believed to be responsible for the enhanced proinflammatory cytokine response. H5N1 NS1 is characterized by a single amino acid change at position 92. By changing the amino acid from glutamic acid to aspartic acid, researchers were able to abrogate the effect of the H5N1 NS1. This single amino acid change in the NS1 gene greatly increased the pathogenicity of the H5N1 influenza virus.
In short, this one amino acid difference in the NS1 protein produced by the NS RNA molecule of the H5N1 virus is believed to be largely responsible for an increased pathogenicity (on top of the already increased pathogenicity of its hemagglutinin type which allows it to  grow in organs other than lungs) that can manifest itself by causing a cytokine storm in a patient's body, often causing pneumonia and death.

## Treatment
Neuraminidase inhibitors are a class of drugs that includes zanamivir and oseltamivir, the latter being licensed for prophylaxis treatment in the United Kingdom. Oseltamivir inhibits  the influenza virus from spreading inside the user's body . It is marketed by Roche as Tamiflu. This drug has become a focus for some governments and organizations trying to be seen as making preparations for a possible H5N1 pandemic.  In August 2005, Roche agreed to donate three million courses of Tamiflu be deployed by the WHO to contain a pandemic in its region of origin. Although Tamiflu is patented, international law gives governments wide freedom to issue compulsory licenses for life-saving drugs.
A second class of drugs, which include amantadine and rimantadine, target the M2 protein, but have become ineffective against most strains of H5N1, due to their use in poultry in China in the 1990's, which created resistant strains. . However, recent data suggest that some strains of H5N1 are susceptible to the older drugs, which are inexpensive and widely available.
Research indicates that therapy to block one cytokine to lessen a cytokine storm in a patient may not be clinically beneficial.

## Mortality rate
From inception through 2007, the number of WHO-confirmed cases stands at 360, with 226 fatalities (as reported by the U.N.on January 3, 2008, confirming earlier deaths) reflecting a 62.78% fatality rate among WHO-confirmed cases.
The global case fatality ratio looks only to the official tally of cases confirmed by the WHO. It takes no account of other cases, such as those appearing in press reports.  Nor does it reflect any estimate of the global extent of mild, asymptomatic, or other cases which are undiagnosed, unreported by national governments to the WHO, or for any reason cannot be confirmed by the WHO.  While the WHO's case count is clearly the most authoritative, these unavoidable limitations result in an unknown number of cases being omitted from it.

# Notes and references
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-  "Vietnam to unveil advanced plan to fight bird flu". Reuters. April 28 2006. Check date values in: |date= (help)
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-  "Expert: Bad vaccines may trigger China bird flu". MSNBC. December 30 2005. Retrieved 2006-09-15. Check date values in: |date= (help)
-  "Bird flu vaccine no silver bullet". BBC. February 22 2006. Retrieved 2006-09-15. Check date values in: |date= (help)
-  "Wild birds and Avian Influenza". FAO. Retrieved 2006-09-15.
-  "Small birds must be kept out of poultry farms". World Poultry. December 12 2006. Check date values in: |date= (help)
-  Donald G. McNeil Jr. (June 4 2006). "Human Flu Transfers May Exceed Reports". New York Times. Check date values in: |date= (help)
-  "Seven Indonesian Bird Flu Cases Linked to Patients". Bloomberg. May 23 2006. Check date values in: |date= (help)
-  "WHO confirms human transmission< in Indonesian bird flu cluster".
-  "Avian influenza  situation in Indonesia  update 17". WHO. June 6 2006. Check date values in: |date= (help)
-  National Center for Infectious Diseases, Division of Global Migration and Quarantine (March 24, 2005). "Interim Guidance about Avian Influenza A (H5N1) for U.S. Citizens Living Abroad". Travel Notices. U.S. Centers for Disease Control and Prevention. Retrieved 2006-10-27.
-  Jennifer Schultz (November 28 2005). "Bird flu vaccine won't precede pandemic". United Press International. Unknown parameter |url-= ignored (help); Check date values in: |date= (help); |access-date= requires |url= (help)
-  Promising research into vaccines includes:
Martin Enserink (August 12 2005). "Avian Influenza: 'Pandemic Vaccine' Appears to Protect Only at High Doses". Science. 309: 996. doi:10.1126/science.309.5737.996b. Check date values in: |date= (help)
"GlaxoSmithKline Initiates Human Trial Programme With Two H5N1 Pandemic Flu Vaccines" (PDF). March 30 2006. Retrieved 2006-10-27. Check date values in: |date= (help)
"Murtha eager to speed vaccine". January 28 2006. Retrieved 2006-10-27. Unknown parameter |source= ignored (help); Check date values in: |date= (help) A promising new bird flu vaccine developed by University of Pittsburgh researchers could provide better protection and be made more quickly than other experimental vaccines.
- Martin Enserink (August 12 2005). "Avian Influenza: 'Pandemic Vaccine' Appears to Protect Only at High Doses". Science. 309: 996. doi:10.1126/science.309.5737.996b. Check date values in: |date= (help)
- "GlaxoSmithKline Initiates Human Trial Programme With Two H5N1 Pandemic Flu Vaccines" (PDF). March 30 2006. Retrieved 2006-10-27. Check date values in: |date= (help)
- "Murtha eager to speed vaccine". January 28 2006. Retrieved 2006-10-27. Unknown parameter |source= ignored (help); Check date values in: |date= (help) A promising new bird flu vaccine developed by University of Pittsburgh researchers could provide better protection and be made more quickly than other experimental vaccines.
-  Jump up to: 25.0 25.1 "Oseltamivir (Tamiflu)". National Institutes of Health. January 13 2000. Check date values in: |date= (help) Revised on January 10 2001.
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-   CIDRAP article Germany finds H5N1 in frozen duck meat published September 10, 2007
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-   Water tech on line article Study: Chlorination inactivates avian flu strain published September 10, 2007 says "Researchers from the US Environmental Protection Agency (EPA), the University of Georgia (Athens, GA) and US Department of Agriculture (USDA) found that the maintenance of a free chlorine residual of 0.52 to 1.08 milligrams per liter (mg/L) was sufficient to inactivate the virus by greater than three orders of magnitude within an exposure time of one minute, according to the study. They noted that EPA specifications for public water supplies that the free chlorine residual values be 6 to 8 mg/L per minute would be more than sufficient to inactivate H5N1 in the water environment."
-   This quote is from page 28 of The Johns Hopkins University - The Impact of Pandemic Influenza on Public Health Use  to find more like this about H5N1 and  about other subjects
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-  T Jacob John (November 12 2005). "Bird Flu: Public Health Implications for India". Economic and Political Weekly. Check date values in: |date= (help)
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-  Menno D. de Jong;  et al. (February 17 2005). "Fatal Avian Influenza A (H5N1) in a Child Presenting with Diarrhea Followed by Coma". New England Journal of Medicine. 352 (7): 686691. Check date values in: |date= (help)CS1 maint: Explicit use of et al. (link)
-  Robert G. Webster and Elizabeth Jane Walker (2003). "Influenza: The world is teetering on the edge of a pandemic that could kill a large fraction of the human population". American Scientist. 91: 122.
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-  Alan Sipress (June 18 2005). "Bird Flu Drug Rendered Useless: Chinese Chickens Given Medication Made for Humans". Washington Post. Check date values in: |date= (help)
"WHO sees role for older antivirals in some H5N1 cases". CIDRAP. May 22 2006. Check date values in: |date= (help)
-   CIDRAP article Study: Inhibiting cytokine response might not reverse H5N1 infections published July 16, 2007
Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO / 3 January 2008
For possible later updates by the WHO, see /
-  The tally may be obtained by clicking a link to the most current date shown by the UN on the WHO's web page entitled Epidemic and Pandemic Alert and Response (EPR) /
-     Options For Influenza Control VI (Conference, Toronto Canada, June 18, 2007)  
     Even those who were in close contact with both infected birds and infected people showed no sign of ever having been infected, Dr. Dejpichai and colleagues found.  
     The study is consistent with findings in Hong Kong, China, and Cambodia, which showed viral seroprevalence of no more than 10% among poultry workers and people living in villages where H5N1 outbreaks occurred, she said.  
     But it contradicts a population-based study in Vietnam, published last year, that concluded that mild cases of the virus were likely to be common. (see Mild Avian Flu Transmission May Be Common)