CDC works very closely with state and local officials in areas where human cases of new H1N1 flu infections have been identified. CDC has deployed staff to several states to assist with the investigation of the impact of the novel H1N1 influenza, including the assessment of the severity of illness, how easily the virus spreads, and the amount of time people may be infectious. In states where EpiAid teams have been deployed, many epidemiological activities are taking place or planned including:

• Active surveillance in the counties where infections in humans have been identified;
• Studies of health care workers who were exposed to patients infected with the virus to see if they became infected;
• Studies of households and other contacts of people who were confirmed to have been infected to see if they became infected; and
• Study to see how long a person with the virus infection sheds the virus.

This virus was originally referred to as “swine flu” because laboratory testing showed that many of the genes in this new virus were very similar to influenza viruses that normally occur in pigs in North America. But further study has shown that this new virus is very different from what normally circulates in North American pigs. It has two genes from flu viruses that normally circulate in pigs in Europe and Asia and avian genes and human genes. Scientists call this a “quadruple reassortant” virus.

Spread of H1N1 (swine) flu can occur in two ways:

• Through contact with infected pigs or environments contaminated with swine flu viruses.
• Through contact with a person with H1N1 (swine) flu. Human-to-human spread of H1N1 (swine) flu has been documented also and is thought to occur in the same way as seasonal flu. Influenza is thought to spread mainly person-to-person through coughing or sneezing of infected people.

If you live in areas where people have been identified with new H1N1 flu and become ill with influenza-like symptoms, including fever, body aches, runny or stuffy nose, sore throat, nausea, or vomiting or diarrhea, you should stay home and avoid contact with other people, except to seek medical care. If you have severe illness or you are at high risk for flu complications, contact your health care provider or seek medical care. Your health care provider will determine whether flu testing or treatment is needed.

Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO (World Health Organization): since 2003

Azerbaijan
cases = 8
deaths = 5

Bangladesh
cases = 1
deaths = 0

Cambodia
cases = 8
deaths = 7

China
cases = 30
deaths = 20

Djibouti
cases = 1
deaths = 0

Egypt
cases = 50
deaths = 22

Indonesia
cases = 139
deaths = 113

Iraq
cases = 3
deaths = 2

Laos
cases = 2
deaths = 2

Myanmar
cases = 1
deaths = 0

Nigeria
cases = 1
deaths = 1

Pakistan
cases = 3
deaths = 1

Thailand
cases = 25
deaths = 17

Turkey
cases = 12
deaths = 4

Viet Nam
cases = 106
deaths = 52

Total
cases = 390
deaths = 246

Total number of cases includes number of deaths.
WHO reports only laboratory-confirmed cases. (12 December, 2008)

Over 60 countries have reported outbreaks of the H5N1 strain of avian influenza since 2003.

More than 300 million birds have died or been destroyed in an effort to prevent further spread of the virus, according to the U.N. Food and Agriculture Organization.
That level of disease among domestic flocks has been characterized as an animal pandemic, and a costly one. $2.5 billion has gone into the international effort to control and eradicate the disease.

Do you remember this?

Hong Kong health authorities closed down a poultry market here Saturday after excrement samples collected from hencoops at the marketplace were confirmed infected with the deadly strain of H5N1 avian influenza virus.

Dr. York Chow, Secretary for Food and Health, announced at a press conference here Saturday afternoon that the Po On Road Market in Kowloon an infected area of the H5N1 virus and ordered the immediate suspension of trading in the market.

Chow said after days of laboratory testings, five of the 20 excrement samples collected from three poultry stores on June 3 were confirmed H5N1 positive and an order was issued immediately to cull about 2,700 chickens in the market.

"We are still investigating on the source of the H5N1 virus infections," he said, adding other 64 poultry markets had reported no H5N1 cases.

Chow said there has been no report of human case of H5N1 infections but the department had decided to raise the response level from "vigilance" to "serious" in the city.

In response to the latest H5N1 virus find, Chow said, the Food and Health Department had suspended immediately the live poultry imports from the Chinese mainland and trading from local chicken farms will be suspended immediately

He said such suspension will last for as long as 21 days if necessary.

Chow said the Hong Kong Special Administrative Region government had noticed the Ministry of Agriculture and the General Administration of Quality Supervision, Inspection and Quarantine on the latest development of bird flu in Hong Kong.

Chow said there had been no unusual incidents reported in the registered chicken farm in the Chinese mainland and none abnormal death of poultry had been reported by store owners during the past days.

Thomas Tsang, Controller of the Center for Health Protection, said the center would conduct health checkups and prescribe anti- virus medicine for those people in close contact with live poultry.

Tsang also called on doctors in the city to quickly report suspected cases of H5N1 infection to the center once they diagnose those patients with a fever.

The Agriculture, Fisheries and Conservation Department said they would strengthen the testing of live poultry on the bird flu virus and disinfecting of poultry whole sale markets.

Scientists are looking at a novel strategy to prevent the spread of pandemic avian influenza. They have developed a vaccine that protects ducks, a known natural reservoir for the virus.

Waterfowl are considered to be the natural reservoir of influenza A viruses due to the isolation of all subtypes from these hosts. Current research indicates that influenza A viruses are continuously evolving within their natural environment and can be transmitted to a variety of animals, including humans. H5N1 avian influenza A viruses are now endemic in domestic poultry in many Asian countries and ducks are believed to be the primary source of infection. Reducing the spread of H5N1 in ducks could play a key role in minimizing the risk of a pandemic outbreak.

In the study researchers first identified dominant pathogenic strains of H5N1 influenza A viruses circulating in Asian poultry and found that four caused symptomatic illness in domestic ducks, but not all were lethal. In addition the researchers reversed the genetics of the viruses in domestic ducks to develop three different inactivated oil emulsion whole-virus H5 influenza vaccines. Following one round of inoculation with the vaccines ducks were completely protected when challenged with a lethal dose of the H5N1 virus.

"The vaccines provided complete protection against the lethal challenge of the homologous and heterologous H5N1 avian influenza A virus with no evidence of morbidity, mortality, or shedding of the challenge virus," say the researchers. "The complete protection offered by these vaccines will be useful for reducing the shedding of H5N1 avian influenza A viruses among vaccinated agricultural avian populations."

The concern is greatest in rural areas of affected countries, where traditional free-ranging ducks, chickens and wildlife mingle, frequently sharing the same source of water, according to a joint statement by the UN Food and Agriculture Organization (FAO), the World Health Organization (WHO) and the Office International des Epizooties (OIE).

Findings pointing to an altered role for domestic ducks join other recent evidence that the H5N1 virus circulating in parts of Asia has increased its virulence in chickens and mice (a laboratory model for mammals), and has expanded its host range to include mammals, such as certain members of the felidae family (e.g. cats and tigers), not previously considered susceptible to infection.

Would you estimate the percentage of movie fans in the world by polling at a cinema? Would you calculate the number of overweight Americans by taking a survey at Weight Watchers locations? Not if you were aiming for any sort of statistical accuracy; such methods would not give you samples at all representative of a larger population.

Regrettably, just this sort of sampling bias may have lead to huge errors in avian flu mortality numbers. While stony-faced newscasters somberly report that more than 50% of people infected with avian flu ultimately die, the death rate may be much lower.

A study published in the January 9th issue of Archives of Internal Medicine found that as many as 600 to 750 people in Vietnam may have come down with a mild variant of the avian flu—one that does not carry lethal consequences. This suggests that current mortality estimates, which are derived from only the most severely ill patients, are biased. We may be underestimating the virus’ transmission rate while overestimating the deadliness of avian flu.
Thorson’s work suggests that the WHO statistics do not account for all cases of H5N1 infection in humans, because many cases go unreported by patients who do not seek medical assistance for milder symptoms.

Christian Sandrock, a physician and an assistant professor at the University of California Davis Health System, as well as a specialist in public health issues, says Thorson’s study brings public attention to a hotly-debated question in the medical community: Is there a mild or asymptomatic version of avian flu?

Sandrock explains that, without serology studies to confirm a patient’s infection with H5N1, Thorson’s study does not fully answer that question.

"It is not at all conclusive," he said.

However, Sandrock thinks that the WHO’s 50% mortality figure will eventually be revised downward.

"There’s going to definitely be some people with the disease that were either asymptomatic or subclinical, that really didn’t come up on radar," Sandrock said. "I think 50% is going to be the high end. How much it’s going to drop, I don’t know. What we’d like to see is that it goes from 50% to 3%. But, I think what we may see is that it goes from 50% to 40%, or 50% to 30%, which is still a phenomenally high mortality."

Low pathogenic avian influenza H5N1 (LPAI H5N1) also called "North American" H5N1 commonly occurs in wild birds. In most cases, it causes minor sickness or no noticeable signs of disease in birds. It is not known to affect humans at all. The only concern about it is that it is possible for it to be transmitted to poultry and in poultry mutate into a highly pathogenic strain.

    * 1975 – LPAI H5N1 was detected in a wild mallard duck and a wild blue goose in Wisconsin.

    * 1981 and 1985 – LPAI H5N1 was detected in ducks by the University of Minnesota conducting a sampling procedure in which sentinel ducks were monitored in cages placed in the wild for a short period of time.

    * 1983 – LPAI H5N1 was detected in ring-billed gulls in Pennsylvania.

    * 1986 – LPAI H5N1 was detected in a wild mallard duck in Ohio.

    * 2005 – LPAI H5N1 was detected in ducks in Manitoba, Canada.

    * 2008 – LPAI H5N1 was detected in ducks in New Zealand.

"In the past, there was no requirement for reporting or tracking LPAI H5 or H7 detections in wild birds so states and universities tested wild bird samples independently of USDA. Because of this, the above list of previous detections might not be all inclusive of past LPAI H5N1 detections. However, the World Organization for Animal Health (OIE) recently changed its requirement of reporting detections of avian influenza. Effective in 2006, all confirmed LPAI H5 and H7 AI subtypes must be reported to the OIE because of their potential to mutate into highly pathogenic strains. Therefore, USDA now tracks these detections in wild birds, backyard flocks, commercial flocks and live bird markets."

H5N1 is a subtype of the species Influenza A virus of the Influenzavirus A genus of the Orthomyxoviridae family. Like all other influenza A subtypes, the H5N1 subtype is an RNA virus. It has a segmented genome of eight negative sense, single-strands of RNA, abbreviated as PB2, PB1, PA, HA, NP, NA, MP and NS.

HA codes for hemagglutinin, an antigenic glycoprotein found on the surface of the influenza viruses and is responsible for binding the virus to the cell that is being infected. NA codes for neuraminidase, an antigenic glycosylated enzyme found on the surface of the influenza viruses. It facilitates the release of progeny viruses from infected cells.[19] The hemagglutinin (HA) and neuraminidase (NA) RNA strands specify the structure of proteins that are most medically relevant as targets for antiviral drugs and antibodies. HA and NA are also used as the basis for the naming of the different subtypes of influenza A viruses. This is where the H and N come from in H5N1.

Influenza A viruses are significant for their potential for disease and death in humans and other animals. Influenza A virus subtypes that have been confirmed in humans, in order of the number of known human pandemic deaths that they have caused, include:

    * H1N1, which caused "Spanish flu" and currently causes seasonal human flu
    * H2N2, which caused "Asian flu"
    * H3N2, which caused "Hong Kong flu" and currently causes seasonal human flu
    * H5N1, the world’s major current pandemic threat
    * H7N7, which has unusual zoonotic potential and killed one person
    * H1N2, which is currently endemic in humans and pigs and causes seasonal human flu
    * H9N2, which has infected three people
    * H7N2, which has infected two people
    * H7N3, which has infected two people
    * H10N7, which has infected two people

The first known strain of HPAI A(H5N1) (called A/chicken/Scotland/59) killed two flocks of chickens in Scotland in 1959; but that strain was very different from the current highly pathogenic strain of H5N1. The dominant strain of HPAI A(H5N1) in 2004 evolved from 1999 to 2002 creating the Z genotype.[14] It has also been called "Asian lineage HPAI A(H5N1)".

Asian lineage HPAI A(H5N1) is divided into two antigenic clades. "Clade 1 includes human and bird isolates from Vietnam, Thailand, and Cambodia and bird isolates from Laos and Malaysia. Clade 2 viruses were first identified in bird isolates from China, Indonesia, Japan, and South Korea before spreading westward to the Middle East, Europe, and Africa. The clade 2 viruses have been primarily responsible for human H5N1 infections that have occurred during late 2005 and 2006, according to WHO. Genetic analysis has identified six subclades of clade 2, three of which have a distinct geographic distribution and have been implicated in human infections: Map

    * Subclade 1, Indonesia
    * Subclade 2, Europe, Middle East, and Africa (called EMA)
    * Subclade 3, China"[10][15][16]

A 2007 study focused on the EMA subclade has shed further light on the EMA mutations. "The 36 new isolates reported here greatly expand the amount of whole-genome sequence data available from recent avian influenza (H5N1) isolates. Before our project, GenBank contained only 5 other complete genomes from Europe for the 2004–2006 period, and it contained no whole genomes from the Middle East or northern Africa. Our analysis showed several new findings. First, all European, Middle Eastern, and African samples fall into a clade that is distinct from other contemporary Asian clades, all of which share common ancestry with the original 1997 Hong Kong strain. Phylogenetic trees built on each of the 8 segments show a consistent picture of 3 lineages, as illustrated by the HA tree shown in Figure 1. Two of the clades contain exclusively Vietnamese isolates; the smaller of these, with 5 isolates, we label V1; the larger clade, with 9 isolates, is V2. The remaining 22 isolates all fall into a third, clearly distinct clade, labeled EMA, which comprises samples from Europe, the Middle East, and Africa. Trees for the other 7 segments display a similar topology, with clades V1, V2, and EMA clearly separated in each case. Analyses of all available complete influenza (H5N1) genomes and of 589 HA sequences placed the EMA clade as distinct from the major clades circulating in People’s Republic of China, Indonesia, and Southeast Asia."[17]