Wednesday, April 29, 2009

Swine Flu

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2009 swine flu outbreak

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The 2009 flu outbreak, commonly called the swine flu, is a spread of a new strain of influenza virus that was clinically identified in April 2009.[57] The new virus strain is a type of influenza A (H1N1) virus.[58] The outbreak has also been called the H1N1 influenza,[59] 2009 H1N1 flu,[60][61] Mexican flu,[62] or swine-origin influenza.[63] It is currently a level 5 outbreak, one level below an official pandemic.
Although the exact time and location of the outbreak is unknown, it is believed to have been first detected when an influenza-like illness was reported by both health agencies and local news media in Mexico. The virus responsible was clinically identified as a new strain on April 24, 2009. Within days, isolated cases (and suspected cases) were identified elsewhere in Mexico, the U.S., and several other countries.
By April 28, the new strain was confirmed to have spread to Spain, the United Kingdom, New Zealand, and Israel, and the virus was suspected in many other nations, with a total of over 4,400 candidate cases, prompting the World Health Organization (WHO) to change its pandemic alert phase to "Phase 5",[64][65][66] which is defined as "...human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short".[67] Despite the scale of the alert, WHO officials noted on April 29 that the majority of people infected with the virus have made a full recovery without need of medical attention or antiviral drugs.[citation needed]
The new strain is an apparent reassortment of four strains of influenza A virus subtype H1N1.[68] Analysis at the United States Centers for Disease Control and Prevention (CDC) identified the four component strains as one endemic in humans, one endemic in birds, and two endemic in pigs (swine).[68] One swine strain was widespread in the United States, the other in Eurasia.[68] Although called swine flu due to it predominantly containing swine strains, the World Organisation for Animal Health have proposed the name North American influenza because this new strain in its entirety has not been found in swine (pigs).[69] Worldwide the common human H1N1 influenza virus affects millions of people every year, according to WHO officials, and "these annual epidemics result in about three to five million cases of severe illness, and about 250,000 to 500,000 deaths."[70] In industrialized countries most of these annual deaths occur in those 65 or older.[70]
In late April officials from both WHO and the CDC expressed serious concern about the situation, stating that the virus had the potential to become a flu pandemic.[71] On April 25, 2009, the WHO formally determined the situation to be a "public health emergency of international concern", with knowledge lacking in regard to "the clinical features, epidemiology, and virology of reported cases and the appropriate responses".[72] Government health agencies around the world also expressed concerns over the outbreak and are monitoring the situation closely. By April 30, 300 U.S. schools had closed as the disease became more widespread in the U.S.[73][74][75][76][77] The Mexican government ordered a multi-day shutdown of all non-essential activities in the government and private sector, amounting to a shutdown of most of the country's economy.[78]



Prior influenza season

Prior to the outbreak, the Northern Hemisphere winter of 2008–2009 had been a comparatively mild season for flu infections,[79] while the preceding Southern 2008 season was described as moderate.[80] Up to April 8, 2009, the U.S. CDC had reported the deaths of 43 children from seasonal flu, compared to 68 in the previous flu season.[79] The improvement was attributed, in part, to an improved Northern Hemisphere winter of 2008–2009 seasonal flu vaccine, for which a rare decision had been made to update all three strains (H1, H3, and B) simultaneously, which ultimately yielded a very good match to the strains of H1N1 and H3N2 which eventually circulated. (This followed the poor performance of the 2007–2008 vaccine, which offered only 2–20% protection rather than the 70–90% achieved in some years.) The U.S. improvement was also attributed to new recommendations there including the vaccination of people 5–18 years of age, who potentially act as "super-spreaders" due to failure to take precautions such as hand-washing.[81][82]
Furthermore, the CDC had in previous years received reports at the approximate rate of one human swine influenza virus infection every one to two years. From December 2005 to February 2009, however, twelve such cases were reported to the agency.[83][84]

Initial outbreaks

First recognized

The new strain of swine flu was first recognized as such when the CDC received a sample on April 14 from a patient who fell ill on March 30 in San Diego County, California. A second case was confirmed on April 17 who had fallen ill on March 28 in Imperial County, California.[85][86]

Spread within Mexico

The outbreak was first detected in Mexico City, where surveillance began picking up a surge in cases of influenza-like illness (ILI) starting March 18.[87] The surge was assumed by Mexican authorities to be "late-season flu" (which usually coincides with a mild Influenzavirus B peak)[88] until April 21,[89][90] when a U.S. Centers for Disease Control and Prevention alert concerning two isolated cases of a novel swine flu was reported in the media.[91] Some samples were sent to the U.S.-based CDC on April 18.[92] The Mexican cases were confirmed by the CDC and the World Health Organization to be a new strain of H1N1.[87][93]
Cases were also reported in the states of San Luis Potosí, Hidalgo, Querétaro and Mexico State.[94] Mexican Health Minister José Ángel Córdova on April 24, said "We’re dealing with a new flu virus that constitutes a respiratory epidemic that so far is controllable."[94] In March and April 2009, over 3000 cases of suspected swine flu in humans were detected in Mexico and the southwestern United States. The disease was detected in several countries on multiple continents within weeks of its initial discovery.
The first death from swine flu occurred on April 13, when a diabetic woman from Oaxaca died from respiratory complications.[95][96] The Mexican fatalities are alleged to be mainly young adults of 25 to 45, a common trait of pandemic flu.[68][97] Although there have been reports of 152 "probable deaths"[98] in Mexico City and "more than 100 dead from swine flu",[99] the WHO had received reports of only 16 confirmed deaths total and explicitly denied the larger figure as of April 29.[100][101]

Seasonal variation

The high humidity of summer typically leads to the end of the flu season as the virus becomes less likely to spread. In Mexico City, May marks the end of the dry season, and experts speculate that the spread of the swine flu may slow.[102] On April 30 Mexican Health Secretary Jose Angel Cordova voiced cautious optimism that the spread of the swine flu might be slowing in that country.[103] However, the outbreak comes at the beginning of the flu season for Southern Hemisphere countries such as New Zealand, Australia, South Africa, and parts of South America.[104]

Genetics and effects


On April 24, the CDC determined that seven samples from suspected cases in Mexico matched the strain from California and Texas. Infecting patients in Texas and California with no known linkages to animals or one another, the strain appeared to be spreading from human to human.[105][71] The CDC determined that the strain contained genes from four different flu viruses – North American swine influenza, North American avian influenza, human influenza, and swine influenza virus typically found in Asia and Europe – "an unusually mongrelised mix of genetic sequences."[68] A CDC investigative team arrived in Mexico City on April 25 to work with Mexican counterparts to study the virus.[89]
Pigs are susceptible to influenza viruses that can also infect both humans and birds, so they may act as a "mixing vessel" in which reassortment can occur between flu viruses of several species.[106][107] Reassortment is a process that happens if two different types of influenza virus infects a single cell and it can produce a new strain of influenza. This is because the virus genome is split between eight independent pieces of RNA, which allows pieces of RNA from different viruses to mix together and form a novel type of virus as new virus particles are being assembled.[108] This new strain appears to be a result of the reassortment of two swine influenza viruses, one from North America and one from Europe.[109] But the North American pig strain was itself the product of previous reassortments, and has carried an avian PB2 gene for at least ten years and a human PB1 gene since 1993.[110] These genes were passed on to the new virus.[111][112]
Gene sequences for every viral gene were made available through the Global Initiative on Sharing Avian Influenza Data (GISAID).[113][114] A preliminary analysis found that the hemagglutinin (HA) gene was similar to that of swine flu viruses present in U.S. pigs since 1999, but the neuraminidase (NA) and matrix protein (M) genes resembled versions present in European swine flu isolates. While viruses with this genetic makeup had not previously been found to be circulating in humans or pigs, there is no formal national surveillance system to determine what viruses are circulating in pigs in the U.S.[115] So far, little is known about the spread of the virus in any pig population. As of April 30 an international team led Juan Lubroth, chief of veterinary investigations for the United Nations Food and Agriculture Organization, in coordination with researchers from the WHO, were in Mexico on the way to La Gloria, in pursuit of what has been dubbed "Pig Zero".[110]
The seasonal influenza strain H1N1 vaccine is thought to be unlikely to provide protection.[116] The virus was also resistant to amantadine and rimantadine, but susceptible to oseltamivir (Tamiflu) and zanamivir (Relenza).[117][118]

Symptoms and severity

See also: Swine_influenza#In_humans, for previous swine flus symptoms on humans.
The CDC does not fully understand why the U.S. cases' symptoms were primarily mild disease while the Mexican cases had led to multiple deaths. However, research on previous pandemic strains has suggested that mortality can vary widely between different countries, with mortality being concentrated in the developing world.[120] Differences in the viruses or co-infection are also being considered as possible causes. In 1918, the 1918 influenza weakened the infected people, and it was then lung infections such as pneumonia which killed 3% of them. Such co-infection can be reduced by the use of antibiotics. In the current outbreak, the first death (13 and 21th April) were diagnosed as 'atypical pneumonias', a pneumonia which, helped by the flu, becomes more dangerous. The CDC's flu chief Nancy Cox said that genetic analysis of the swine flu strain did not reveal the markers for virulence found in the 1918 flu virus.[121]
At a press briefing on April 27, acting CDC director Dr. Richard Besser stated that out of 40 confirmed cases in the United States at that point, only one individual was hospitalized. He also revealed that the median age was 16 years "with a range in age of 7 to 54 years."[122] By April 29, the U.S. had 91 confirmed cases with 5 hospitalizations and one death.[123]
Whereas most influenza strains affect the elderly and young children worst, this strain has primarily caused deaths in people between the ages of 25 and 50.[124]

International cases and responses

Confirmed cases followed by death Confirmed cases Unconfirmed or suspected cases See also: Live map of swineflu, H1N1 live map
The new strain has spread widely beyond Mexico, with confirmed cases in fourteen countries and suspected cases in more than forty. Many countries have advised their inhabitants not to travel to infected areas.[weasel words] Countries including Australia, China, Iceland, India, Indonesia, Malaysia, Philippines, Singapore, South Korea and Thailand are monitoring visitors returning from flu-affected areas to identify people with fever and respiratory symptoms. Many countries have also issued warnings to visitors of flu-affected areas to contact a doctor immediately if they had flu-like symptoms.
Although there is no evidence that the virus is transmitted by food,[125] and influenza A viruses are generally not heat resistant,[125] some countries banned import and sale of pork products "as a precaution against swine flu".[126][127]
Despite the lack of any evidence that the virus is present in swine anywhere in the world, Egypt's parliament called for the nation's 250,000 pigs to be killed immediately,[128] a move the World Organization for Animal Health called "scientifically unjustified".[125]
Mexico's schools, universities, and all public events will be closed from April 24, 2009 to May 6, 2009.[129][130] On April 27, 2009, a few schools in the U.S. closed due to confirmed cases in students.[131][132][133]

Pandemic concern

WHO and CDC officials are concerned that this outbreak may become a pandemic, for the following reasons:[71]
  • New strain
The virus is a new strain of influenza, from which human populations have not been vaccinated or naturally immunized.[134] In the United States, cases infected 25% of family members. Seasonal flu tends to sicken 5% to 20% of family members.[135]
  • Widespread human transmission
The virus infects by human-to-human transmission. Investigations of infected patients indicated no direct contact with swine, such as at a farm or agricultural fair.[93] The strain was later confirmed to have been transmitted between humans.[136] In contrast, for example, disease transmission in the last severe human outbreak of influenza, the bird flu that peaked in 2006, was determined to be almost entirely from direct contact between humans and birds.[citation needed]
  • Virulence
For reasons not yet well understood, all but one of the fatalities to date have been in Mexico. Furthermore, in Mexico (but not elsewhere) the reported deaths from the illness have primarily been young, healthy adults.[137] Most other influenza strains produce the worst symptoms in young children, the elderly, and others with weaker immune systems.[93][138] However, the CDC has indicated that symptoms reported from this strain so far are similar to those of normal seasonal flu.[139] While some media outlets have speculated that this virus could cause a cytokine storm in patients,[137] there is presently no evidence for this hypothesis, with the CDC stating that there is "insufficient information to date about clinical complications of this variant of swine-origin influenza A (H1N1) virus infection."[139]
  • Lack of data
That other crucial factors are still largely unknown, such as transmission rates and patterns (epidemicity) and effectiveness of current influenza treatments, combined with the innate unpredictability of influenza strains, means that reliable forecasts cannot be made.[72]
As noted, predicting the size and severity of influenza outbreaks is a very inexact science. In 1976 the U.S. government incorrectly predicted a swine flu pandemic that never materialized.[140]
WHO officials observed that because there are "human cases associated with an animal influenza virus, and because of the geographical spread of multiple community outbreaks, plus the somewhat unusual age groups affected, these events are of high concern".[93]
By the end of April, however, some scientists believed that this strain was unlikely to cause as many fatalities as earlier pandemics, and may not even be as damaging as a typical flu season.[141]

WHO alert phases

Phase 3

Prior to the swine flu outbreak, the WHO worldwide pandemic alert was set at Phase 3 due to H5N1 avian flu, which spread widely in birds with occasional cases in humans.[143][144][145] A Phase 3 alert means that a new virus has been confirmed but there is no or limited evidence of human-to-human transmission - insufficient to sustain community-level outbreaks. The WHO decided not to raise the level of the worldwide pandemic alert after its first meeting, on April 25.[145]

Phase 4

Following the second meeting of the Emergency Committee on April 27, the pandemic alert level was raised to Phase 4.[146] Phase 4, "Sustained Human to Human Transmission," entails community-wide outbreaks.[142]
As of April 29, World Health Organization acting assistant director-general Dr. Keiji Fukuda stated:
[that the organization was] moving closer to Phase 5. What we are trying to do right now is make absolutely sure that we are dealing with sustained transmission in at least two or more countries.[147]

Phase 5

On April 29, the Emergency Committee met for the third time,[148] and WHO raised the pandemic alert level to five,[149] the second-highest level, indicating that a pandemic is "imminent". Human-to-human transmission cases have been recorded in multiple regions.[150] In Spain, officials confirmed the first European case of an infection in a person who had not traveled to Mexico, in a person whose girlfriend had done so.[151]

Prevention and treatment

Recommendations to prevent infection by the virus consist of the standard personal precautions against influenza. This includes frequent washing of hands with soap and water or with alcohol-based hand sanitizers, especially after being out in public. The CDC advises not touching the mouth, nose or eyes, as these are primary modes of transmission. When coughing, they recommend coughing into a tissue and disposing of the tissue, then immediately washing the hands.[152]
There is no risk of flu transmission from the consumption of properly-cooked pork products.[153]
The previously recommended influenza vaccines for the southern and northern hemispheres, including that for the 2009/2010 flu season, are ineffective against the new strain.[154] Current development, large-scale manufacturing, distribution and delivery of a new vaccine takes several months.[155][156] The WHO Director-General announced that production of the unchanged seasonal vaccine should continue for now, and that the WHO would assist the development process for an effective vaccine.[146] U.S.-based medical product company Baxter International has requested a virus sample from the WHO in order to begin development of a new vaccine.[157] Sanofi-Aventis (Sanofi-Pasteur) is manufacturing the conventional seasonal flu vaccine and has not been asked to produce a vaccine against the new H1N1 strain, which would be difficult to manufacture without diverting facilities from current production.[158]
Of the available antiviral treatments for influenza, the WHO stated that the viruses obtained from the human cases with swine influenza in the United States were sensitive to oseltamivir (Tamiflu)[159] and zanamivir (Relenza) but resistant to amantadine and rimantadine.[160] Tamiflu and Relenza also have a preventative effect against Influenzavirus A.[161] On April 27, the CDC recommended the use of Tamiflu and Relenza for both treatment and prevention of the new strain.[162] Roche and the U.S. government had already extended the shelf life of federally stockpiled Tamiflu from the original five years to seven years because studies indicated that the medication continues to maintain its effectiveness.[163]
Due to a more convenient method of administration, treatment with oseltamavir is typically preferred, but in H3N2 flu treatment leads to resistance in 0.4% of adult cases and 5.5% of children. The resistant strains are typically less transmissible, but that is not certain, and resistant human H1N1 viruses have become widely established. Fortunately, simulations reveal that using a second effective antiviral such as zanamivir (Relenza) to treat even 1% of cases will delay the spread of resistant strains. Even a drug such as amantadine (Symmetrel) for which resistance frequently emerges may be useful in combination therapy.[164][165]

Train commuters in Mexico City wearing surgical masks
There is so far little data available on the risk of airborne transmission of this particular virus. Mexican authorities are distributing surgical masks to the general public. The UK Health Protection Agency considers facial masks unnecessary for the general public.[166] Many authorities recommend the use of respirators by health-care workers in the vicinity of pandemic flu patients, in particular during aerosol generating procedures (e.g. intubation, chest physiotherapy, bronchoscopy).
On April 28, the WHO flu expert Keiji Fukuda pointed out that it is too late to contain the swine flu. "Containment is not a feasible operation. Countries should now focus on mitigating the effect of the virus," he said.[98] He also stressed that the experts did not recommend closing borders or restricting travel. "With the virus being widespread... closing borders or restricting travel really has very little effects in stopping the movement of this virus."[98] However, on April 28, the U.S. CDC began "recommending that people avoid non-essential travel to Mexico."[167] The WHO's early reaction was that it saw no need at this point to issue travel advisories warning travellers not to go to parts of Mexico or the United States. The spokesperson said that the situation might change "depending on what the situation in the field is".[168] WHO Director-General Dr. Margaret Chan also said that it was too premature to issue such recommendations without better analysis and understanding of the situation at this stage.[169] Many countries confirmed that inbound international passengers will be screened. Typical airport health screening involves asking passengers which countries they have visited and checking whether they feel or appear particularly unwell. Thermographic equipment was put into use at a number of airports to screen passengers. In the USA, two confirmed cases were detected through their border infectious disease surveillance.[155] A number of countries advised against travel to known affected regions.
Dr. Ira Longini, a specialist in the mathematical and statistical theory of epidemics, suggests that if those infected stay at home or seek medical care, public meeting places are closed, and anti-flu medications are made widely available, then in simulations the sickness is reduced by nearly two-thirds. "The name of the game is to slow transmission until a well-matched vaccine can be made and distributed. I am fairly optimistic we can do that".

Name of the disease

Popular name and scientific name

According to researchers cited by The New York Times, "based on its genetic structure, the new virus is without question a type of swine influenza, derived originally from a strain that lived in pigs".[170] This origin gave rise to the nomenclature "Swine flu", largely used by mass media in the first days of the epidemic. Despite this origin, the current strain is now a human-to-human issue, requiring no contact with swine. On April 30 the World Health Organization stated that no pigs in any country have been determined to have the illness, but farmers remain alert due to concerns that infected humans may pass the virus to their herds.[171]
Scientific nomenclature designates influenza virus strains with names such as "A/California/09/2009(H1N1)-like",[172] which are too complex to achieve widespread use.

Debate for more suitable name

Some authorities object to calling the flu outbreak "swine flu". U.S. Agriculture Secretary Tom Vilsack expressed concerns that this would lead to the misconception that pork is unsafe for consumption.[173] Israeli deputy health minister Yaakov Litzman proposed the name "Mexican flu" because Muslims and Jews consider pork to be unclean,[174] but the Israeli government retracted this proposal following Mexican complaints.[175] Although the South Korean Ministry for Food, Agriculture, Forestry and Fisheries asked the press to use the term “Mexican Virus” on April 29,[176] most of South Korean press and people prefer to use SI (short for Swine Influenza). Taiwanese authorities suggested the names “H1N1 flu” or “new flu”, which most local media now use.[177] The World Organization for Animal Health has proposed the name "North American influenza".[178] The European Commission uses the term "novel flu virus".[175]
The WHO announced they would refer to the new influenza virus as influenza A(H1N1) or "Influenza A (H1N1) virus, human"[175] as opposed to "swine flu", in an attempt to not confuse the public about risks of pork products.[179] They confirmed that you cannot contract Influenza A (H1N1) by eating any properly cooked pork products.[180]
Others such as Henry Niman of Recombinomics object to the name change: "It's clearly swine. It's a flu virus from a swine, there's no other name to call it."[181]


Media Response

Since the outbreak began, there has been a week of near constant media attention.[182] When a health emergency was officially declared[where?], the story of the outbreak spread quickly through news networks.[183] Multiple news conferences were aired in the United States by government officials. By the next day, it was the main topic of discussion.[183] The amount of media attention suggested a full-blown crisis, resulting in public fear.[183] According to Mark Feldstein, a former correspondent for NBC, ABC and CNN, the reason for such extensive coverage is that "If you scare people, they'll tune in more."[183]
Epidemiologists caution that the number of cases reported in the early days of an outbreak can be very inaccurate and deceptive.[184] This can be due to several causes, including selection bias, media bias, and incorrect reporting by governments.
Selection bias, as authorities in different countries may be looking at different patient populations. For example, doctors in Mexico may be concentrating on patients in hospitals, rather than the larger vulnerable population, and this may explain the higher mortality recorded in the country.[184] Media bias in reporting swine flu cases and deaths may skew incidence maps based on these media reports. Countries with poor health care systems and poor laboratory facilities may take longer to identify suspected cases and analyse those cases. Passive data collection methodologies (waiting for the patient to arrive at a health care facility) are considered inferior to active data collection techniques (performing random stratified sampling) because of various forms of selection bias.[185]
Also, if national governments and local health care services do not accurately report their own data on suspected cases and deaths this will produce a bias in any conclusions drawn for such data. For instance, World Health Organization accused China of under-reporting cases of SARS during the 2002 SARS outbreak.[186] Gathering accurate data for the flu outbreak is further complicated by the possibility of further mutations of the virus,[187] and because laboratory facilities to perform swift genetic tests on patient samples are not widely available.[184]

Government actions against pigs and pork

Several countries, including Serbia, China and Russia banned the import of pork products from North America in general as a response to the outbreak, despite assurances from the WHO that the disease is not spread through pork.[188] On April 29, the Egyptian Government decided to kill all 300,000 pigs in Egypt, despite none of them having been suspected to be infected. They have also sent medics to vaccinate farmer families against the common flu, which have no link with, nor provide protection against, the current Mexico epidemic.[189][190]

See also


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External links

UN World Health Organization (WHO)
USA Centers for Disease Control (CDC)
European Centre for Disease Prevention and Control (ECDC)
Pan-American Health Organization (PAHO)