2009 swine flu pandemic

Negative stain electronic microscope image of a reassorted A(H1N1) flu virus.

The 2009 swine flu outbreak is an epidemic that began in April 2009 with a new strain of influenza virus. Although commonly called swine flu, this new strain has not been found in swine. It is also known as Mexican flu, North American influenza, and 2009 H1N1 flu. On April 30, 2009, the World Health Organization began to call it influenza A(H1N1). The outbreak is believed to have started in March 2009. Local outbreaks of an influenza-like illness were first detected in three areas of Mexico, but the virus responsible was not clinically identified as a new strain until April 24, 2009. Following the identification, its presence was soon confirmed in various Mexican states and in Mexico City. Within days, isolated cases (and suspected cases) were identified elsewhere in Mexico, the U.S., and several other Northern Hemisphere 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 3,000 candidate cases, prompting the World Health Organization (WHO) to change its pandemic alert phase to "Phase 5", which denotes "widespread human infection". Despite the scale of the alert, the WHO stated 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.

The new strain is an apparent reassortment of four strains of influenza A virus subtype H1N1. 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). One swine strain was widespread in the United States, the other in Eurasia. The common human H1N1 influenza virus affects millions of people every year, according to the WHO, "In annual influenza epidemics 5–15% of the population are affected with upper respiratory tract infections. Which results in between 250,000 and 500,000 deaths every year around the world. " In industrialized countries most of these deaths occur in those 65 or older.

In late April both the United Nations WHO and the U.S. CDC expressed serious concern about the situation, as it had the potential to become a flu pandemic due to the novelty of the influenza strain, its transmission from human to human, and the unusually high mortality rate in Mexico. 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". Government health agencies around the world also expressed concerns over the outbreak and are monitoring the situation closely. Up to around 300 U.S. schools have closed as the disease became more widespread in the U.S., the same day the Mexican government ordered a shutdown of all non-essential activities in the government and private sector, amounting to a shutdown of most of the country's economy.

Prior influenza season

Template:Globalize/USA Prior to the outbreak, the Northern Hemisphere winter of 2008–2009 had been a comparatively mild season for flu infections. 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. 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.

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.

Initial outbreaks

Further information: 2009 swine flu outbreak timeline

First recognized

The new strain of swine flu was first recognized by the CDC in a sample received 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 gotten ill on March 28 in Imperial County, California.

Smithfield Foods

Beginning in early March, a flu that progressed in many cases to respiratory illness affected 60% of the residents of the town of La Gloria, Veracruz, Mexico. La Gloria is located near a pig farming operation that raises nearly one million pigs per year, and town residents have long been bothered by flies that multiply in the pig farm's manure lagoons. The Mexican Social Security Institute stated in early April that these flies may have been the original disease vector of the virus.

The owner of the pig farm is Smithfield Foods, the world’s largest pork producer and processor. Smithfield Foods stated that it had found no clinical signs or symptoms of the presence of swine influenza in the company's swine herd, nor in its employees at its joint ventures in Mexico, and that it routinely administers influenza virus vaccination to their swine herds and conducts monthly testing for the presence of swine influenza. After the U.S. discovery of the novel swine flu virus, Mexico sent several samples to the U.S. for testing. One of these tests from a 5-year-old from La Gloria is the earliest confirmed case in Mexico, and is widely considered to possibly be patient zero for the outbreak. However, no further cases of swine flu have been confirmed in the town and the reported date of his infection, April 2, is after the reported dates of the first two confirmed U.S. cases, March 28 and March 30.

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. The surge was assumed by Mexican authorities to be "late-season flu" (which usually coincides with a mild Influenzavirus B peak) until April 21, 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. This new strain was promptly confirmed in Mexico, connecting the new strain to the ongoing outbreak of ILI. The first death from swine flu occurred on April 13, when a diabetic woman from Oaxaca died from respiratory complications. Some samples were sent to the U.S.-based CDC on April 18.

In March and April 2009, over 9000 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 strain appears to be unusually lethal in Mexico but not in other countries. Although there have been reports of 152 "probable deaths" in Mexico City and "more than 100 dead from swine flu", the WHO had received reports of only 7 confirmed deaths total and explicitly denied the larger figure as of April 29.

Mexico's schools, universities, and all public events will be closed from April 24, 2009 to May 6, 2009. On April 27, 2009, a few schools in the U.S. closed due to confirmed cases in students.

There have also been cases reported in the states of San Luis Potosí, Hidalgo, Querétaro and Mexico State. Some cases in Mexico and the United States have been confirmed by the World Health Organization to be a new strain of H1N1. The Mexican fatalities are mainly young adults of 25 to 45, a common trait of pandemic flu. 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."

Reporting bias

Epidemiologists caution that the number of cases reported in the early days of an outbreak can be very inaccurate and deceptive. This can be due to several causes:

• 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.
• 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 come to you) are considered inferior to active data collection techniques (performing random stratified sampling) because of various forms of selection bias.
• 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.

Gathering accurate data for the flu outbreak is further complicated by the possibility of further mutations of the virus, and because laboratory facilities to perform swift genetic tests on patient samples are not widely available. As of April 2009 there are no properly controlled epidemiological studies for the 2009 swine flu outbreak.

Genetics and effects

The CDC has confirmed that U.S. cases were found to be made up of genetic elements 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." Pigs have been shown to act as a potential "mixing vessel" in which reassortment can occur between flu viruses of several species. This new strain appears to be a result of the reassortment of two swine influenza viruses, which themselves are descended from previous reassortments in pigs. Influenza viruses readily undergo reassortment because their genome is split between eight pieces of RNA (see Orthomyxoviridae). The virus was resistant to amantadine and rimantadine, but susceptible to oseltamivir (Tamiflu) and zanamivir (Relenza).

Pigs, as well as humans, can harbor influenza viruses adapted to other species, allowing the viruses to exchange genes and create a pandemic strain.

Gene sequences for every viral gene were made available through the Global Initiative on Sharing Avian Influenza Data (GISAID). Preliminary genetic characterization 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. The six genes from American swine flu are themselves mixtures of swine flu, bird flu, and human flu viruses. 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. The seasonal influenza strain H1N1 vaccine is thought to be unlikely to provide protection.

Main symptoms of swine flu in humans
See also: "Symptoms of swine flu on YouTube". Centers for Disease Control and Prevention.

The CDC does not fully understand why the U.S. cases 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. Differences in the viruses or co-infection are also being considered as possible causes. Of the fourteen initial samples from Mexico tested by the CDC, seven were found to match the American strain. The virus likely passes through several cycles of infection with no known linkages between patients in Texas and California, and that containment of the virus is "not very likely". The U.S. embassy reported that a CDC investigative team arrived in Mexico City on April 25 to work with Mexican counterparts to study the virus.

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." By April 29, the U.S. had 91 confirmed cases with 5 hospitalizations and one death.

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.

Pandemic concern

See also: Pandemic Severity Index

The WHO and CDC are concerned that this outbreak may become a pandemic, for the following reasons.

• New strain

The virus is a new strain of influenza, from which human populations have not been vaccinated or naturally immunized.

• 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. The strain was later confirmed to have been transmitted between humans. 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. U.S. Vice President Joe Biden announced that he had advised his family not to travel by air or subway but later repudiated his statement.

• 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. Most other influenza strains produce the worst symptoms in young children, the elderly, and others with weaker immune systems. However, the CDC has indicated that symptoms reported from this strain so far are similar to those of normal seasonal flu. While some media outlets have speculated that this virus could cause a cytokine storm in patients, 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."

• 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.

As noted, predicting the size and severity of influenza outbreaks is a very inexact science. The U.S. government was famously wrong in predicting, in 1976, a swine flu pandemic that never materialized.

In a statement, the WHO said "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".

WHO alert phases

Phases 1 and 2

The WHO Phases refer to the current threat of any pandemic. Phase 1 is the normal case, with no threats being tracked. Prior to the first report of the 2009 swine flu, WHO had already raised the world pandemic alert level first to phase 2 and then to phase 3, because WHO was tracking the avian flu. WHO and other agencies were not aware of the 2009 swine flu when it was at the phase 2 level.

Phase 3

The WHO decided not to raise the level of the worldwide pandemic alert after its first meeting, on April 25. 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 Phase 3 alert was initially set due to the avian flu.

Phase 4

Following the second meeting of the Emergency Committee on April 27, the pandemic alert level was raised to Phase 4. Phase 4, "Sustained Human to Human Transmission," entails community-wide outbreaks.

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.

Phase 5

On April 29, the Emergency Committee met for the third time, and WHO raised the pandemic alert level to five, the second-highest level, indicating that a pandemic is "imminent". Human-to-human transmission cases have been recorded in multiple regions. 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.

Prevention and treatment

Further information: [[:Influenza: Prevention and Influenza 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.

There is no risk of flu transmission from consumption of pork. (Health authorities still recommend that pork be cooked to a minimum internal temperature of 160°F/70°C to ensure safety for reasons unrelated to influenza.)

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. Current development, large-scale manufacturing, distribution and delivery of a new vaccine takes several months. 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. 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.

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) and zanamivir (Relenza) but resistant to amantadine and rimantadine. Tamiflu and Relenza also have a preventative effect against Influenzavirus A. On April 27, the CDC recommended the use of Tamiflu and Relenza for both treatment and prevention of the new strain. 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.

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. 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. 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." However, on April 28, the U.S. CDC began "recommending that people avoid non-essential travel to Mexico." 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". 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. 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. A number of countries advised against travel to known affected regions.

Dr. Ira Longin, 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". In the northern hemisphere the flu season will soon end. However, "Timing is terrible for people in the Southern Hemisphere—places like New Zealand, Australia, South Africa, parts of South America. They are just coming into their flu season."

International cases and responses

  Confirmed deaths

  Confirmed cases

  Unconfirmed cases

Main article: 2009 swine flu outbreak by country

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. 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, and influenza A viruses are generally not heat resistant, some countries banned import and sale of pork products "as a precaution against swine flu".

Despite no 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, a move the World Organization for Animal Health called "scientifically unjustified".

Name of the disease

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". 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, and therefore the name of Swine flu may be misleading.

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. Israeli deputy health minister Yaakov Litzman proposed the name "Mexican flu" because Muslims and Jews consider pork to be unclean, but the Israeli government retracted this proposal following Mexican complaints. Although the South Korean Ministry for Food, Agriculture, Forestry and Fisheries asked the press to use the term “Mexican Virus” on April 29, but the 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. The World Organization for Animal Health has proposed the name "North American influenza". The European Commission uses the term "novel flu virus".

A more technical term used for the virus is "Influenza A (H1N1) virus, human".

The World Health Organization announced on April 30 it will refer to the new influenza virus as influenza A(H1N1) as opposed to swine flu in an attempt to not confuse the public about risks of pork products.

Media response

Since the outbreak began, there has been a week of near constant media attention. When a health emergency was officially declared on April 19, the story of the outbreak spread quickly through news networks. Multiple news conferences were aired in the United States by government officials. By the next day, April 20, it was the main topic of discussion.

The amount of media attention suggested a full-blown crisis, resulting in public fear. 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."

See also

• 1976 swine flu outbreak
• 1918 flu pandemic (Spanish flu)
• Hong Kong Flu (1968–1969)
• Influenza pandemic
• Severe acute respiratory syndrome (SARS)
• Health care in Mexico

External links

• U.S. Government swine, avian and pandemic flu portal
• Pandemic Flu Planning Checklist for Individuals and Families
• Global map of reported H1N1 outbreaks in 2009
• H1N1 swine flu outbreak timeline
• Swine Flu Outbreak, Influenza Virus Resource — sequences and related resources (GenBank, NCBI)
• BioHealthBase Bioinformatics Resource Center Database of influenza genomic sequences and related information.
• Medical Encyclopedia Medline Plus: Swine Flu

UN World Health Organization (WHO)

• Swine influenza, at the World Health Organization
  • RSS feed
• WHO's current Pandemic Influenza Phase
• @whonews twitter account

USA Centers for Disease Control (CDC)

• Swine Influenza (Flu) portal
  • Guidance for Clinicians on Identifying and Caring for Patients with Swine-origin Influenza A (H1N1) Virus Infection
  • Interim Guidance on Case Definitions for Swine Influenza A (H1N1) Human Case Investigations for state and local health department investigations, defines confirmed, probable and suspected
• Social Media Tools, inc. Swine Flu (mobile information, widgets, videos, podcasts, RSS feeds, social networking, etc.)

Pan-American Health Organization (PAHO)

• Swine Influenza portal
  • Influenza cases by a new sub-type: Regional Update (28 April 2009 13:00 WDC) (Epidemiological Alerts Vol. 6, No. 14)

European Centre for Disease Prevention and Control (ECDC)

• Threat Assessment for Swine Influenza at 19:00 hours 24 April 09
• Swine Influenza Information Home
  • ECDC H1N1 Situation Report
  • Swine Influenza FAQs
  • ECDC Pandemic Preparedness Report