The 2009 flu pandemic is a global outbreak of a new strain of influenza A virus subtype H1N1, officially referred to as novel H1N1, first identified in April 2009 and commonly called swine flu. The virus is a mixing (re-assortment) of four known strains of influenza A virus: one endemic in humans, one endemic in birds, and two endemic in pigs (swine). Transmission of the new strain is human-to-human, and eating cooked pork products will not transmit the virus.

The outbreak began in Mexico, with evidence that there had been an ongoing epidemic for months before it was officially recognized as such. The Mexican government soon closed most of Mexico City’s public and private offices and facilities to contain the spread of the virus. As the virus quickly spread globally, clinics were overwhelmed by testing and treating patients, and the WHO and the U. S. Centers for Disease Control and Prevention (CDC) eventually stopped counting all cases and focused instead on tracking major outbreaks. In early June 2009, the World Health Organization (WHO) declared the outbreak to be a pandemic, but also noted that most of the illnesses were of moderate severity.

The illness is generally mild, except in some cases for people in higher risk groups, such as those with asthma, diabetes, obesity, heart disease, or who are pregnant or have a weakened immune system. In addition, even in people who were previously healthy, secondary infections, such as those caused by bacterial pneumonia or a relapse of the illness with worse symptoms, are considered very serious and require medical treatment.

Like other influenza viruses, novel H1N1 influenza is spread by coughing, sneezing, or touching contaminated surfaces and then touching the nose or mouth. Symptoms, which last up to a week, are similar to those of seasonal flu, and can include fever, sneezing, sore throat, cough, headache, and muscle or joint pains. To avoid spreading the infection, the CDC recommended that those with symptoms stay home from school, work, and crowded settings; in general, wearing facial masks was not recommended, except in healthcare settings.

Annual influenza epidemics are estimated to affect 5–15% of the global population. Although most cases are mild, these epidemics still cause severe illness in 3–5 million people and 250,000–500,000 deaths worldwide. In industrialized countries, severe illness and deaths occur mainly in the high-risk populations of infants, the elderly, and chronically ill patients, although the swine flu outbreak (as well as the 1918 Spanish flu) differs in its tendency to affect younger, healthier people.

In addition to these annual epidemics, Influenza A virus strains caused three global pandemics during the 20th century: the Spanish flu in 1918, Asian flu in 1957, and Hong Kong flu in 1968–69. These virus strains had undergone major genetic changes for which the population did not possess significant immunity. Recent genetic analysis has revealed that three-quarters, or six out of the eight genetic segments of the 2009 flu pandemic strain arose from the North American swine flu strains circulating since 1998, when a new strain was first identified on a factory farm in North Carolina, and which was the first-ever reported triple-hybrid flu virus.

The great majority of deaths in the 1918 flu pandemic were the result of secondary bacterial pneumonia. The influenza virus damaged the lining of the bronchial tubes and lungs of victims, allowing common bacteria from the nose and throat to infect their lungs. Subsequent pandemics have had many fewer fatalities due to the development of antibiotic medicines that can treat pneumonia.

The influenza virus has also caused several pandemic threats over the past century, including the pseudo-pandemic of 1947, the 1976 swine flu outbreak, and the 1977 Russian flu, all caused by the H1N1 subtype. The world has been at an increased level of alert since the SARS epidemic in Southeast Asia (caused by the SARS coronavirus). The level of preparedness was further increased and sustained with the advent of the H5N1 bird flu outbreaks because of H5N1’s high fatality rate, although the strains currently prevalent have limited human-to-human transmission (anthroponotic) capability, or epidemicity.

People who contracted flu before 1957 appeared to have some immunity to H1N1. Dr. Daniel Jernigan of the CDC has stated: “Tests on blood serum from older people showed that they had antibodies that attacked the new virus [...] That does not mean that everyone over 52 is immune, since Americans and Mexicans older than that have died of the new flu.”

It is not known where the virus originated. Analyses in scientific journals have suggested that the H1N1 strain responsible for the current outbreak first evolved in September 2008, and circulated among humans for several months before being identified as a new strain of flu.

The virus was first reported in two US children in March 2009, but health officials have reported that it apparently infected people as early as January 2008 in Mexico. The outbreak was first detected in Mexico City on March 18, 2009; immediately after the outbreak was officially announced, Mexico requested material support from the US, and within days of the outbreak Mexico City was “effectively shut down”. Some countries canceled flights to Mexico while others halted trade. Calls to close the border to contain the spread were rejected. Mexico already had hundreds of cases before the outbreak was officially recognized, and was therefore in the midst of a “silent epidemic”. As a result, Mexico was reporting only the most serious cases, possibly leading to a skewed initial estimate of the case fatality rate.”

The new strain was first identified by the CDC in two children, neither of whom had been in contact with pigs. The first case, from San Diego County, California, was confirmed from clinical specimens (nasopharyngeal swab) examined by the CDC on April 14, 2009. A second case, from nearby Imperial County, California, was confirmed on April 17. The patient in the first confirmed case had flu symptoms including fever and cough on clinical exam on March 30, and the second on March 28. It was not identified as a new strain in Mexico until April 24.