Updated: Nov. 11, 2009

OVERVIEW

The outbreak of swine flu that was first detected in Mexico was declared a global pandemic on June 11, 2009, in the first designation by the World Health Organization of a worldwide pandemic in 41 years. The virus traveled the globe in the spring, worked its way across the Southern Hemisphere during the summer and reemerged as a widespread outbreak across the United States in the fall.

The initial outbreak raised fears of a repeat of the 1919 swine flu epidemic that left millions dead around the world. As more cases emerged, it became clear that the H1N1 virus, as it is officially called, was "moderate" in severity, in the words of Margaret Chan, the W.H.O.'s director general, with the overwhelming majority of patients experiencing only mild symptoms and a full recovery, often in the absence of any medical treatment.

But it the new swine flu has proved more serious than expected for pregnant women and healthy young people -- a sharp contrast to the seasonal flu, which is more dangerous to older people and those with compromised immune systems. In November, the federal Centers for Disease Control estimated that 4,000 people had died in the United States as a result of swine flu.

In October, federal health officials began delivering a swine flu vaccine which had been hurriedly developed. A total of 200 million doses are expected to be delivered, but the production fell significantly behind schedule when the vaccine proved to grow in eggs much more slowly than predicted. Some vaccination sites reported long lines and anxiety among parents hoping to have their children get one of the limited number of shots. A debate raged, primarily online, over whether the vaccine was safe, while many other Americans appeared to simply shrug off the flu's spread.

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ORIGINS

The origins of the flu are unclear; it seems to have first surfaced in Mexico or the southwestern United States. The outbreak was first identified in March 2009 in Mexico, where health authorities became alarmed over the deaths of several young and healthy adults.

Mexico's first known case, which was later confirmed, was from Perote, in Veracruz State, according to Health Minister José Ángel Córdova. The case involved a 5-year-old boy named Edgar, who recovered.

Yet contrary to the popular assumption that the new swine flu pandemic arose on factory farms in Mexico, federal agriculture officials in late June 2009 said they believed that it most likely emerged in pigs in Asia, then traveled to North America in a human. But they emphasized that there was no way to prove their theory and only sketchy data underpinning it.

There is no evidence that this new virus, which combines Eurasian and North American genes, has ever circulated in North American pigs, while there is tantalizing evidence that a closely related "sister virus" has circulated in Asia. American breeding pigs, possibly carrying North American swine flu, are frequently exported to Asia, where the flu could have combined with Asian strains. But because of disease quarantines that make it hard to import Asian pigs, experts said, it is unlikely that a pig brought the new strain back West.

On April 30, the W.H.O. said that it would stop referring to the virus as swine flu, after a number of countries banned pork imports or slaughtered pig hers, opting for the more clinical sounding A(H1N1). The virus has pieces of North American swine, bird and human flus and of Eurasian swine flu, according to the C.D.C.

PREPARING FOR AN EXPECTED SURGE IN CASES

As anecdotal reports and at least one poll showed that many Americans were nervous about the vaccine, federal health officials emphasized that the new shots were nearly identical to seasonal ones, and said they were doing what they could to debunk myths about the vaccine, such as the rumor that the shot causes the flu.

The top priority group for vaccinations, 150 million Americans, or about half the population, would include health care workers and emergency medical responders, because their jobs are critical. It would also include people with the highest risk of complications and severe illness from the new H1N1 virus: pregnant women; children and young adults from 6 months to 24 years; and people ages 25 to 64 with medical problems like asthma, diabetes and heart disease. The vaccine is also recommended for people caring for infants under 6 months, to prevent them from infecting the babies.

Defying expectations of experts, clinical trials show that the new swine flu vaccine protects most people with only one dose instead of two, so the vaccine supplies will go twice as far as had been predicted. Immune responses are different in each individual, but clinical trials suggest most people will be protected after 8 to 10 days.

Barring production delays, the government hopes to have in hand 195 million doses by the end of 2009.

Even as the C.D.C. released the first doses of the vaccine in early October, doctors, especially pediatricians, struggled to figure out how to administer perhaps thousands of doses quickly in small offices with limited staff, while dealing with other illnesses. Some said they were considering hiring nurses just for the vaccinations and setting aside days when children would be vaccinated in alphabetical order.

SYMPTOMS AND TRANSMISSION

The most common method of transmission is airborne, and it is also possible to become infected by touching a surface with the virus on it and then touching one's mouth or nose. The C.D.C. has advised people to wash their hands frequently, and also to avoid surfaces that might be contaminated.

Most people lack immunity to this new virus. But in one sign that the disease may not be as serious as feared, Mexican Health Minister José Ángel Córdova said that the flu appears only slightly more contagious than the seasonal flu, less than thought. Each sufferer is, on average, passing the disease along to between 1.4 and 1.8 people, a statistic known as the R factor.

Among the many unknowns, perhaps the biggest is how deadly A(H1N1) will be.

Even a flu with a low percentage of lethality can cause a large number of deaths if vast swaths of populations are infected -- seasonal flus kill an estimated 250,000 to 500,000 people worldwide each year. This outbreak has caused concern because officials have never seen this particular strain of the flu passing among humans before, said Dr. Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases.

PANDEMIC VIRUSES

By late September 2009, federal health officials said the swine flu virus had not mutated in any threatening way since the spring of 2009 and that the new vaccine was still a good match for it.

Much of the initial worry concerned the ages of the victims in Mexico. Unlike typical flu seasons, when infants and the aged are the most vulnerable, none of the initial deaths in Mexico were in people older than 60 or younger than 3, a spokeswoman with the World Health Organization said.

Pandemic flus -- like the 1918 flu and outbreaks in 1957 and 1968 -- often strike young, healthy people the hardest. This flu strain it appears to infect an unusually high percentage of young people. The median age of patients is 17.

The sudden detection of the new virus occurred just as scientists were focusing on behavioral changes observed in another virus, the A(H5N1) bird flu strain, in Egypt. Virologists have tracked the avian virus since its discovery in Hong Kong in 1997.

The avian flu has kept world health authorities anxious for years because 257 of the 421 people who contracted it died, or 61 percent. But it has shown very little ability to pass from person to person, mainly infecting poultry, and some experts have suggested that there may be something about the H5N1 virus that makes it inherently less transmissible among people.

As a benchmark, the deadliest influenza pandemic in the past century, the Spanish influenza of 1918 to 1919, had an estimated mortality rate of around 2.5 percent but killed tens of millions of people because it spread so widely. Many of those lives would have been saved if anti-flu drugs, antibiotics and mechanical ventilators had existed.

The virus that caused widespread panic in Asia in 2003, SARS -- severe acute respiratory syndrome -- is both easily spread and virulent. In the 2003 outbreak in Hong Kong, it killed 299 of the 1,755 people infected, or 17 percent.

RESPONSE FROM PUBLIC HEALTH OFFICIALS

Health authorities around the world took extraordinary measures to combat the epidemic and mitigate its effects as it quickly spread across the globe in late April and early May 2009. The W.H.O. raised its alert level on H1N1 flu to Phase 5 on April 29, based on the flu's continuing spread in the United States and Mexico. It was the first time that Phase 5, the next-to-highest level, has been declared since the W.H.O. system was introduced in 2005 in response to the avian influenza crisis.

Phase 6 means a pandemic is underway. A W.H.O. spokesman, Dick Thompson, said in mid-May there was still not enough evidence to conclude that the disease was spreading in a sustained way outside of North America, which would be required for the organization to raise its pandemic alert level to 6.

Britain, Japan and other nations have urged the W.H.O. to change the way it decides to declare a pandemic - saying the agency must consider how deadly the virus is, not just how fast it is spreading. There has been concern that by raising the global alert level to 5, the United Nations health agency had unduly raised alarm.

International health experts, who say the epidemic will spread regardless of attempts at containment, advised against closing borders. They encouraged governments to focus on mitigating the disease's spread through public health measures.

For the W.H.O., the approach is an about-face from the strategy that has contained the H5N1 avian flu. The avian flu was contained in 1997 by killing every chicken in Hong Kong, and later cases have been met with aggressive efforts at culling nearby birds and vaccinating poultry in a ring around them.

Many countries ignored the advice against containment efforts, leading to a welter of bans, advisories and alerts on certain pork products. In China, authorities quarantined Mexican travelers in hospitals and hotels - many of whom had shown no sign of illness.

Mexico City, one of the world's largest cities, temporarily closed schools, gyms, swimming pools, restaurants and movie theaters. Mexicans donned masks for protection outdoors.

THE VIRUS IN NEW YORK CITY

In the early days of the swine flu outbreak in the United States the cases were concentrated in New York City. The city's first reported cases were diagnosed in late April 2009 among teenagers from a high school in Queens who had traveled to Mexico for spring break.

In the following weeks the public schools seemed to become an incubator for the flu, and numerous facilities were closed. But after an early period of high alert when the virus was first detected, officials toned down their concern.

On May 17, 2009, Mitchell Wiener, the assistant principal at a school in Queens, became the first person to die from the virus in New York.  Health officials said that the death was not surprising, since even in a normal flu season, thousands of victims die of complications from the disease, and because he had a history of medical problems that may have put him at greater risk.

In the fall of 2009, as the city girded for a second wave of the swine flu pandemic that already had killed more than 50 people in New York City, Mayor Michael R. Bloomberg outlined a strategy that included free vaccinations for students, health clinics transformed into "flu centers" to relieve hospitals, emergency room statistics reported on the Web daily and schools closing only as a last resort.

FLU DRUGS

A single shot of the new swine flu vaccine appears to protect most children and teenagers nearly as well as it protects adults, according to federal officials. Clinical trials indicate that children 6 months to 9 years old received some protection from one shot, but not enough, so health officials are recommending they get two shots 21 days apart.

Federal health officials expressed particular worry about pregnant women. As of late August 2009, 100 had been hospitalized in intensive care, and 28 had died since the beginning of the outbreak in April. Pregnant women were urged to get swine flu shots as soon as they became available.

As a small fraction -- some 2.4 million doses -- of the nasal spray vaccine began arriving the first week of October at local health departments, plans for limited distribution were being formulated on the fly or dusted off from earlier in the decade, when fears of an avian flu pandemic sparked a rush of emergency preparedness.

In large part, chaos seems to have been averted, at least initially. Many people seem to be more eager to receive the injectable form of the vaccine, which is not yet available. And the nasal spray, called FluMist, has some limits on who may use it. It is not recommended for infants, the elderly or pregnant women.

Health officials were still struggling to communicate that information to the public and make the general population aware that the first doses were not being widely distributed. So for most people, there was nothing to do but wait.

Federal officials said there was little they could do to avoid the shortages. Vaccine production relies on a process of growing strains of the virus in eggs, and the swine flu virus grew unexpectedly slowly. But they acknowledged that their optimistic statements in the months leading up to the flu season may have contributed to the confusion.

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