2009 swine flu pandemic

The 2009 flu pandemic is a global outbreak of a new strain of influenza A virus subtype H1N1, identified in April 2009 and commonly referred to as swine flu, which infects and is transmitted between humans. It is thought to be a mutation —more specifically, a reassortment— of four known strains of influenza A virus subtype H1N1: one endemic in humans, one endemic in birds, and two endemic in pigs (swine). A June 10, 2009 update by the U.N.'s World Health Organization (WHO) states that "74 countries have officially reported 27,737 cases of influenza A(H1N1) infection, including 141 deaths".

WHO officially declared the outbreak to be a "pandemic" on June 11, but stressed that the new designation was a result of the global "spread of the virus," not its severity. The WHO stated the pandemic appears to have moderate severity in comparatively well-off countries, however it is prudent to anticipate a bleaker picture as the virus spreads to areas with limited resources, poor health care, and a high prevalence of underlying medical problems. The case fatality rate (CFR) of the pandemic strain is estimated at 0.4% (range 0.3%-1.5%)

The virus typically spreads from coughs and sneezes or by touching contaminated surfaces and then touching the nose or mouth. As of June 2009, there is no vaccine available to prevent infection although companies are developing one; estimates of availability range from six months to twelve months. There is also concern that the virus could mutate later in the year and become more virulent and less susceptible to any vaccine developed to protect from an earlier strain. This concern is partly due to the memory of the 1918 flu pandemic, which killed approximately 600,000 in the United States alone, and was preceded by a mild "herald" wave of cases in the spring.

As of May 24, 2009, nearly 90% of reported deaths had taken place in Mexico. This has led to speculation that Mexico may have been in the midst of an unrecognized epidemic for months prior to the current outbreak, thereby showing a fatality rate that was much higher than it would have been if earlier cases had been counted. According to the US Centers for Disease Control and Prevention, the fact that the flu's infection activity is now monitored more closely may also help explain why more flu cases than normal are being recorded in many countries.

Historical context

Annual influenza epidemics are estimated to affect 5–15% of the global population, resulting in severe illness in 3–5 million patients and causing 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.

In addition to these annual epidemics, Influenza A virus strains caused three major global epidemics during the 20th century: the Spanish flu in 1918, Asian flu in 1957 and Hong Kong flu in 1968–69. These pandemics were caused by strains of Influenza A virus that had undergone major genetic changes and for which the population did not possess significant immunity. The overall effects of these pandemics and epidemics are summarized in the table below.

20th and 21st century Flu pandemics
Pandemic	Year	Influenza A virus subtype	People infected (approx)	Deaths (est.)	Case fatality rate
1918 pandemic flu	1918–19	H1N1	500 million - 1 billion	20 to 100 million	>2.5%
Asian flu	1957	H2N2		2 million	<0.1%
Hong Kong flu	1968–69	H3N2		1 million	<0.1%
2009 flu pandemic	2009	H1N1	36,000 (confirmed)	183 (confirmed)	0.5% est. (range 0.3%-1.5%)
Seasonal flu	Every year	mainly A/H3N2, A/H1N1, and B	5-15% (340 million - 1 billion)	250,000-500,000	<0.05%

      Not a pandemic, but listed to compare the several flu strains endemic in humans which produce seasonal flu with the rare new strain that results in a flu pandemic

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 prior to 1957 may have some immunity. A May 20, 2009 New York Times article stated: “Tests on blood serum from older people showed that they had antibodies that attacked the new virus, Dr. Daniel Jernigan, chief flu epidemiologist at the Centers for Disease Control and Prevention, said in a telephone news conference. That does not mean that everyone over 52 is immune, since some Americans and Mexicans older than that have died of the new flu.”

Initial outbreaks

A semi-logarithmic chart of laboratory-confirmed A(H1N1) influenza cases by date according to WHO reports.

Further information: 2009 flu pandemic timeline

Further information: 2009 flu pandemic table

It is not known where the virus originated. Analysis has suggested that the H1N1 strain responsible for the current outbreak first evolved around September 2008 and circulated in the human population for several months before the first cases were identified as being due to a new strain.

Mexico

Further information: [[:2009 flu pandemic in Mexico]]

The virus was first reported in two U.S. children in March, but health officials have said that it apparently infected people as early as last January in Mexico. The outbreak was first detected in Mexico City on March 18, 2009 where surveillance began picking up a surge in cases of influenza-like illness. "In early April, Mexico had noticed that it had high numbers of serious respiratory illnesses and some deaths. It began sending samples to Canada and the United States, asking for help genotyping the new virus." Health Secretary Jose Angel Cordova confirmed that a 4-year-old boy was part of an outbreak in Veracruz state that began in February. Residents of the town of Perote worried at the time that they had contracted a new and aggressive flu, and publicly demonstrated against the pig farm they initially blamed for their illness. It was only after U.S. labs confirmed a swine flu outbreak that Mexican officials sent the boy's sample in for testing, and it tested positive for swine flu. While there was speculation that the outbreak may have started at the pig plant in Veracruz, the plant owners said that no pigs had tested positive for the virus.

After the outbreak was officially announced, Mexico immediately requested material support from the U.S. and worked closely with the CDC and Canada, sending them suspected samples for testing. Soon after, the CDC helped Mexico build their own lab capability to do faster diagnosis and confirmation of the H1N1 virus in Mexico. According to one commentator, "in the face of mounting hysteria, the response of both Mexico and the United States was an almost perfect display of the cooperation and partnership . . . ." Within a few days Mexico City was "effectively shut down," and some countries hastily canceled flights to Mexico while other halted trade. Although many in the U.S. called for shutting the border to help contain the spread, President Obama rejected the idea and Homeland Security Secretary Janet Napolitano called it "pointless," as the virus had already crossed into the U.S., and felt that "closing the border would have done nothing more than wreak economic havoc on both economies."

As the outbreak spread throughout Mexico and into the U.S., however, scientists were trying to understand why there were so many deaths in Mexico while infections in the United States and Canada were relatively mild and not unusually dangerous compared to seasonal flus. "If that continues to be true," wrote the Washington Post, "then it may help explain the mysteriously high mortality in Mexico." The newspaper noted that "it may be that Mexico already has had hundreds of thousands, and possibly millions, of cases—all but the most serious hidden in the 'noise' of background illness in a crowded population." They added, "the fact that most people infected in other countries had recently been to Mexico—or were in direct contact with someone who had been—is indirect evidence that the country may have been experiencing a silent epidemic for months." A study published May 11, 2009 in the journal Science estimated Mexico alone may have already had 23,000 cases of swine flu by April 23, 2009, the day it announced the epidemic.

As experts struggled to explain why so many deaths had initially occurred in Mexico and nowhere else, the CDC on May 1, 2009 suggested a simple explanation: "there are many cases in Mexico, most are mild, and just the bad ones have been seen so far." It noted that recent severe cases had focused on patients seeking care in hospitals and acknowledged that there could in fact be a large number of undetected cases of illness, which would explain the much higher mortality rate. Other experts agreed: "The central question every flu expert in the world would like answered, is how many mild cases Mexico has had," said Dr. Martin Cetron, director of global migration and quarantine for the Centers for Disease Control, in an interview. "We may just be looking at the tip of the iceberg, which would give you a skewed initial estimate of the case fatality rate," as he also speculated that there may have been tens of thousands of unreported mild infections, which would then make the number of deaths seemingly low, and as the flu spreads, the number of people who become seriously ill would remain relatively small.

United States

Further information: [[:2009 flu pandemic in the United States]]

The new strain was first diagnosed in two children by the CDC, first on April 14, 2009 in San Diego County, California and a few days later in nearby Imperial County, California (it was not identified as a new strain in Mexico until 24 April). Neither child had been in contact with pigs.

World governments and media response

Main article: 2009 swine flu outbreak by country

  Confirmed cases followed by death

  Confirmed cases

  Unconfirmed or suspected cases

See also: H1N1 live map, WHO updates

U.S. response analyzed

According to Dr. Thomas Frieden, the new CDC director on June 8, 2009: "There’s no question that a new strain of influenza spreading rapidly throughout the world is a major problem and requires a major response. So far, it doesn’t seem to be any more severe than seasonal flu, but seasonal flu kills 36,000 Americans a year."

Federal officials and other groups felt that six years of worrying about H5N1 avian flu did much to prepare the United States for the current swine flu outbreak. Jeffrey Levi, executive director of the monitoring group Trust for America’s Health, notes that after H5N1 emerged widely in Asia in 2003, killing about 60 percent of the humans infected by it, many countries took steps to prevent any crisis that would emerge if that virus were to acquire the ability to jump easily from human to human, and the measures taken in preparation were helpful. Levi also said that little vaccine would be available by the fall, even if there were no major delays in production.

Dr. Schuchat, summarizing much of the country's quick response says "This really was a wake-up call for the world. We actually have been preparing for a pandemic for many years now." The avian flu outbreak more than five years ago led the CDC and state and local public health departments to prepare for a nationwide pandemic. "I would say these exercises worked immensely," Schuchat said, especially development of disease diagnosis and tracking and communication. "There has been a lot of payoff for worrying about bird flu."

But recognizing that the responses were not perfect, she also said the CDC will now use the current lull to take stock of the nation's response to the new H1N1 flu and attempt to patch any gaps in the public health safety net before flu season starts this fall. She cited a new report which found that recent cuts in public health departments have meant many did not have adequate resources to carry out flu plans. The U.S. Government Accountability Office also said the U.S. flu preparedness plan needed improvement, including better coordination between federal, state and local governments and the private sector.

The report found problems in plans for school closures and limiting mass gatherings, and even with a mild outbreak, it found hospital emergency departments and other parts of the healthcare delivery system were overwhelmed. It urged government health officials to improve coordination at all levels of government and with other countries, and develop better strategies for school closures, sick-leave policies and other ways to limit public gatherings during periods of rapid infection. The report specifically urged a halt to planned layoffs at state and local health departments, and recommended hospitals improve strategies for handling a large influx of patients.

Data reporting and accuracy

See also: National Influenza Centers, Disease surveillance, and Clinical surveillance

The initial outbreak received a week of near-constant media attention. Epidemiologists cautioned that the number of cases reported in the early days of an outbreak can be very inaccurate and deceptive due to several causes, among them selection bias, media bias, and incorrect reporting by governments. Inaccuracies could also be caused by authorities in different countries looking at differing population groups. Furthermore, countries with poor health care systems and older laboratory facilities may take longer to identify or report cases.

In late April, experts predicted there would be 2,000 to 2,500 U.S. cases by the end of May. However, by May 15, 2009, the Centers for Disease Control and Prevention estimated that there were "upwards of 100,000" cases in the country, even though only 7,415 had been confirmed at that point. The CDC in late May stated that counting confirmed cases had become "largely irrelevant," and switched instead to its traditional surveillance systems for monitoring flu-like symptoms by looking for patterns, clusters and changes in flu activity nationwide. According to the CDC, surveillance methods, along with rapid isolation and treatment, only makes sense at the very earliest stage of an outbreak, and "becomes irrelevant" once the virus is spreading widely within the community, as it is in the United States.

In some instances, governments accused other countries of intentionally underreporting cases. Moscow, for instance, hinted that the Caribbean nation of the Dominican Republic was underreporting its number of swine flu cases to "boost tourism," and on May 30 advised its citizens not to travel there. In early May, Cuba's Fidel Castro accused Mexico of hiding the scope of the epidemic until after President Obama visited the country in April, and a study published in the journal Science on May 11, estimated Mexico alone may have had 23,000 cases of swine flu by April 23, the day it announced the epidemic.

In the U.S. data accuracy has also become an issue, with some school districts deciding to keep the names of students and schools that have reported infections confidential, one stating that "it would not be fair to single out one school," since doing so would likely trigger requests by parents to have their children tested despite their health not being in danger, and the schools lack the ability to test everyone. Dr. Hector Gonzalez, Director of the Laredo Health Department, said that according to CDC guidelines, physicians only need to submit samples for testing if the patient is a child under 5 years of age, is pregnant, has an underlying medical condition or is suffering from respiratory distress requiring urgent care.

In early June, WHO and the U.S. FDA acknowledged that a new laboratory test used to identify the potentially deadly virus is only about 90 per cent accurate, and suggested that the newly developed rRT-PCR "rapid" testing method gives only a "presumptive positive" rather than a "definitive positive" result for H1N1 influenza. As this test is currently used in Australia, reports indicate that Australians may have been falsely diagnosed with human swine flu while others with the disease may have been sent home with a negative result.

Travel advisories

The new strain has spread widely beyond Mexico and the U.S., with confirmed cases in fifty-four countries and suspected cases in fifty-nine. Many countries had earlier advised citizens to avoid travelling to infected areas, especially Mexico, and were monitoring visitors returning from flu-affected areas for possible flu symptoms. In late April 2009 Mexico closed all of its schools and public places for a week to control its spread.

At first, most cases outside North America were recent travellers to Mexico or the U.S. However, intra-national infections have now also been reported from Canada, Japan, Panama, the UK, Spain, Germany, Australia, Italy, and Belgium.

On May 15, 2009, CDC’s "Travel Health Warning" recommending against non-essential travel to Mexico, in effect since April 27, 2009, was downgraded to a "Travel Health Precaution for Mexico." In lifting its warning, the CDC said, "There is evidence that the Mexican outbreak is slowing down in many cities though not all.” It also said that the “risk of severe disease” from the H1N1 virus "now appears to be less than originally thought."

Actions concerning pigs

Main article: 2009 swine flu outbreak actions concerning pigs

Swine infections

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 a human-to-human transmitted virus, requiring no contact with swine. On May 2 it was announced that a carpenter on an Alberta farm who had returned from Mexico had transmitted the disease to a herd of pigs, showing that the disease can still move between species.

Pork import bans

International health officials from the CDC, WHO, FAO, OIE and other food organizations have reaffirmed that pork is safe to eat and hogs are not to blame for the epidemic. However, as of early June, China, Russia and more than a dozen other countries were still banning pork imports from the U.S.

On June 12, the World Trade Organisation (WTO) planned to highlight the pork bans in a forthcoming report on protectionism due in the coming weeks. WHO's World Organisation for Animal Health (OIE) and U.N.'s Food and Agriculture Organisation reiterated that pork is not a source of infection and is safe to eat provided it is prepared properly. However, the WTO report is likely to limit itself to listing the meat import restrictions and "not comment on whether they are justified, for fear of prejudging any trade disputes that arise from them." Russia is not a WTO member, and along with Argentina, are among the most prominent countries still banning pork imports from affected countries.

This has also led some U.S. industry and government officials to "speculate that the issue is more about market share than health concerns." The bans, instituted in the wake of the swine flu outbreak, cost the U.S. hog industry millions of dollars every week. "It's politics and not science," said John Lawrence, a professor and livestock economist at Iowa State University. "The product is safe. So why restrict imports?" About 20 percent of U.S. pork is exported, and China and Russia are among the biggest buyers.

Pork culls

In late April, 2009, the Egyptian Government began to kill all 300,000 pigs in Egypt, despite a lack of evidence that the pigs had, or were even suspected of having, the virus. This led to clashes between pig owners and the police in Cairo. Most of Egypt's 80-million population are Muslims, whose religion forbids them from eating pork, but an estimated six to ten percent are Christian Copts, who eat pork. On June 5, the UK-based Compassion in World Farming organization warned Egypt that its brutal measures and its mass slaughter of pigs could negatively affect Egypt's tourism industry. Philip Lymbery the chief executive of the group was quoted saying that "Britons and people from around the world have joined the international storm of protest against this atrocity in Egypt, with many saying they'll no longer consider Egypt as a possible holiday destination,"

In Canada in early June, an Alberta pig farmer whose herd was infected with the new swine flu virus culled his entire herd. In May he had already culled 500 animals from his herd which was believed to have been infected by a worker who had been vacationing in Mexico. The farm owner said the animals cannot be marketed because they are under quarantine and he is facing a problem with overcrowding.

Surveillance of pig populations

At the beginning of June 2009, the U.S. Agriculture Department said it would launch a pilot surveillance project to look for new strains of flu virus in pigs. Some experts claim that global health officials have underestimated the risk that pig herds might be a source of new influenza strains, choosing instead to focus on the threat of bird flu. "This virus most likely evolved from recent swine viruses," Gerardo Nava of the National Autonomous University of Mexico wrote in a report published in the online journal Eurosurveillance.

Until recently, health experts have done very little surveillance of influenza among pigs—even though the virus is very common in the animals and just as transmissible as it is among people. Flu viruses have also been shown to pass from pigs to people and from people to pigs. "These observations also reiterate the potential risk of pig populations as the source of the next influenza virus pandemic," Nava and colleagues wrote. "Although the role of swine as 'mixing vessels' for influenza A(H1N1) viruses was established more than a decade ago, it appears that the policy makers and scientific community have underestimated it. . . . The problem is that the virus is recombining (in the pig's body) and getting new sequences, new genes."

Nomenclature debate

H1N1 influenza virus

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. The CDC began referring to it as "Novel influenza A (H1N1)". In the Netherlands, it was originally called "pig flu", then called "Mexican flu" by the national health institute and in the media. South Korea and Israel briefly considered calling it the "Mexican virus". Later, the South Korean press used "SI", short for "swine influenza". Taiwan suggested the names "H1N1 flu" or "new flu", which most local media now use. The World Organization for Animal Health proposed the name "North American influenza". The European Commission adopted the term "novel flu virus".

After initially opposing changing the name from "swine flu", the WHO announced they would refer to the new influenza virus as Influenza A (H1N1) or "Influenza A (H1N1) virus, human", also to avoid suggestions that eating pork products carried a risk of infection.

The outbreak was also called the "H1N1 influenza", "2009 H1N1 flu", or "swine-origin influenza". However, Seth Borenstein, writing for the Associated Press quoted several experts who objected to any name change at all.

Virus characteristics

Main article: 2009 A/H1N1

The virus is a novel strain of influenza from which human populations have been neither vaccinated nor naturally immunized. The CDC, after examining virus samples from suspected cases in Mexico, matched the strain with those from cases in Texas and California, and found no known linkages to either to animals or one another. It was also determined that the strain contained genes from four different flu viruses: North American swine influenza; North American avian influenza; human influenza; and two swine influenza viruses typically found in Asia and Europe. Further analysis showed that several of the proteins of the virus are most similar to strains that cause mild symptoms in humans, leading virologist Wendy Barclay to suggest on May 1 that the virus was unlikely to cause severe symptoms for most people. Scientists in Winnipeg completed the first full genetic sequencing of the virus on 6 May.

Virus origins

In early June, Oxford University's Department of Zoology, reported test results that "show that this strain has been circulating among pigs, possibly among multiple continents, for many years prior to its transmission to humans." The research team that worked on this report also believe that it was "derived from several viruses circulating in swine," and that the initial transmission to humans occurred several months before recognition of the outbreak. The team concluded that "despite widespread influenza surveillance in humans, the lack of systematic swine surveillance allowed for the undetected persistence and evolution of this potentially pandemic strain for many years."

Structure of the influenza virion. The hemagglutinin (HA) and neuraminidase (NA) proteins are shown on the surface of the particle. The viral RNAs that make up the genome are shown as red coils inside the particle and bound to Ribonuclear Proteins (RNPs).

According to the researchers, movement of live pigs between Eurasia and North America "seems to have facilitated the mixing of diverse swine influenza viruses, leading to the multiple reassortment events associated with the genesis of the (new H1N1) strain." They also stated that this new pandemic "provides further evidence of the role of domestic pigs in the ecosystem of influenza A."

Rate of infection

According to the World Health Organization, 66 countries had officially reported 19,723 cases of infection, including 117 deaths, as of June 3, 2009. Notably, the cases in Argentina, Australia and El Salvador more than doubled in each of WHO reporting cycle updates 41 and 42 (29 May and 1 June respectively). But according to CDC experts, however, the flu outbreak in the U.S. is dying down in the country as a whole. As of May 30, Wisconsin had more cases than any other state: 1,430, but Wisconsin officials said that this was "nothing to worry about," pointing out that the higher numbers largely reflected the state's efficiency in testing suspected cases. Spokesman Seth Boffeli added that the Wisconsin cases had been relatively mild.

Some news reports indicated that the swine flu was spreading more widely than official figures indicate, with outbreaks in Europe and Asia following those of North and South America. According to the CDC, about one in 20 cases was being officially reported in the U.S. In the U.K., according to virologist professor John Oxford, the virus may be 300 times more widespread than health authorities have said, with total infections estimated at 30,000 as of 24 May 2009. Oxford's estimate comes as leading scientists are warning that estimates by the U.K. and other governments on the spread of the disease are "meaningless" and hiding its true extent. He also estimates that Japan may have approximately 30,000 cases. Professor Michael Osterholm, one of the world's top flu experts and an adviser to the U.S. government, also called the official figures "meaningless," claiming that officials were not hiding cases, but were not hunting very hard to find them. Oxford also believes that thousands of people have caught the virus and "suffered only the most minor symptoms," or none at all, over the past weeks.

Although the United States was past its flu season, the Southern Hemisphere, where the virus had also spread, was entering the cold months when influenza cases increase. Jeffery Taubenberger, a National Institutes of Health researcher, stated that "I am loath to make predictions about what an influenza virus that mutates so rapidly will do," but he believes it will spread across the planet. Other experts concur, adding that "the new swine flu virus is almost certain to eventually infect every continent and country, although that may take years."

Virulence

Most fatalities have been in Mexico (72%, as of June 5, 2009) where, according to the New York Times, the deaths from the illness have primarily been young, healthy adults. The WHO Rapid Pandemic Assessment Collaboration estimated the case fatality ratio in Mexico prior to mid-April to be 0.4%. This is comparable to that of the 1957 Asian flu, a category 2 pandemic that killed approximately 1 to 4 million people.

By May 27, 2009, the CDC was reporting 6764 U.S. cases in 47 states resulting in fourteen deaths, but noted that for the most part, the infections continue to be mild—similar to seasonal flu—and recovery is extremely quick. Furthermore, analysis hasn't turned up any of the markers which scientists associate with the virulence of the 1918 "Spanish flu" virus, said Nancy Cox, head of the CDC's flu lab. In the state of New York, as of June 7, eight people have died from the outbreak, which has sparked "panic in schools, fear in hospitals and unease on the subways'," writes the New York Daily News. Belinda Ostrowsky, a doctor at Montefiore Medical Center's division of infectious diseases notes that the deaths so far are "a tiny fraction of the up to 2,000 New Yorkers who die every year from seasonal flu - with barely a public murmur." She adds, "When there's something that's new and unknown, it scares people."

Mutation potential

On May 22, 2009, WHO chief Dr. Margaret Chan said that the virus must be closely monitored in the southern hemisphere, as it could mix with ordinary seasonal influenza and change in unpredictable ways. "In cases where the H1N1 virus is widespread and circulating within the general community, countries must expect to see more cases of severe and fatal infections," she said. "This is a subtle, sneaky virus."

This led other experts to become concerned that the new virus strain could mutate over the coming months. Guan Yi, a leading virologist from the University of Hong Kong, for instance, described the new H1N1 influenza virus as "very unstable", meaning it could mix and swap genetic material when exposed to other viruses. During an interview he said "Both H1N1 and H5N1 are unstable so the chances of them exchanging genetic material are higher, whereas a stable (seasonal flu) virus is less likely to take on genetic material." The H5N1 virus is mostly limited to birds, but in rare cases when it infects humans it has a mortality rate of between 60% to 70%. Experts worry about the emergence of a hybrid of the more virulent Asian-lineage HPAI (highly pathogenic avian influenza) A/H5N1 strain (media labeled "bird flu") with more human-transmissible Influenza A strains such as this novel 2009 swine-origin A/H1N1 strain (media labeled "swine flu"), especially since the H5N1 strain is and has been for years endemic in a variety of wild bird species in countries like China, Indonesia, Vietnam and Egypt. (See the suite of H5N1 articles for details.)

Nor had federal health officials in the U.S. dismissed the possibility that the worst was yet to come. "Far from it," Ann Schuchat of the CDC says, noting that the horrific 1918 flu epidemic, which killed hundreds of thousands in the United States alone, was preceded by a mild "herald" wave of cases in the spring, followed by devastating waves of illness in the fall. "That 1918 experience is in our minds," she said.

However, as of early June 2009, Schuchat reported "encouraging news" regarding any mutations to date, by announcing that samples of the virus from points around the globe are "genetically identical" to the strain found in the United States. "We have tested isolates from a wide geographic area, from the Americas, Europe, from Asia and New Zealand and we are not seeing variations in isolates from the genetic testing we do here." Although cases have been relatively mild and patients recover quickly, health officials have warned that the virus could mutate into a more virulent form, putting greater numbers of people at risk.

Pandemic declared

Further information: [[:CDC Pandemic Severity Index and WHO pandemic phases]]

On June 11, 2009, the WHO's Chan declared the outbreak had become a pandemic. The WHO declared a Pandemic Alert Level of six, out of a maximum six, describing the degree to which the virus had been able to spread among humans. In the same briefing, Chan stressed that the WHO pandemic level was not linked to severity. On a separate scale for severity, WHO assessed the global severity as "moderate."

WHO had hesitated to raise its alert level and declare a phase 6 pandemic as the virus to date has caused generally mild symptoms. Having raised it to level 6 may cause many countries to adopt a variety of plans, such as shutting borders, banning events and curtailing travel. A move to phase 6 means that "emergency plans are instantly triggered around the globe." In addition, at phase 6, many pharmaceutical companies may switch from making seasonal flu shots to pandemic-specific vaccine, "potentially creating shortages of an immunization to counter the normal winter flu season." Keiji Fukuda, WHO's assistant director general of health security and environment, stated that a move to phase 6 would "signify a really substantial increase in risk of harm to people." He also cautioned that "one of the critical issues is that we do not want people to over-panic if they hear that we are in a pandemic situation."

WHO to focus on developing countries

On June 12, the day after the pandemic was declared, WHO stated that its "primary concern is to strengthen and support health systems in countries with less resources." It emphasized that developing countries, where medical care systems are weak and supplies of antivirals insufficient, "will be the frontline of their battle against pandemic flu." They also noted that the virus has so far caused mostly mild symptoms in rich countries such as Canada and the United States, with "most patients recovering without even going to a doctor." But WHO experts felt that it could prove far more deadly to poor populations "already weakened by malnutrition, chronic conditions like asthma and diabetes, or low immunity due to HIV/AIDS." They were also working to make stocks of antivirals and antibiotics and an eventual pandemic vaccine more accessible and affordable to developing countries.

Northern Hemisphere

As of early June 2009, the flu has been reported in more than 60 countries, mostly in the Northern Hemisphere, with the United States reporting the most cases — more than 10,000, including at least 18 deaths, according to the World Health Organization.

As of May 30, 2009, seasonal flu is down, circulating at low levels; while the non-seasonal new H1N1 flu strain continues to spread and constitutes approximately 82% of all influenza viruses reported to CDC in the last week of May 2009.

Southern Hemisphere

It is predicted that the virus will likely continue to spread worldwide, especially in the Southern Hemisphere, where countries are entering the winter months and the traditional flu season. South America already has had more than 3,000 cases, including 2,335 cases and two deaths in Chile and one death in Colombia. Keiji Fukuda of WHO has stated that swine flu has already caused more infections than seasonal influenza at the start of Chile's winter flu season.

On June 6, 2009, Australia's second largest city, Melbourne, was reported to be the "swine flu capital of the world"; on 8 June there were 1,011 cases in Victoria, mostly in Melbourne. In the entire country, confirmed cases have reached 1,542. However, according to professor Robert Booy from the University of Sydney, the reason Victoria has the highest per capita rate of swine flu in the world "may simply be down to Australia's tough testing regime," and "is probably the best in the world at detecting this influenza virus." As a result, he feels that the U.S. and Mexico probably had more cases than have been reported, stating "I would be quite certain that there's ten to a hundredfold more cases in the US than are confirmed. In early June WHO and the U.S. Food and Drug Administration suggested that one of the testing methods used in Australia gives only a "presumptive positive" rather than a "definitive positive" result for H1N1 influenza and is only about 90 percent accurate. As a result, they stated that some Australians may have been given a false diagnosis.

Symptoms and expected severity

CDC's CAPT Dr. Joe Bresee describes symptoms.

The signs of infection with swine flu are similar to other forms of influenza, and include a fever, coughing, headaches, pain in the muscles or joints, sore throat, chills, fatigue and runny nose. Diarrhea and vomiting have also been reported in some cases. People at higher risk of serious complications included people age 65 years and older, children younger than 5 years old, pregnant women, and people of any age with underlying medical conditions, such as asthma, diabetes, obesity, heart disease, or a weakened immune system (e.g., taking immunosuppressive medications or infected with HIV).

Most cases mild

Evidence mounted through May 2009 that the symptoms were milder than health officials initially feared. As of May 27, 2009, most of the 342 confirmed cases in New York City had been mild and there had been only 4 confirmed deaths from the virus. Similarly, Japan had reported 279, mostly mild flu cases, and no deaths, with the government reopening schools as of May 23, stating that the "virus should be considered more like a seasonal flu." Furthermore, Australia has had upwards of 1500 cases with no deaths. In Mexico, where the outbreak began in April, Mexico City officials lowered their swine flu alert level as no new cases had been reported for a week.

Symptoms that may require medical attention

Certain symptoms may require emergency medical attention. In children, for instance, those might include blue lips and skin, dehydration, rapid breathing, excessive sleeping and significant irritability that includes a lack of desire to be held. In adults, shortness of breath, pain in the chest or abdomen, sudden dizziness or confusion may indicate the need for emergency care. In both children and adults, persistent vomiting or the return of flu-like symptoms that include a fever and cough may require medical attention.

Underlying conditions may worsen symptoms

WHO reported that almost one-half of the patients hospitalized in the United States had underlying conditions. "Among 30 patients hospitalized in California," stated the WHO report, "64 percent had underlying conditions and two of five pregnant women developed complications, including spontaneous abortion and premature rupture of membranes." And on June 5, health officials in six states that reported deaths from swine flu said that all six patients had been diagnosed with other health problems.

However, doctors in New York suggested that people with "underlying conditions" who had flu symptoms should consult their doctors first. "Visiting an emergency room full of sick people may actually put them in more danger," wrote the New York Times. Dr. Steven J. Davidson, the chairman of emergency medicine department at Maimonides Medical Center in Brooklyn commented "Like the asthmatics, we’d really prefer that pregnant women would stay away from the emergency departments." Approximately one-third of New Yorkers have one of the underlying conditions recognized by the city.

Prevention

Further information: [[:Influenza prevention and standard personal precautions against influenza]]

Containment and quarantine

Chinese inspectors on an airplane, checking passengers for fevers, a common symptom of swine flu

On April 28, 2009, WHO's Dr. Keiji Fukuda said that it was 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 therefore did not recommend closing borders or restricting travel, stating that "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." Many other countries confirmed that inbound international passengers would 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. A number of countries also advised against travel to known affected regions, while experts suggested 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.

Some countries began quarantining foreign visitors suspected of having or being in contact with others who may have been infected. In late May 2009, the Chinese government confined 21 U.S. students and three teachers to their hotel rooms because a passenger on their plane to China, suspected of having swine flu, had been seated within four rows of the students. In Hong Kong, an entire hotel was quarantined with 240 guests after one person staying there was found to have swine flu.

Other governments took or threatened similar actions: The government of Australia ordered a cruise ship with 2000 passengers to stay at sea because of a swine flu threat; Egyptians who went on the annual Muslim pilgrimage to Mecca risked being quarantined upon their return.

At the end of April 2009, when the outbreak began, Russia and Taiwan said they would quarantine visitors showing symptoms of the virus, and in Southern California, a marine confirmed to have swine flu was placed in quarantine along with about 30 other Marines. In early May, Japan quarantined 47 airline passengers in a hotel for a week after three travelers who arrived on the same plane from Canada tested positive for H1N1 swine flu, and Mongolia quarantined 109 Russian airline passengers in Ulaanbaatar.

On June 8, 2009 China reported that New Orleans Mayor Ray Nagin, his wife and a security guard, although symptom free, were being held in quarantine after flying on a plane carrying a passenger who exhibited symptoms. Nagin was traveling to China and Australia on an economic development trip. However, according to Fox News, "they don't even allow phone calls," reporting that the Chinese were also screening his calls "to keep him safe," and have refused even to pass on telephone messages without the permission of government health officials.

In India, after four airline passengers from London tested positive, the government ordered that all the 231 passengers of the flight should be administered the anti viral drug oseltamivir. Health authorities also asked that all the passengers not move out of their homes till further orders and quarantined at least one of the infected passengers. And in Egypt, a foreign students' dormitory for the American University in Cairo, with 140 students, was put under quarantine after two U.S. students were diagnosed with swine flu. According to the BBC, police wearing face masks "stood at barriers outside the elegant seven-floor AUC dormitory in Zamalek," and pizzas were delivered to the building during the day but none of the residents were allowed in or out.

Other governments have given health officials the "increased power" to order people into quarantine to control the spread of swine flu. The government of New Zealand, for instance, gave medical officers the power to order people to be quarantined at home if they have been in close contact with someone who has swine flu.

School closures

U.S.

The early days of the swine flu outbreak led to numerous school closures in a number of states. However, with signs that the virus was milder than initially feared, schools reopened and the closures stopped, although officials accept that the virus is continuing to spread nationwide.

In California, school administrators have noted that throughout the U.S. during the early weeks in the swine flu outbreak, counties recommended that schools close if a student was infected, but since early May, as the virus spread widely across the state and country, public health experts agreed that closing schools wasn't helping contain the disease. It's not yet known whether school closures will remain relatively rare or whether more will close before summer break begins, as many schools point out that closures could become more problematic, with finals and graduations coming up.

In New York City, more than 50 public schools were closed for short periods since early May, and as of June 5, 2009, with 780 confirmed cases in the state, the majority of cases have been mild. However, attendance dropped at other schools as worried parents kept their children home. As of early June, a few schools were still closed. Similarly, 858 Texas schools had also closed during the outbreak with most now reopened. And in Connecticut school officials are debating the value of keeping schools closed, with 480 confirmed cases and most of them mild. There, if more than 15 percent of the pupils had flu-like symptoms, the school would be advised to close.

Other countries

In Australia, a small number of schools have been closed with some to provide schoolwork via the websites, email and mail, however some school administrators have noted major inconveniences. One principal stated "We needed this like a hole in the head for our year 11 and 12 students - their exams start on June 15, 2009 and that's just six days away." Schools in New South Wales have also been known to forbid students to return to school for 7 days if they have visited urban Victoria. In the Philippines, college classes were postponed for a week. The Hong Kong government has announced that all nurseries, kindergartens and primary schools in Hong Kong would be closed for two weeks starting from 12 June, 2009, after 12 confirm cases in a secondary school on 11 June, 2009.

Spread in the workplace

The CDC advised sick people to stay home from work, school, or social gatherings and to generally limit contact with others to avoid infecting them. However, 48% of workers in the U.S. have no paid sick time, and sick adults attending work have been cited as a major weakness in the American response.

Hygiene

Airborne transmission

Little data is available on the risk of airborne transmission specific to this particular virus. Many authorities recommend the use of respirators by health-care workers in the vicinity of pandemic flu patients, particularly during aerosol generating procedures (e.g. intubation, chest physiotherapy, bronchoscopy). Masks may be of benefit in "crowded settings" or for people who are in "close contact" with infected persons, defined as 1 meter or less by the World Health Organization and 6 feet or less by the U.S. Occupational Safety and Health Administration. In these cases the CDC recommended respirators classified as N95, but it is unknown whether they would prevent swine flu infection. According to mask manufacturer 3M, there are no "established exposure limits for biological agents" such as swine flu virus.

Although Mexican authorities distributed surgical masks to the general public, the UK Health Protection Agency considered facial masks unnecessary for the general public. A Los Angeles official stated that masks may lead to a false sense of security, may be effective only for a limited time and may be contaminated if taken on and off. Masks were not generally provided by airport security or airlines. Although the CDC recommends the use of surgical masks in its guidelines, other U.S. officials stated in May that if the flu virus does in fact reach pandemic proportions, "there won't be enough face masks to go around."

Contact with infected surfaces

Infection can be caused by touching a surface contaminated with flu viruses and then touching the eyes, nose, or mouth. The CDC advised avoiding such contact and frequent washing of hands with soap and water or with alcohol-based hand sanitizers, especially after being out in public. Those coughing should use a tissue, dispose of the tissue, then wash hands right away. Transmission was also reduced by disinfecting household surfaces with a disinfectant or a diluted bleach solution.

No danger from pork consumption

The leading international health agencies stressed that the "influenza viruses are not known to be transmissible to people through eating processed pork or other food products derived from pigs."

Airline hygiene precautions

U.S. airlines have made no major changes as of the beginning of June, but continued standing practices that include looking for passengers with symptoms of flu, measles or other infections, and rely on in-flight air filters to ensure that aircraft are sanitized. "We take our guidance from the professionals (such as the CDC)", stated an Air Transport Association spokesman. The CDC has not recommended that airline crews wear face masks or disposable overcoats.

Outside the U.S. however, some airlines have modified hygiene procedures to minimize travel health risks on international flights. Asian carriers have stepped up cabin cleaning, installed state-of-the-art air filters and allowed in-flight staff to wear face masks, with some replacing used pillows, blankets, headset covers and headrest covers, while others have begun disinfecting the cabins of all aircraft. In China, some airline flight attendants are required to wear disposable facial masks, gloves and hats and even disposable overcoats during flights to select destinations.

Singapore has been thermal-screening everyone coming into the country, with Singapore Airlines giving passengers traveling to the United States health kits that include a thermometer, masks and antiseptic towels. Its cabin and flight crews are getting mandatory temperature checks before flights. The government recently quarantined a passenger who was later found to have the flu along with about 60 other people on the same flight who were sitting within three rows. A consultant for the microbiology division at National University Hospital in Singapore, said hygiene practices such as covering the nose and mouth when sneezing or coughing in confined areas may be the best way to limit infection and safety measures such as costly air filters may be of limited use for carriers.

Vaccination

Main article: 2009 A/H1N1 vaccine

Further information: [[:Influenza vaccine#2009-2010 season (Northern Hemisphere)|Influenza vaccine § 2009-2010 season (Northern Hemisphere)]]

Preparation of a vaccine against a new strain of flu is nothing new, but limitations on national production capacity, and the cost of production are all significant issues, and there are concerns that the virus might mutate or undergo reassortment that makes the new vaccine ineffective. However, John Sterling, Editor in Chief of Genetic Engineering & Biotechnology News, said on June 2, "It can take five or six months to come up with an entirely novel influenza vaccine. There is a great deal of hope that biotech and pharma companies might be able to have something ready sooner." As of June 4, 2009, Anne Schuchat, the Immunization Director of the CDC believed that little pandemic vaccine would be available by the fall, even if nothing goes wrong or delays production. The U.S. goal of pandemic plans is to make 600 million doses in six months, enough for two doses for each American, according to experts, with an estimated cost of $8 billion.

The seasonal flu vaccine is not believed to protect against the new strain, therefore any existing stock would not be useful. The CDC has considered an "earlier rollout of seasonal vaccine," which usually is made available in September in the United States, peaking in November. The new vaccine may be given in a second round of vaccinations rather than being added to the seasonal flu vaccine or replacing one of its three components with the new H1N1 virus.

Treatment

Further information: [[:Influenza treatment]]

Home treatment remedies

The Mayo Clinic suggested a number of measures to help ease symptoms, including adequate hydration and rest, soup to ease congestion, and over-the-counter drugs to relieve pain. The latter would relieve symptoms, but not treat the condition, and runs the risk of overdose or harm to children if used incorrectly. In general, most patients were expected to recover without requiring medical attention, with the exception of individuals with pre-existing or acquired complications.

Antiviral drugs

According to the CDC, antiviral drugs can be given to treat those who become severely ill. These antiviral drugs are prescription medicines (pills, liquid or an inhaler) and act against influenza viruses, including the 2009 pandemic virus. There are two such medications that are recommended for use against the 2009 H1N1 swine flu virus, oseltamivir (Tamiflu) and zanamivir (Relenza). A recent study published in the June Issue of Nature Biotechnology emphasized the urgent need for augmentation of oseltamivir (Tamiflu) stockpiles with additional antiviral drugs (including zanamivir (Relenza)) based on an evaluation of the performance of these drugs in the scenario that the 2009 H1N1 neuraminidase (NA) were to acquire the tamiflu-resistance (His274Tyr) mutation which is currently wide-spread in seasonal H1N1 strains. This finding was based on observations of NA-drug interactions that shed light on the polar glycerol C6 group in zanamivir (Relenza) being better suited than the corresponding hydrophobic pentyloxy group in oseltamivir (Tamiflu) to engage the active site hydrogen bond network in the His274Tyr mutant form of 2009 H1N1 NA. This study also underlined the need for prudent administration of antivirals in general, in order to reduce the probability of encountering tamiflu-resistant 2009 swine flu viruses.

The CDC has noted that as the flu pandemic spreads, antiviral drugs such as oseltamivir (Tamiflu) and zanamivir (Relenza) might become in short supply. Therefore, the drugs would be given first to those people who have been hospitalized or are at high risk of complications. The drugs work best if given within 2 days of becoming ill, but might be given later if illness became severe or to those at a high risk for complications.

In H3N2 strains, Tamiflu treatment has led to resistance in 0.4% of adult cases and 5.5% of children. Resistant strains usually are less transmissible. Nonetheless resistant human H1N1 viruses became widely established in previous flu seasons. Marie-Paule Kiely, WHO vaccine research director, said that it was "almost a given" that the new strain would undergo reassortment with resistant seasonal flu viruses and acquire resistance, but it was not yet known at what level resistance would appear. Simulations suggest that if physicians chose a second effective antiviral such as zanamivir (Relenza) as first-line treatment in even a few percent of cases, this could greatly delay the spread of resistant strains. Even a drug such as amantadine (Symmetrel) for which resistance frequently emerges may be useful in combination therapy, however it must be noted that adamantane-derivative drugs amantadine (Symmetrel) and rimantadine (Flumadine) are ineffective individually against the 2009 H1N1 strains owing to the presence of the prototypic Ser31Asn mutation on their M2 protein as determined by a recent study published in Nature Biotechnology. If the virus develops oseltamivir resistance, the "world’s Tamiflu stockpiles will be all but worthless," doctors would have to switch to the more expensive and harder to take, Relenza.

When buying these medications, some agencies warn against buying from online sources, with WHO estimating that half the drugs sold by online pharmacies without a physical address are counterfeit. Medical experts were also concerned that people "racing to grab up antiviral drugs just to feel safe" might eventually lead to the virus developing drug resistance. Partly as a result, experts suggested the medications should be reserved for only the very ill or people with severe immune deficiencies.

Emergency planning

See also: Influenza pandemic § Government preparations for a potential H5N1 pandemic (2003-2009)

Emergency preparedness experts suggest that organizations, such as corporations, should be making plans now in case something big and unexpected happens with the Swine Flu or other potential pandemic viruses. Kevin Nixon, an emergency planning expert who has testified before Congress and served on the Disaster Recovery Workgroup for the Office of Homeland Security, and the Federal Trade Commission, stresses that private companies "should be hammering out a game plan for who would do what and where if the government decided to restrict our movements to contain an outbreak." He states that "companies and employers that have not done so are being urged to establish a business continuity plan should the government direct state and local governments to immediately enforce their community containment plans."

Emergency planning would include some of the following: Asking people with symptoms, and members of an ill person's household, to voluntarily remain at home for up to 7 days; sending students home from school, including public and private schools as well as colleges and universities, and recommending out-of-school social distancing; and recommending social distancing of adults which could include cancelling public gatherings or changing workplace environments.

Crime risk

In early June, the Australian Crime Commission, in a written public report, warned that criminals may exploit a swine flu pandemic. They pointed out that illicit markets, robbery and fraud through false charities were all potential targets for organised crime, and the emergence of a black market for medicine was also a concern. "Criminal groups may also seek to infiltrate legitimate markets such as transport, finance and government sectors to help facilitate criminal activity and confuse the line between their illegal and legal activities," the report said. It warns of potential robbery and extortion, counterfeit medicine scams, black markets, charity fraud, welfare fraud and possibly increased community influence." Industrial drug sites might be targeted for robbery along with retail chemists.

See also

• 1918 flu pandemic
• 1976 swine flu outbreak
• 2009 swine flu outbreak by country
• GISAID - The Global Initiative on Sharing All Influenza Data
• Health care in Mexico
• Hong Kong Flu (1968–1969)
• Severe acute respiratory syndrome (SARS)

Further reading

• Soundararajan, Venkataramanan (2009). "Extrapolating from sequence — the 2009 H1N1 'swine' influenza virus" (PDF). Nature Biotechnology. 27 (6): 510–513. doi:10.1038/nbt0609-510. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)

• Smith, Gavin (2009). "Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic". Nature. Forthcoming. doi:10.1038/nature08182. {{cite journal}}: Cite has empty unknown parameter: |month= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

External links

• Influenza: H1N1 at Curlie
• Swine flu: Bihar gears up to meet possible threat
• Official swine flu advice and latest information from the UK National Health Service
• Swine influenza, at the World Health Organization
• Pan-American Health Organization (PAHO) Swine Influenza portal
• H1N1 Influenza (Flu) portal at the U.S. Centers for Disease Control (CDC)
• Influenza A(H1N1) at the European Centre for Disease Prevention and Control (ECDC)
• International Society for Infectious Diseases PROMED-mail news updates
• U.S. Government swine, avian and pandemic flu portal
• Medical Encyclopedia Medline Plus: Swine Flu
• Swine Flu Outbreak, Influenza Virus Resource Sequences and related resources (GenBank, NCBI)
• BioHealthBase Bioinformatics Resource Center Database of influenza genomic sequences and related information.
• Human/Swine A/H1N1 Influenza Origins and Evolution Analysis of genetic data for the origin and evolution of swine flu virus.
• Swine flu charts and maps Numeric analysis and approximation of current active cases