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Homeland Security


I. Introduction and Charge


In April 2009, a novel influenza A/H1N1 virus (2009-H1N1) appeared in Mexico, causing pneumonias and 59 deaths in Mexico City alone. The virus soon spread to the United States and to other continents. Within two months, the World Health Organization (WHO) declared that the viral outbreak met the criteria of a level 6 pandemic. As of August 2009, the virus continues to spread in the United States and elsewhere.

Although initial concerns of an extremely high fatality rate have receded, the expected resurgence of 2009-H1N1 in the fall poses a serious health threat to the United States. Further, although most cases are mild, serious complications arise in some individuals, especially those with underlying medical complica­ tions such as pregnant women and those with neurological conditions. Under some models, seriously ill influenza patients could require 50 to 100 percent of intensive care unit (ICU) beds at the epidemic’s peak, stressing the medical and public health systems to the point of overwhelming some hospitals, and could cause from 30,000 to 90,000 deaths, concentrated among children and young adults.

Since the initial report of the outbreak, the Federal Government, through various departments, agen­cies and offices, has been actively studying the course of events, responding to them, and planning for a resurgence of the pandemic this fall.

Under the aegis of the President’s Council of Advisors on Science and Technology (PCAST), a Working Group on 2009-H1N1 influenza was formed in response to the President’s request for an expert external review of the epidemic and the nation’s response to an anticipated resurgence in the fall of 2009 . Overall, the Working Group was deeply impressed by the efforts underway across the Federal Government—including the breadth of issues being anticipated and addressed, the depth of thinking, the overall level of energy being devoted, and the awareness of potential pitfalls.

The Working Group did identify some potential ways to strengthen the response, and it has provided recommendations. In many cases, the relevant agencies are already aware of these opportunities and are taking steps in these directions. The Working Group’s recommendations are intended to provide support for and additional focus to such efforts.

On April 15, 2009, the first case of infection with novel influenza A (H1N1) virus (“swine flu,” hereafter “2009-H1N1”) was confirmed in the United States. In March and April, Mexico had experienced an outbreak of unexplained pneumonia, with hundreds of reported cases and 59 deaths in Mexico City alone. It soon became clear that 2009-H1N1 was associated with the Mexican pneumonia outbreak and that the virus was spreading within North America; it was soon detected in many other countries. On April 29, the World Health Organization (WHO) raised its influenza pandemic alert level to Phase 5, just short of declaring that a global influenza pandemic was underway. In those early days of the outbreak, severe cases were the most readily counted because they were usually hospitalized. As of April 29, 8 of 148 individuals with confirmed 2009-H1N1 infection worldwide had died (5.4 percent), initially raising

the possibility that the virus was extremely virulent, comparable to or even worse than the viral strain that caused the 1918-19 influenza pandemic. But uncertainty about the number of unconfirmed cases— especially infected individuals with mild or no symptoms—made it impossible to assess severity accu­ rately. In fact, subsequent data revealed that the case-fatality ratio was actually much lower—although still a cause for serious public concern.

As more cases were confirmed around the United States in late April and early May, the Centers for Disease Control and Prevention (CDC), in coordination with state and local public health departments, increased surveillance efforts and issued interim guidance to control the virus’s spread. Intensified sur­ veillance rapidly clarified that many mild cases had been missed in the early phases of the epidemic, easing concerns that the new virus was extremely virulent, but still leaving uncertain the overall spec­trum of illness and incidence. Media coverage was intense. Advisories warned against travel to Mexico and soon against travel to the United States. In regions of the United States with reported cases, some schools were closed just days or weeks short of the end of the school year. By June 11, the virus had spread to 74 countries and all continents but Antarctica, and WHO declared the outbreak an influenza pandemic (Phase 6) on the basis of its geographic spread. As summer began and schools adjourned, travel advisories were rescinded and media and public attention waned.

Although influenza usually becomes almost undetectable during the summer, transmission of 2009- H1N1 virus continues in the United States (albeit at a lower level) and in other Northern Hemisphere countries, notably the United Kingdom. While monitoring of clinical outcomes to date suggests that most 2009-H1N1 infections are mild, there have been notable reports of people with severe illnesses, many of them requiring intensive hospital care, and deaths, predominantly among relatively young people. Certain groups—such as the First Nation people in rural Manitoba, Canada—appear to have been particularly hard hit. And even mild outbreaks have in many cases been socially disruptive.

The Southern Hemisphere’s regular influenza season is now underway, and 2009-H1N1 has spread rapidly within Argentina, Australia, Chile, and New Zealand, appearing to eclipse infection with the expected seasonal influenza virus and stressing the medical and public health systems to the point of overwhelming some hospitals and filling some intensive care units (ICUs) to capacity. For example, in Australia, 11 percent of over 20,000 confirmed cases of 2009-H1N1 influenza have been hospitalized. And of the 410 cases now hospitalized, 110 are in ICUs.

As the influenza season in the Northern Hemisphere approaches and schools reopen, the pandemic is expected to accelerate, with the potential for significant health consequences in the United States, Europe, and other regions. Based on past pandemics, this acceleration is likely to occur before the normal (i.e., seasonal) influenza season, starting in September and peaking in October. In a typical (non-pan­ demic) season, influenza becomes prevalent in winter and causes an estimated 30,000 to 40,000 deaths in the United States, with about 90 percent of those deaths occurring in patients ages 65 years or older.

A plausible scenario, given current data (and described in more detail in Chapter 3), is that 2009-H1N1 influenza could place enormous stress on U.S. medical and public health systems, as well as on an American economy already under stress. It could cause anywhere from 30,000 to 90,000 deaths in the United States in fall 2009, mainly among younger adults and children (unlike the situation with seasonal influenza, which causes death mainly in the elderly) and those with certain pre-existing conditions.

Moreover, as much as 50 to 100 percent of ICU capacity in the United States could be required solely to treat 2009-H1N1 patients at the peak caseload, in hospital units that typically run at 80 percent of capacity. Such stress on ICUs and emergency departments would cause severe disruption of hospital function, necessitating marked curtailment of all but the most urgent admissions and surgeries.

These estimates assume that the clinical severity of infection with the 2009-H1N1 virus will be the same this fall as it was in the spring. Even so, the estimates of serious disease and death could be off by several-fold because the total number of infected persons to date—and proportion of severe infec­ tions—remain extremely uncertain. In addition, there is a possibility, difficult to quantify, that severity could change, either up or down, as the virus evolves (see Box 1A). Various public health measures can be taken to attempt to mitigate the pandemic. It is clear, however, that many of the decisions about whether and when to employ these mitigation measures will have to be made rapidly, before many uncertainties are resolved.

Since the outbreak began in late April 2009, the Federal Government—through various departments, agencies, and offices, especially the Department of Health and Human Services (DHHS), the Department of Homeland Security (DHS), and components of the White House staff—has been actively studying the course of events, responding to them, and planning for a resurgence of the pandemic this fall. As a consequence of concerns since 2004 about the possibility of a pandemic involving the highly patho­ genic avian (H5N1) influenza virus, the United States has been especially well positioned to organize a response to the 2009-H1N1 pandemic. Preparedness activities have included:

  • releasing antiviral drugs from the national stockpile;
  • contracting with several pharmaceutical companies to develop and manufacture vaccines against 2009-H1N1 as quickly as possible;
  • removing restrictions on the use of unapproved medical treatments and tests under public health emergency conditions;
  • increasing surveillance at multiple levels (e.g., virus identification and characterization; data on outpatients, hospitalized patients, and mortality);
  • convening a summit of states, tribes, and territories to plan responses to the epidemic;
  • overseeing congressional passage of an emergency funding measure (described in greater detail below) for a variety of uses, including purchase of vaccines and drugs, support of non-Federal public health initiatives, and additional needs at CDC and the Food and Drug Administration (FDA);
  • providing funds to state and local public health offices and health care systems to step up their preparedness efforts;
  • undertaking public communication efforts; and
  • issuing guidance for the general public, clinicians, laboratories, pregnant women, schools, and communities.


In the few months since its first isolation, the 2009-H1N1 influenza virus has been quickly subjected to intense study of its molecular properties, illustrating the capacities of modern virology and genetics.

Like other influenza viruses, the genes of the 2009-H1N1 virus are arrayed on eight segments of single-stranded RNA that, in the aggregate, constitute the viral genome. Genomes of these viruses are inherently unstable, with frequent changes in each RNA segment accounting for genetic “drift,” and reassortment of segments when cells are co-infected with two or more viruses, accounting for more dramatic genetic “shift.” The 2009-H1N1 virus is a “triple reassortant,” as it contains RNA segments from avian-, human-, and swine-origin viruses. The majority of RNA segments, including the segment cod­ ing for the hemagglutinin protein, come from swine-origin viruses. Hemagglutinin mediates immune protection against influenza viruses, is notable for rapid changes in its composition, and forms the basis for the annual reformulation of influenza virus vaccines. It is also one of the two major proteins on the viral surface, hemagglutinin (H) and the neuraminidase (N), that determine the subtype classification of type A influenza viruses as ‘H1N1,’ ‘H3N2,’ etc.

Of all of the H1 subtype hemagglutinins in viruses isolated from humans in the 20th and 21st centuries, the hemagglutinin of the 2009-H1N1 appears to be genetically most similar to those of the 1918-19 H1N1 pandemic virus and of the H1N1 virus of swine-origin that caused the limited human outbreak at an army base in New Jersey in 1976. It is less closely related to the hemagglutin in other strains of H1N1 virus responsible for seasonal influenza in recent years.

The relatively low virulence of 2009-H1N1 virus may be attributed, in part, to the absence of a major determinant of virus virulence—the expression of a protein called PB1-F2 that is known to cause cell death and was found in viruses responsible for the major influenza pandemics of 1918-19 (H1N1), 1957 (H2N2), and 1968 (H3N2).

The 2009-H1N1 virus is atypical in some ways, including its transmissibility during warm seasons and its apparent infection of the gastrointestinal tract in approximately one-third of serious cases. These and other properties of the new virus will be subject to more intensive study and comparisons with earlier isolates in the near future in order to understand its mode of pathogenesis, virulence, transmission rate, and immunogenic properties.

On June 24, 2009, President Obama signed into law the Supplemental Appropriations Act, 2009 (Public Law 111-32). Within the Act, Congress appropriated $7.65 billion to DHHS to prepare for the 2009-H1N1 influenza outbreak, including a $5.8 billion contingent appropriation. After spending an initial $1.85 billion on procurement of vaccines, expansion of surveillance activities, and preparation for a possible immunization campaign, on July 16 the President designated an additional $1.825 billion as emergency funds to support additional measures related to influenza vaccination efforts, leaving $3.975 billion in reserve as contingency funds.

In early July, President Obama asked his Council of Advisors on Science and Technology (PCAST) to provide an expert external assessment of the epidemic and to offer guidance about the nation’s plans to respond to its likely resurgence in the fall. PCAST established a Working Group on 2009-H1N1, co- chaired by Drs. Harold Varmus and Eric Lander, consisting of experts in the fields of virology, public health, and medicine, with experience in the academic, governmental, philanthropic, and industrial sectors.

PCAST’s charge was several-fold:

  • to identify critical questions for which timely answers are needed by decision-makers;
  • to survey and assess preparations currently underway in the Federal Government;
  • to highlight major challenges and gaps; and
  • to make specific recommendations concerning additional opportunities to help mitigate a serious 2009-H1N1 flu pandemic this fall.

The Working Group worked on an accelerated schedule during the month of July 2009 to respond to its charge. It met July 16–17, 2009, in Washington, D.C., to hear presentations from Federal agency leaders, epidemiologists, state and international public health officials, vaccine and drug developers, and experts in social mitigation strategies, including public information and marketing. In addition, interviews were conducted at other times with government officials and experts on various aspects of the influenza epidemic.

The Working Group’s goal was not to predict the severity of any next wave of the epidemic or to pre scribe specific responses. Instead, the goal was to provide guidance to support and strengthen the many efforts already underway to prepare the country for the expected resurgence of 2009-H1N1 in the fall.


Overall, the Working Group was deeply impressed by the efforts underway across the Federal Government—including the breadth of issues being anticipated and addressed, the depth of think­ing, the overall level of energy being devoted, and the awareness of potential pitfalls. The response is probably the best effort ever mounted against a pandemic, reflecting both past preparedness efforts and the quality and commitment of the people involved.

The Working Group did identify some potential ways to strengthen the response. In many cases, the relevant agencies are already aware of these opportunities and are taking steps to address them, while recognizing that time is short and that some goals may not be achievable. The Working Group’s recommendations are intended to provide support for and additional focus to such efforts

To present its observations in a logical narrative, this report is organized in chapters focused on the Nation’s prior experience with influenza; scenario planning; surveillance of the current epidemic; decision-making about measures to mitigate the epidemic; lowering legal and economic barriers to response; communications; and steps to strengthen the response to future epidemics. In addition to providing specific guidance to relevant agencies, the report aims to provide sufficient background to be readable by members of the general public, who are understandably concerned about the current outbreak and the Nation’s response.

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