The Severity of Pandemic H1N1 Influenza in the United States, from April to July 2009: A Bayesian Analysis
Publication Date
December 08, 2009
Journal
PLOS Medicine
Authors
Anne M. Presanis, Daniela De Angelis, The New York City Swine Flu Investigation Team 3 ¶, Angela Hagy, et al
Volume
6
Issue
12
Pages
e1000207
DOI
https://dx.plos.org/10.1371/journal.pmed.1000207
Publisher URL
http://journals.plos.org/plosmedicine/article?id=10.1371%2Fjournal.pmed.1000207
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19997612
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784967
Europe PMC
http://europepmc.org/abstract/MED/19997612
Web of Science
000273060600018
Scopus
74049092311
Mendeley
http://www.mendeley.com/research/severity-pandemic-h1n1-influenza-united-states-april-july-2009-bayesian-analysis
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"scopus_author_id"=>"26633361600"}, {"first_name"=>"Donald", "last_name"=>"Walker", "scopus_author_id"=>"55468079000"}, {"first_name"=>"Connie", "last_name"=>"Warner", "scopus_author_id"=>"7102594756"}, {"first_name"=>"Isaac", "last_name"=>"Weisfuse", "scopus_author_id"=>"6701495309"}, {"first_name"=>"Don", "last_name"=>"Weiss", "scopus_author_id"=>"15133713500"}, {"first_name"=>"Antoinette", "last_name"=>"Williams-Akita", "scopus_author_id"=>"6506046754"}, {"first_name"=>"Elisha", "last_name"=>"Wilson", "scopus_author_id"=>"35390136800"}, {"first_name"=>"Eliza", "last_name"=>"Wilson", "scopus_author_id"=>"57190006685"}, {"first_name"=>"Marie", "last_name"=>"Wong", "scopus_author_id"=>"55458938600"}, {"first_name"=>"Charles", "last_name"=>"Wu", "scopus_author_id"=>"35390304400"}, {"first_name"=>"David", "last_name"=>"Yang", "scopus_author_id"=>"35390498800"}, {"first_name"=>"Mohammad", "last_name"=>"Younis", "scopus_author_id"=>"35390434900"}, {"first_name"=>"Sulaimon", "last_name"=>"Yusuff", "scopus_author_id"=>"35390460300"}, {"first_name"=>"Christopher", "last_name"=>"Zimmerman", "scopus_author_id"=>"7103371821"}, {"first_name"=>"Jane", "last_name"=>"Zucker", "scopus_author_id"=>"16237791900"}], "year"=>2009, "source"=>"PLoS Medicine", "identifiers"=>{"pui"=>"358104138", "doi"=>"10.1371/journal.pmed.1000207", "isbn"=>"1549-1676", "pmid"=>"19997612", "issn"=>"15491277", "scopus"=>"2-s2.0-74049092311", "sgr"=>"74049092311"}, "id"=>"cc55e46f-2f2b-3613-ad8e-2f915b056e3d", "abstract"=>"BACKGROUND: Accurate measures of the severity of pandemic (H1N1) 2009 influenza (pH1N1) are needed to assess the likely impact of an anticipated resurgence in the autumn in the Northern Hemisphere. Severity has been difficult to measure because jurisdictions with large numbers of deaths and other severe outcomes have had too many cases to assess the total number with confidence. Also, detection of severe cases may be more likely, resulting in overestimation of the severity of an average case. We sought to estimate the probabilities that symptomatic infection would lead to hospitalization, ICU admission, and death by combining data from multiple sources.\\n\\nMETHODS AND FINDINGS: We used complementary data from two US cities: Milwaukee attempted to identify cases of medically attended infection whether or not they required hospitalization, while New York City focused on the identification of hospitalizations, intensive care admission or mechanical ventilation (hereafter, ICU), and deaths. New York data were used to estimate numerators for ICU and death, and two sources of data--medically attended cases in Milwaukee or self-reported influenza-like illness (ILI) in New York--were used to estimate ratios of symptomatic cases to hospitalizations. Combining these data with estimates of the fraction detected for each level of severity, we estimated the proportion of symptomatic patients who died (symptomatic case-fatality ratio, sCFR), required ICU (sCIR), and required hospitalization (sCHR), overall and by age category. Evidence, prior information, and associated uncertainty were analyzed in a Bayesian evidence synthesis framework. Using medically attended cases and estimates of the proportion of symptomatic cases medically attended, we estimated an sCFR of 0.048% (95% credible interval [CI] 0.026%-0.096%), sCIR of 0.239% (0.134%-0.458%), and sCHR of 1.44% (0.83%-2.64%). Using self-reported ILI, we obtained estimates approximately 7-9 x lower. sCFR and sCIR appear to be highest in persons aged 18 y and older, and lowest in children aged 5-17 y. sCHR appears to be lowest in persons aged 5-17; our data were too sparse to allow us to determine the group in which it was the highest.\\n\\nCONCLUSIONS: These estimates suggest that an autumn-winter pandemic wave of pH1N1 with comparable severity per case could lead to a number of deaths in the range from considerably below that associated with seasonal influenza to slightly higher, but with the greatest impact in children aged 0-4 and adults 18-64. These estimates of impact depend on assumptions about total incidence of infection and would be larger if incidence of symptomatic infection were higher or shifted toward adults, if viral virulence increased, or if suboptimal treatment resulted from stress on the health care system; numbers would decrease if the total proportion of the population symptomatically infected were lower than assumed.", "link"=>"http://www.mendeley.com/research/severity-pandemic-h1n1-influenza-united-states-april-july-2009-bayesian-analysis", "reader_count"=>103, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>9, "Librarian"=>3, "Student > Doctoral Student"=>5, "Researcher"=>29, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>12}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>9, "Librarian"=>3, "Student > Doctoral Student"=>5, "Researcher"=>29, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>12}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Environmental Science"=>1, "Nursing and Health Professions"=>1, "Mathematics"=>13, "Agricultural and Biological Sciences"=>26, "Medicine and Dentistry"=>38, "Veterinary Science and Veterinary Medicine"=>2, "Physics and Astronomy"=>2, "Psychology"=>1, "Social Sciences"=>2, "Computer Science"=>2, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>38}, "Social Sciences"=>{"Social Sciences"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Mathematics"=>{"Mathematics"=>13}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Vietnam"=>1, "Hong Kong"=>1, "United States"=>4, "China"=>1, "Brazil"=>1, "United Kingdom"=>4, "Italy"=>1, "Israel"=>1, "Australia"=>1, "France"=>1, "Kenya"=>1, "Spain"=>1}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/872847"], "description"=>"<p>Cases at each level of severity.</p>", "links"=>[], "tags"=>["infectious diseases/viral infections", "public health and epidemiology/infectious diseases"], "article_id"=>543302, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cases_at_each_level_of_severity_/543302", "title"=>"Cases at each level of severity.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-12-08 00:55:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/872654"], "description"=>"<p>Approach 1 used three datasets to estimate successive steps of the severity pyramid. Approach 2 used self-reported ILI for the denominator, and confirmed deaths for the numerator, both from New York City. Both approaches used prior distributions, in some cases informed by additional data, to inform the probability of detecting (confirming and reporting) cases at each level of severity (not shown in the diagram; see <a href=\"http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1000207#pmed.1000207.s001\" target=\"_blank\">Text S1</a>). The Bayesian evidence synthesis framework was used as a formal way to combine information and uncertainty about each level of severity into a single estimate and associated uncertainty that reflected all of the uncertainty in the inputs.</p>", "links"=>[], "tags"=>["approaches", "estimating"], "article_id"=>543110, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagram_of_two_approaches_to_estimating_the_sCFR_/543110", "title"=>"Diagram of two approaches to estimating the sCFR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-12-08 00:51:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/872810"], "description"=>"<p>Posterior median (95% CI) estimates of the sCFR, sCIR, and sCHR, by age group, using self-reported ILI as the denominator of symptomatic cases.</p>", "links"=>[], "tags"=>["median", "estimates", "self-reported", "ili", "denominator", "symptomatic"], "article_id"=>543255, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.t004", "stats"=>{"downloads"=>8, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Posterior_median_95_CI_estimates_of_the_sCFR_sCIR_and_sCHR_by_age_group_using_self_reported_ILI_as_the_denominator_of_symptomatic_cases_/543255", "title"=>"Posterior median (95% CI) estimates of the sCFR, sCIR, and sCHR, by age group, using self-reported ILI as the denominator of symptomatic cases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-12-08 00:54:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/872738"], "description"=>"<p>The key quantities of interest, sCHR, sCIR, and sCFR, are products of the relevant conditional probabilities. (A) Approach 1, synthesizing data from New York City and Milwaukee. Note that <i>c<sub>M</sub></i><sub>|<i>S</i></sub> (double circle) is informed by prior information <a href=\"http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1000207#pmed.1000207-Reed1\" target=\"_blank\">[19]</a> rather than observed data. (B) Approach 2, using data from New York City only, including the telephone survey. Variables: <i>c<sub>D</sub></i><sub>|<i>M</i></sub>: the ratio of non-hospitalized deaths to medically-attended cases; <i>c<sub>D</sub></i><sub>|<i>H</i></sub>: the ratio of deaths to hospitalized cases; <i>c<sub>I</sub></i><sub>|<i>H</i></sub>: the ratio of cases admitted to intensive care or using mechanical ventilation to hospitalized cases; <i>c<sub>H</sub></i><sub>|<i>M</i></sub>: the ratio of hospitalized cases to medically attended cases; <i>c<sub>M</sub></i><sub>|<i>S</i></sub>: the ratio of medically attended cases to symptomatic cases; <i>c<sub>D</sub></i><sub>|<i>S</i></sub>: the ratio of deaths to symptomatic cases; <i>c<sub>H</sub></i><sub>|<i>S</i></sub>: the ratio of hospitalized cases to symptomatic cases.</p>", "links"=>[], "tags"=>["observed", "conditional", "probabilities"], "article_id"=>543193, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_illustration_of_the_relationship_between_the_observed_data_rectangles_and_the_conditional_probabilities_blue_circles_/543193", "title"=>"Schematic illustration of the relationship between the observed data (rectangles) and the conditional probabilities (blue circles).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-12-08 00:53:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/432933"], "description"=>"<div><h3>Background</h3><p>Accurate measures of the severity of pandemic (H1N1) 2009 influenza (pH1N1) are needed to assess the likely impact of an anticipated resurgence in the autumn in the Northern Hemisphere. Severity has been difficult to measure because jurisdictions with large numbers of deaths and other severe outcomes have had too many cases to assess the total number with confidence. Also, detection of severe cases may be more likely, resulting in overestimation of the severity of an average case. We sought to estimate the probabilities that symptomatic infection would lead to hospitalization, ICU admission, and death by combining data from multiple sources.</p><h3>Methods and Findings</h3><p>We used complementary data from two US cities: Milwaukee attempted to identify cases of medically attended infection whether or not they required hospitalization, while New York City focused on the identification of hospitalizations, intensive care admission or mechanical ventilation (hereafter, ICU), and deaths. New York data were used to estimate numerators for ICU and death, and two sources of data—medically attended cases in Milwaukee or self-reported influenza-like illness (ILI) in New York—were used to estimate ratios of symptomatic cases to hospitalizations. Combining these data with estimates of the fraction detected for each level of severity, we estimated the proportion of symptomatic patients who died (symptomatic case-fatality ratio, sCFR), required ICU (sCIR), and required hospitalization (sCHR), overall and by age category. Evidence, prior information, and associated uncertainty were analyzed in a Bayesian evidence synthesis framework. Using medically attended cases and estimates of the proportion of symptomatic cases medically attended, we estimated an sCFR of 0.048% (95% credible interval [CI] 0.026%–0.096%), sCIR of 0.239% (0.134%–0.458%), and sCHR of 1.44% (0.83%–2.64%). Using self-reported ILI, we obtained estimates approximately 7–9× lower. sCFR and sCIR appear to be highest in persons aged 18 y and older, and lowest in children aged 5–17 y. sCHR appears to be lowest in persons aged 5–17; our data were too sparse to allow us to determine the group in which it was the highest.</p><h3>Conclusions</h3><p>These estimates suggest that an autumn–winter pandemic wave of pH1N1 with comparable severity per case could lead to a number of deaths in the range from considerably below that associated with seasonal influenza to slightly higher, but with the greatest impact in children aged 0–4 and adults 18–64. These estimates of impact depend on assumptions about total incidence of infection and would be larger if incidence of symptomatic infection were higher or shifted toward adults, if viral virulence increased, or if suboptimal treatment resulted from stress on the health care system; numbers would decrease if the total proportion of the population symptomatically infected were lower than assumed.</p><h3></h3><p><em>Please see later in the article for the Editors' Summary</em></p></div>", "links"=>[], "tags"=>["severity", "pandemic", "h1n1", "influenza", "united", "april", "july", "bayesian"], "article_id"=>145419, "categories"=>["Cancer", "Biological Sciences"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Severity_of_Pandemic_H1N1_Influenza_in_the_United_States_from_April_to_July_2009_A_Bayesian_Analysis/145419", "title"=>"The Severity of Pandemic H1N1 Influenza in the United States, from April to July 2009: A Bayesian Analysis", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-12-08 01:30:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/872889"], "description"=>"<p>Posterior median (95% CI) estimates of the sCFR, sCIR, and sCHR, by age group, based on a combination of data from New York City and Milwaukee, and survey data on the frequency of medical attendance for symptomatic cases.</p>", "links"=>[], "tags"=>["median", "estimates", "york", "symptomatic"], "article_id"=>543341, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.t003", "stats"=>{"downloads"=>10, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Posterior_median_95_CI_estimates_of_the_sCFR_sCIR_and_sCHR_by_age_group_based_on_a_combination_of_data_from_New_York_City_and_Milwaukee_and_survey_data_on_the_frequency_of_medical_attendance_for_symptomatic_cases_/543341", "title"=>"Posterior median (95% CI) estimates of the sCFR, sCIR, and sCHR, by age group, based on a combination of data from New York City and Milwaukee, and survey data on the frequency of medical attendance for symptomatic cases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-12-08 00:55:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/872929"], "description"=>"<p>Detection probabilities and their prior distributions.</p>", "links"=>[], "tags"=>["probabilities"], "article_id"=>543382, "categories"=>["Infectious Diseases", "Computational Biology"], "users"=>["Anne M. Presanis", "Daniela De Angelis", "Angela Hagy", "Carrie Reed", "Steven Riley", "Ben S. Cooper", "Lyn Finelli", "Paul Biedrzycki", "Marc Lipsitch"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1000207.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_probabilities_and_their_prior_distributions_/543382", "title"=>"Detection probabilities and their prior distributions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-12-08 00:56:22"}

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Relative Metric

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