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This presentation is made available through a Creative Commons Attribution- Noncommercial license. Details of the license and permitted uses are available at © 2010 Dr. Juliet Pulliam and the Clinic on the Meaningful Modeling of Epidemiological Data Title: Introduction to Infectious Disease Data Attribution: Dr. Juliet Pulliam, Clinic on the Meaningful Modeling of Epidemiological Data Source URL: For further information please contact Dr. Juliet Pulliam

Introduction to infectious disease data Clinic on the Meaningful Modeling of Biological Data and BSc Honours Course in Biomathematics African Institute for the Mathematical Sciences Muizenberg, South Africa 26 May 2010 Dr. Juliet Pulliam RAPIDD Program, DIEPS Fogarty International Center, NIH, USA and Department of Ecology & Evolutionary Biology University of California at Los Angeles (UCLA)

What is an infectious disease?

Disease A deviation from the normal physiological status of an organism that negatively affects its survival or reproduction

Disease A deviation from the normal physiological status of an organism that negatively affects its survival or reproduction Infectious Disease A disease in one organism (the host) that is caused by another organism (pathogen or parasite) which has entered the host’s body

Case definition “a set of standard criteria for deciding whether a person has a particular disease [or infection]”

Case definition “a set of standard criteria for deciding whether a person has a particular disease [or infection]” Person: Place: Time: Clinical description:

A “case” study

Case definition “a set of standard criteria for deciding whether a person has a particular disease [or infection]” Person: Residents of Mexico, recent visitors to Mexico Place: North America (Mexico, US, Canada) Time: On or after March 15, 2009 Clinical description: severe influenza-like illness (fever, cough, sore throat, body aches, headache, chills, fatigue, and/or severe respiratory distress)

Sunday, 26 April

Confirmed case: signs and symptoms plus laboratory confirmation Probable case: signs and symptoms in an individual meeting person, place, and time criteria plus contact with a known case or more specific clinical signs Possible case: signs and symptoms in an individual meeting person, place, and time criteria plus a physician diagnosis Suspect case: signs and symptoms in an individual meeting person, place, and time criteria Not a case: failure to fulfill the criteria for a confirmed, probable, possible, or suspect case

Sunday, 26 April

Monday, 27 April

Tuesday, 28 April

Wednesday, 29 April

Thursday, 30 April

Friday, 1 May

Saturday, 2 May

Sunday, 3 May

Monday, 4 May

Tuesday, 5 May (?) X

? ? Monday, 4 May

Case definition “a set of standard criteria for deciding whether a person has a particular disease [or infection]” Person: Place: Time: Clinical description:

Case definition Person: Residents of and recent visitors to North America, and their close contacts or others in their community Place: Worldwide Time: On or after March 15, 2009 Clinical description: fever, cough, sore throat, body aches, headache, chills, fatigue, and/or severe respiratory distress; diarrhea and vomiting do not rule out diagnosis

Incidence of disease Date of onset

Mathematical expression? Incidence of infection

Ways of collecting data on cases Surveillance Hampson et al Surveillance + Contact Tracing/Outbreak investigation

Ways of collecting data on cases Epidemiological studies

Prevalence of infection of disease of antibodies (seroprevalence) Mathematical expression? Source: UNAIDS HIV Surveillance Database

Seroprevalence Can be related to: Prevalence of infection Past exposure May or may not be: Prevalence of resistance Specific to infection of interest

Seroprevalence Can be related to: Prevalence of infection Past exposure May or may not be: Prevalence of resistance Specific to infection Pulliam et al. (In review)

Seroconversion Mathematical expression?

Levels of data aggregation Aggregated data De-identified data Personally identifying data

Sources Slides 8 and 10-22: Images are reproduced from The New York Times (online edition), April Slide 25: Data are available from The Centers for Disease Control and Prevention, Atlanta, GA, USA. - Image available at: Slide 27: Hampson et al. (2009) Transmission dynamics and prospects for the elimination of canine rabies. PLoS Biology 7(3): e doi: /journal.pbio Slide 29: Data from UNAIDS HIV Surveillance Database, provided courtesy of USAID. Slide 31: Pulliam et al. (In review) Agricultural intensification, priming for persistence, and the emergence of Nipah virus, a lethal bat-borne zoonosis.