1. This presentation is made available through a Creative Commons Attribution- Noncommercial license. Details of the license and permitted uses are available at http://creativecommons.org/licenses/by-nc/3.0/ © 2010 Dr. Juliet Pulliam http://creativecommons.org/licenses/by-nc/3.0/ Title: Introduction to Infectious Disease Dynamics, Part I Attribution: Dr. Juliet Pulliam, Topics in Biomedical Sciences Source URL: http://lalashan.mcmaster.ca/theobio/mmed/index.php/Honours Coursehttp://lalashan.mcmaster.ca/theobio/mmed/index.php/Honours Course For further information please contact Dr. Juliet Pulliam (juliet.mmed.clinic@gmail.com).

2. Introduction to infectious disease dynamics I Introduction to Biomedical Sciences BSc Honours Course in Biomathematics African Institute for the Mathematical Sciences Muizenberg, South Africa 17 May 2010 Dr. Juliet Pulliam RAPIDD Program Division of International Epidemiology Fogarty International Center National Institutes of Health (USA)

3. Terminology Infectious diseases Exposure - potentially infectious contact between a parasitic organism and a potential host Exposed

4. Terminology Infectious diseases Infection - a parasitic organism enters a host Exposed Infected

5. Terminology Infectious diseases Transmission - a parasitic organism replicates within an infected host, and the infected host sheds infectious individuals (the host is said to be “infectious” or “transmitting”) Exposed Infected Infectious

6. Terminology Infectious diseases Pathogenesis - a parasitic organism causes changes in the physiology of an infected host, affecting survival and/or reproduction (the host is said to be “diseased”) Exposed Infected InfectiousDiseased

7. Terminology Infectious diseases Infectious disease dynamics are determined -- to a large extent -- by the duration of these states, as well as the degree and timing of overlap Exposed Infected InfectiousDiseased

8. Terminology Infectious diseases Exposed Infected InfectiousDiseased InfectionOnset of symptoms Onset of shedding

9. Terminology Infectious diseases InfectionOnset of symptoms Onset of shedding Incubation periodClinical disease Infectious periodLatent period

10. Terminology Infectious diseases InfectionOnset of symptoms Onset of shedding Infection Onset of symptoms Onset of shedding Serial interval

11. Transmission Infectious diseases Mode of transmission Direct transmission Direct contact Droplet spread Indirect transmission Airborne Vehicle-borne (fomites) Vector-borne (mechanical or biological) Portal of entry Portal of exit

12. Immunity Infectious diseases Active immunity Requires stimulation of antibody production Response to many infections Induced by most vaccines Long-lasting Passive immunity Presence of antibodies without stimulating production Maternal antibodies Immunoglobulin injections Transient

13. Infectious disease dynamics Traditional epidemiology Outbreak investigation Disease surveillance On-the-ground management Mathematical epidemiology General principles Explanation of patterns Prediction of spread and control Assessment of necessary data

14. Terminology Shoe-leather epidemiology Endemic level of disease (“hyperendemic”) Epidemic Disease outbreak Pandemic Sporadic cases and clusters

15. Epidemic curves Shoe-leather epidemiology Common source epidemics point source exposure

16. Epidemic curves Shoe-leather epidemiology Common source epidemics continuous exposure

17. Epidemic curves Shoe-leather epidemiology Common source epidemics intermittent exposure

18. Epidemic curves Shoe-leather epidemiology Propagated epidemics Centers for Disease Control. Measles outbreak—Aberdeen, S.D. MMWR 1971;20:26.

19. Epidemic curves Shoe-leather epidemiology Mixed epidemics Lee LA, Ostroff SM, McGee HB, et al. An outbreak of shigellosis at an outdoor music festival. Am J Epidemiol 1991;133:608-615.

20. This presentation is made available through a Creative Commons Attribution- Noncommercial license. Details of the license and permitted uses are available at http://creativecommons.org/licenses/by-nc/3.0/ © 2010 Dr. Juliet Pulliam http://creativecommons.org/licenses/by-nc/3.0/ Title: Introduction to Infectious Disease Dynamics, Part II Attribution: Dr. Juliet Pulliam, Topics in Biomedical Sciences Source URL: http://lalashan.mcmaster.ca/theobio/mmed/index.php/Honours Coursehttp://lalashan.mcmaster.ca/theobio/mmed/index.php/Honours Course For further information please contact Dr. Juliet Pulliam (juliet.mmed.clinic@gmail.com).

21. Introduction to infectious disease dynamics II Introduction to Biomedical Sciences BSc Honours Course in Biomathematics African Institute for the Mathematical Sciences Muizenberg, South Africa 17 May 2010 Dr. Juliet Pulliam RAPIDD Program Division of International Epidemiology Fogarty International Center National Institutes of Health (USA)

22. Infectious disease dynamics Traditional epidemiology Outbreak investigation Disease surveillance On-the-ground management Mathematical epidemiology General principles Explanation of patterns Prediction of spread and control Assessment of necessary data

23. Terminology Infectious diseases Exposed Infected InfectiousDiseased InfectionOnset of symptoms Onset of shedding

24. A simpler view of the world Infectious diseases Infected InfectiousDiseased InfectionOnset of symptoms Onset of shedding Infectivity = 1

25. A simpler view of the world Infectious diseases Infected Infectious Infection Onset of shedding Infectivity = 1 Don’t worry about symptoms and disease!

26. A simpler view of the world Infectious diseases Infected=Infectious Infection Onset of shedding Infectivity = 1 Don’t worry about symptoms and disease! ^ much!

27. A simpler view of the world Infectious diseases ^ much! Infectious

28. A simple view of the world Infectious diseases InfectiousSusceptibleRecovered

29. A simple view of the world Infectious diseases InfectiousSusceptibleRecovered

30. A simple view of the world Infectious diseases InfectiousSusceptibleRecovered

31. Health-related states Infectious diseases InfectiousSusceptibleRecovered

32. State variables Infectious diseases SIR

33. Transition rates Infectious diseases SIR

34. A simple disease model Infectious diseases SIR

35. A simple disease model Infectious diseases SIR

36. A simple disease model Infectious diseases SIR

37. A simple disease model Infectious diseases SIR

38. Phase portrait