Systems biology of epidemiology From genes to environment

Juan Gutierrez (April 10, 2014)

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Slides

0:01 Systems Biology of Epidemiology: From Genes to Environment
0:59 Collaborators
1:44 The Pioneers
2:50 Epidemics are Driven by Cellular and Molecular Interactions
4:28 Epidemics are Driven by Cellular and Molecular Interactions Continued
5:31 Epidemics are Driven by Cellular and Molecular Interactions Continued
6:15 Immunoepidemiology
7:14 Challenges of omic data
12:33 Molecular Changes vs. Physiological State
14:43 Molecular Changes vs. Physiological State Continued
15:26 Molecular Changes vs. Physiological State Continued
17:28 Molecular Changes vs. Physiological State Continued
21:22 Within-Host Dynamics
21:40 Within-Host Dynamics Continued
22:13 A Change in Perspective
23:20 A Shift in the Paradigm
24:01 A Shift in the Paradigm Continued
24:17 Basic Propagation Number
24:52 Basic Propagation Number Continued
25:04 Basic Propagation Number Continued
25:15 Basic Propagation Number Continued
25:21 Basic Propagation Number Continued
26:29 Between-Host Dynamics
27:43 Diffusion on a Manifold
28:15 Diffusion on a Manifold Continued
29:31 Diffusion on a Manifold Continued
30:22 Key Aspects of Infectious Disease Can Hardly Be Studied with Existing Paradigms
30:34 Asymptomaticity is Very Important
30:57 Vector Behavior is Very Important
31:45 Vector Behavior is Very Important Continued
32:05 The Malaria Case
33:55 The Malaria Case Continued
33:58 The Malaria Case Continued
34:02 From Cells to Continent
35:39 Summary
36:04 The Bottom Line

Abstract

Traditional epidemiological models consists of compartmentalizing hosts into susceptible, exposed, infected, recovered (SEIR), and variations of this paradigm (e.g. SIR, SIR/SI, etc.). These models are challenged when the within-host dynamics of disease is taken into account with aspects such as: (i) Simultaneous Infection: Simultaneous presence of several distinct pathogen genomes, from the same or multiple species, thus causing individual to belong to multiple compartments simultaneously. (ii) Antigenic diversity and variation: Antigenic variation, defined as the ability of a pathogen to change antigens presented to the immune system during an infection, and antigenic diversity, defined as antigenic differences between pathogens in a population, are central to the pathogen's ability to 1) infect previously exposed hosts, and 2) maintain a long-term infection in the face of the immune response. Immune evasion facilitated by this variability is a critical factor in the dynamics of pathogen growth, and therefore, transmission. This talk explores an alternate mechanistic formulation of epidemiological dynamics based upon studying the influence of within-host dynamics in environmental transmission. A basic propagation number is calculated that could guide public health policy.