Spatio-Temporal Analysis of Surveillance Data

Authored by: Jon Wakefield , Tracy Qi Dong , Vladimir N. Minin

Handbook of Infectious Disease Data Analysis

Print publication date:  November  2019
Online publication date:  November  2019

Print ISBN: 9781138626713
eBook ISBN: 9781315222912
Adobe ISBN:


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This chapter looks at the basic concepts from the viewpoint of identifying the key epidemiological parameters to understand the spread of infectious diseases. The parameters discussed in this chapter are relevant to understanding the progression of disease, transmission, and severity. This chapter describes how to estimate basic intervals that are important to understanding the progression and transmission dynamics of disease. These parameters include the time intervals that characterize the duration of a typical infection cycle, such as the generation interval and the serial interval. An alternative way to characterize the duration of a typical infection cycle is by the duration of the latent period and infectious period of an infected human host. The duration between the moment of infection and symptom onset is the incubation period. In addition to the serial interval and generation interval, the reproductive number characterizes important transmission dynamics of the disease. Finally, there are parameters to characterize the severity of infection, such as the probability that a case will be hospitalized, be admitted to intensive care, or will die. The estimation of these key parameters is illustrated using R-code and data collected during the 2009 influenza A H1N1 pandemic in South Africa and in the USA.

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