Methods for Outbreaks Using Genomic Data

Authored by: Don Klinkenberg , Caroline Colijn , Xavier Didelot

Handbook of Infectious Disease Data Analysis

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

Print ISBN: 9781138626713
eBook ISBN: 9781315222912
Adobe ISBN:

10.1201/9781315222912-13

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Abstract

In most methods described in other chapters, outbreaks were analysed using host data such as day of symptom onset, age, sex, or profession, and environmental data such as daily temperature or presence of particular control measures. These data were used to infer individual-level parameters such as incubation periods and risk factors for infection, and population-level parameters such as the basic reproduction ratio and the reduction in transmission due to control. A third type of data can greatly contribute to these analyses: genomic data from the pathogen. Molecular typing data from viruses or bacteria isolated from infected individuals can contain additional information on the likely links in the contact network that have led to transmission. Higher genetic similarity between isolates is likely indicative of a closer link in the transmission chain.

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