Chapter 3 : Epidemiological and Evolutionary Dynamics of Pathogens

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Studies relating to the epidemiology and evolutionary dynamics of pathogens are just beginning to emerge with some exciting insights. This chapter reviews some of the basic evolutionary approaches that might give insights into the population dynamics of infectious disease and that would link well with epidemiological data to give a more complete picture of population dynamics over time and insights into more appropriate intervention strategies. The author reviews these applications of evolutionary techniques through a series of examples throughout the chapter. The key factors in the evolutionary response of pathogens to their environments can be measured by assessing the genetic diversity, the impact of natural selection in shaping that existing diversity, and the impact of recombination in redistributing that diversity, sometimes into novel combinations. Natural selection at the phenotypic level is generally agreed upon, and there are abundant examples, perhaps the most famous of which are Darwin’s finches. One of the main goals of genomic science is to elucidate the relationships between genotypes and phenotypes. Population genetic approaches can provide a statistical framework within which one can test such associations. Phenotypes associated with each sequence can then be evaluated using a nested analysis of variance. In summary, a diversity of quantitative approaches are now available for analyzing microbial data and linking genetic diversity with epidemiological factors.

Citation: Crandall K, Pérez-Losada M. 2008. Epidemiological and Evolutionary Dynamics of Pathogens, p 21-30. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch3
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Image of Figure 1.
Figure 1.

Evolutionary history of HIV diversity estimated using maximum likelihood phylogeny estimation based on genetic diversity of the protease gene.

Citation: Crandall K, Pérez-Losada M. 2008. Epidemiological and Evolutionary Dynamics of Pathogens, p 21-30. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch3
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Image of Figure 2.
Figure 2.

Host-switching of polyoma viruses (hosts on the left with viruses on the right and associations drawn in a dotted line). See Pérez-Losada et al., 2006b, for details.

Citation: Crandall K, Pérez-Losada M. 2008. Epidemiological and Evolutionary Dynamics of Pathogens, p 21-30. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch3
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Image of Figure 3.
Figure 3.

The rapid accumulation of influenza whole genome sequence data in GenBank within the past year.

Citation: Crandall K, Pérez-Losada M. 2008. Epidemiological and Evolutionary Dynamics of Pathogens, p 21-30. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch3
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