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Quantitative Viral Ecology

PSL Master in Life Sciences - ENS IMaLiS


Year and Semester : M2 S1
Credits/hours : 3 ECTS / 30 hours
First and last day of class : October 26-30, 2020
Hours : 9am-12pm, 2pm-5pm
Venue : ENS Biology Department

Coordination

Joshua Weitz (ENS Chaire Blaise Pascal, Georgia Tech)
Régis Ferrière (IBENS & UMI iGLOBES CNRS, ENS, Univ. Arizona)

Keywords

Viral life cycle. Viral life-history traits. Virus-microbe infection networks. Coevolutionary dynamics. Ocean Viruses. Viral shunt.

Course Prerequisites

The targeted audience is advanced undergraduates and graduate students in ecology and evolutionary biology and related fields, with experience and a strong interest in mathematical modeling. Participants trained in other fields are welcome given the following prerequisites :
• Introductory ecology : population dynamics, population regulation (density-dependence), exponential growth, logistic model, Lotka-Volterra model.
• Basic systems modelling : non-linear differential equations, equilibrium, stability analysis.
• Some experience in programming (Python).

Course objectives and description

When we think about viruses we tend to consider ones that afflict humans—such as those that cause influenza, HIV, and Ebola. Yet, vastly more viruses infect single-celled microbes. Diverse and abundant, microbes and the viruses that infect them are found in oceans, lakes, plants, soil, and animal-associated microbiomes. Taking a vital look at the “microscopic” mode of disease dynamics, the course presents a theoretical foundation from which to model and predict the ecological and evolutionary dynamics that result from the interaction between viruses and their microbial hosts.
Three major questions will be addressed : What are viruses of microbes and what do they do to their hosts ? How do interactions of a single virus-host pair affect the number and traits of hosts and virus populations ? How do virus-host dynamics emerge in natural environments when interactions take place between many viruses and many hosts ? The course will provide a framework for tackling new challenges in the study of viruses and microbes and how they are connected to ecological processes—from the laboratory to the Earth system.
This is a one-week intensive course. Lecture-style presentations will be complemented by computer-based tutorials. In the tutorial sessions, students will work to implement the theory and numerically study model examples. This will involve the guided writing of simple code in Python.

Evaluation

Evaluation is based on the students presenting the work they carried out in the tutorial sessions.
The presentations will take place at the end of the week.

Course material

Readings, slides, computer simulation tutorial, and video-recorded presentations will be made available to enrolled students.

Suggested readings

Weitz JS (2016) Quantitative Viral Ecology : Dynamics of Viruses and their Microbial Hosts. Monographs in Population Biology, Princeton University Press.