(Internal) The evolution of SARS-CoV-2 (COVID-19) variants: evolutionary and ecological modelling

Advisor: Ryan Gregory, Integrative Biology

Proposed computational advisor: Stefan Kremer, Justin Slater, Ayesha Ali, Rozita Dara, Lorna Deeth, Khurram Nadeem, Gurjit Randhawa, Yan Yan

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has evolved rapidly over the course of the pandemic. More than 3,000 subvariants have been designated, some of which (Alpha, Delta, Omicron BA.1, BA.2, BA.5) caused large waves of illness, and it has so far been necessary to update vaccines three times in the face of evolving variants that can escape prior immunity.

The virus evolves at two different levels: within hosts (through persistent infection or recombination) and among hosts. Understanding the factors that influence the evolution of new viral variants at each of these levels and allow them to spread is essential in ongoing efforts to contain the virus. This project will involve developing conceptual, mathematical, and/or computational models to identify the ways in which multiple properties of individual hosts, host populations, and viral variants influence the transmissibility, virulence, and public health impacts of new variants. Whereas many studies use epidemiological models to study SARS-CoV-2, this project will draw more heavily from models and theory in evolutionary biology and ecology.

This can be a one-semester or two-semester project. More than one student can work on a project involving this topic.
 

Knowledge/Skills

Background in mathematical or computational modelling, willingness to learn new conceptual frameworks, comfort with exploring new approaches to a complex problem