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

Advisor: Ryan Gregory, Integrative Biology

Proposed computational co-advisor: Stefan Kremer, Computer Science

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, while more recently a complex and dynamic “variant soup” consisting of multiple variant lineages (e.g., BQ*, XBB.1.5*, XBB.1.16*, XBB.1.9*, EG.5*), which rise and fall in relative frequency, has kept the baseline of infections high for long periods of time. It has been necessary to update vaccines twice so far in the face of evolving variants that can escape prior immunity.

Understanding the factors that influence the evolution of new variants and allow them to spread is essential in ongoing efforts to contain the virus. This project will involve developing conceptual and 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.