(Internal) The evolution of SARS-CoV-2 (COVID-19) variants: analysis of large genomic datasets

Advisor: Ryan Gregory, Integrative Biology

Proposed computational co-advisor: Stefan Kremer, Computer Science

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is unprecedented in human history in terms of both the number of hosts available, the degree of repeated infection, and the amount of global travel. At the same time, there has never before been such a detailed dataset of genome sequences that has allowed the evolution of the virus to be tracked in real-time. 

This project will involve the use of bioinformatics tools to pose and answer empirical questions related to the evolution of SARS-CoV-2 variants. This may include tracking the effects and interactions of specific mutations, the role of within-host versus among-host evolution, and the mechanisms that generate very divergent variants (e.g., long-term within-host infections, recombination among lineages, evolution in non-human host species). 

This can be a one-semester or two-semester project.