The fast spread of SARS-Cov-2 sparked much interest in understanding the underlying genomics of this 30,000bp Coronavirus. Thus far, thousands of genome assemblies are available, yet they feature only a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have evolved while rapidly spreading throughout the world. In this talk, I will describe the mutational landscape of thousands of SARS-Cov-2 genomes and take a deep dive into the intrahost diversity of this devastating virus. Specifically, I will discuss within-host minor variants that are found across hosts and describe population-wide structural variations that highlight this underexplored intrahost diversity. Implications of these findings include both high false-negative rates of qPCR-based tests and as a key tool in transmission analyses.

Learning Objectives:
1. Differentiating consensus-level vs within-host variation of SARS-CoV-2

2. Discovering the potential impact of single nucleotide variation on COVID-19 diagnostics

3. Understanding the utility of minor variants on tracking SARS-CoV-2 transmission