Next-Generation Sequencing (NGS) has been a key technology during the COVIID-19 pandemic and has helped researchers characterize the SARs-CoV-2 genome, perform strain-typing for molecular epidemiology, study host genetics to identify patients with elevated genetic risk, determine effects of co-infections, and monitor host immune response.   In this talk we will give an overview of the key methods used to study the SARS-CoV-2 RNA genome as well as other respiratory pathogens.  We will compare the three main NGS methods for studying RNA viruses: shotgun meta-transcriptome sequencing, targeted RNA enrichment and PCR amplicon methods.  Finally, we will discuss how NGS can be used as a surveillance tool in the future to help control future breakouts.

Learning Objectives:

1. NGS enables precision diagnosis and characterization of respiratory pathogens

2. NGS can be used to understand host genetics, inflammatory and immune response Surveillance using

3. NGS will be critical to identify and control future pandemics