​​Emerging viruses can cause new diseases in humans and animals and proper epidemiological surveillance is essential to detect and characterize such viruses. Given the enormous impact of the COVID-19 pandemics, this course will cover the assembly of the SARS-CoV-2 genome from human patients, characterization of viral variants, and identification of variants of concern (VOCs). The course will also present some innovative methods that can improve the detection of evolutionarily remote viruses. Among other methods, the course will cover the construction of profile HMMs and their application to screening metagenomic datasets for both known and novel viruses.

Virtual machines:

• All students will receive an account in a virtual machine (VM) 
• The VMs will be running Linux and all programs used throughout the course will be available to students
• Access to the VMs will be granted throughout the entire duration of the course. 
• No programs are needed on the local computer, except Zoom