What to know
The Office of Advanced Molecular Detection presents this toolkit to address topics related to the application of genomics to epidemiologic investigations and public health response to SARS-CoV-2. The COVID-19 Genomic Epidemiology Toolkit is meant to further the use of genomics in responding to COVID-19 at the state and local level.
Welcome and Overview
Overview: CDC's Dr. Greg Armstrong gives an introduction to the COVID-19 Genomic Epidemiology Toolkit and describes the role for genome sequencing in public health.
Posted: 01/08/21
Presenter: Gregory L. Armstrong, MD Director, Advanced Molecular Detection Program, CDC
Part 1: Introduction
Module 1.1 – What is Genomic Epidemiology?
Module 1.2 – The SARS-CoV-2 Genome
Module 1.3 – How to read a phylogenetic tree
Module 1.4 – Emerging variants of SARS-CoV-2
Part 2: Case Studies
Module 2.1 – SARS-CoV-2 sequencing in Arizona
Module 2.2 – Healthcare cluster transmission
Module 2.3 – Investigating workplace-community transmission
Module 2.4 – Superspreading event in a pre-symptomatic population
Module 2.5 – Confirming SARS-CoV-2 reinfection with whole genome sequencing
Module 2.6 – Detecting and prioritizing SARS-CoV-2 variants
Module 2.7 – Wastewater-based variant tracking for SARS-CoV-2
Part 3: Implementation
Module 3.1 – Getting started with Nextstrain
Module 3.2 – Getting started with MicrobeTrace
Module 3.3 – Real-time phylogenetics with UShER
Module 3.4 – Walking through Nextstrain trees
Module 3.5 – Public genome repositories for SARS-CoV-2
Module 3.6 – Sequencing strategies for SARS-CoV-2