COVID-19 Genomic Epidemiology Toolkit

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.

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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?
This training module provides an introduction to genomic epidemiology.
Module 1.2 – The SARS-CoV-2 Genome
This module describes the basics of microbial genomes, with specific refence to the SARS-CoV-2 genom...
Module 1.3 – How to read a phylogenetic tree
This module describes how to interprete phylogenetic trees in the context of transmission
Module 1.4 – Emerging variants of SARS-CoV-2
This module discusses emerging variants and why genomic surveillance is important.

Part 2: Case Studies

Module 2.1 – SARS-CoV-2 sequencing in Arizona
This case study from Arizona describes using sequencing for surveillance and investigation
Module 2.2 – Healthcare cluster transmission
Case study investigating outbreaks in two skilled nursing facilities in Minnesota
Module 2.3 – Investigating workplace-community transmission
This case study describes using sequencing to differentiate  workplace and community transmission at...
Module 2.4 – Superspreading event in a pre-symptomatic population
How sequencing uncovered a super-spreading event in a congregate care setting in Massachusetts
Module 2.5 – Confirming SARS-CoV-2 reinfection with whole genome sequencing
A case study from California shows how whole genome sequencing can identify cases of true reinfectio...
Module 2.6 – Detecting and prioritizing SARS-CoV-2 variants
A case study from Colorado describes the use of genomic sequencing in COVID-19 investigation and con...
Module 2.7 – Wastewater-based variant tracking for SARS-CoV-2
A case study from Vermont describes the detection of SARS-CoV-2 RNA in wastewater to detect communit...

Part 3: Implementation

Module 3.1 – Getting started with Nextstrain
Introducing Nextstrain, an interactive tool for visualizing phylogenetic trees
Module 3.2 – Getting started with MicrobeTrace
Introducing MicrobeTrace, an interactive tool for transmission network analysis
Module 3.3 – Real-time phylogenetics with UShER
An introduction to UShER, an easy to use web portal for fast phylogenetic tree calculation.
Module 3.4 – Walking through Nextstrain trees
How to use Nextstrain to analyze genomic epidemiological data
Module 3.5 – Public genome repositories for SARS-CoV-2
Sharing and searching for genome sequence data in two public repositories
Module 3.6 – Sequencing strategies for SARS-CoV-2
The Office of Advanced Molecular Detection presents this toolkit to address topics related to the ap...
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