Advanced Molecular Detection (AMD)

COVID-19 Genomic Epidemiology Toolkit

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.

Each module includes a dedicated survey to inform future training development. We value your input.

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Welcome and Overview
Part1: Introduction
Part 2: Case Studies
Part 3: Implementation

Welcome and Overview

Module 0 - Introduction

Low Resolution Video

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

ToolkitModule_0 pdf icon[PDF – 15 slides]

Part 1: Introduction

What is genomic epidemiology?

How genome sequencing supports epidemiologic investigation of COVID-19

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The SARS-CoV-2 genome

Key features of microbial genomes, focusing on SARS-CoV-2

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How to read a phylogenetic tree

Interpreting phylogenetic trees in the context of transmission

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Emerging variants of SARS-CoV-2

How variants emerge and why genomic surveillance is important

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Part 2: Case Studies

SARS-CoV-2 sequencing in Arizona

Using sequencing for surveillance and investigation

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Healthcare cluster transmission

Investigating outbreaks in two skilled nursing facilities

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Investigating workplace-community transmission

How sequencing helped distinguish between workplace and community transmission

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Superspreading event in a pre-symptomatic population

How sequencing uncovered a super-spreading event in a congregate care setting

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Confirming SARS-CoV-2 reinfection with whole genome sequencing

How sequencing can be used to identify cases of true reinfection

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Detecting and prioritizing SARS-CoV-2 variants

Describes the detection and genome sequencing of SARS-CoV-2 variants to prioritize COVID-19 investigation and contact tracing activities

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Wastewater-based variant tracking for SARS-CoV-2

Describes the detection of SARS-CoV-2 RNA in wastewater to better understand community transmission

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Part 3: Implementation

Getting started with Nextstrain

Introducing Nextstrain, an interactive tool for visualizing phylogenetic trees

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Getting started with MicrobeTrace

Introducing MicrobeTrace, an interactive tool for transmission network analysis

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Real-time phylogenetics with UShER

Introducing UShER, a web portal for fast calculation of phylogenetic trees

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Walking through Nextstrain trees

How to use Nextstrain to analyze genomic epidemiological data

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Public genome repositories for SARS-CoV-2

Sharing and searching for genome sequence data in two public repositories

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Sequencing strategies for SARS-CoV-2

Strategies for using genome sequencing to assist with epidemiologic surveillance and investigation of SARS-CoV-2.

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More modules and materials will be added to this toolkit, so please check back for updates or subscribe to the mailing list.

Page last reviewed: November 17, 2021

Content source: Centers for Disease Control and Prevention

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