The CDC Advanced Molecular Detection (ADM) program developed this toolkit to support the application of genomics in epidemiologic investigations and the public health response to SARS-CoV-2. It is designed to strengthen genomics use for COVID-19 at the state and local level, and also includes cross-cutting modules to enhance practical skills of professionals working in genomic epidemiology.

Part 1: Introduction

• 1.1 – What is Genomic Epidemiology?
• 1.2 – The SARS-CoV-2 Genome
• 1.3 – How to read a phylogenetic tree
• 1.4 – Emerging variants of SARS-CoV-2

Part 2: Case Studies

• 2.1 – SARS-CoV-2 sequencing in Arizona
• 2.2 – Healthcare cluster transmission
• 2.3 – Investigating workplace-community transmission
• 2.4 – Superspreading event in a pre-symptomatic population
• 2.5 – Confirming SARS-CoV-2 reinfection with whole genome sequencing
• 2.6 – Detecting and prioritizing SARS-CoV-2 variants
• 2.7 – Wastewater-based variant tracking for SARS-CoV-2

Part 3: Implementation

• 3.1 – Getting started with Nextstrain
• 3.2 – Getting started with MicrobeTrace
• 3.3 – Real-time phylogenetics with UShER
• 3.4 – Walking through Nextstrain trees
• 3.5 – Public genome repositories for SARS-CoV-2
• 3.6 – Sequencing strategies for SARS-CoV-2