COVID-19 Genomic Epidemiology Toolkit
More modules and materials will be added to this toolkit, so please check back for updates or subscribe to the mailing list.
The Office of Advanced Molecular Detection released 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.
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.
Presenter: Gregory L. Armstrong, MD
Director, Advanced Molecular Detection Program, CDC
This module provides an introduction to genomic epidemiology, with specific reference to SARS-CoV-2 sequencing for epidemiologic investigations.
Presenter: Nancy Chow, PhD
Bioinformatics and Informatics Lead, CDC
- Pathogen Genomics in Public Health. Armstrong et al. 2019 NEJM. www.ncbi.nlm.nih.gov/pmc/articles/PMC7008580/external icon
- Towards a genomics-informed, real-time, global pathogen surveillance system. Gardy and Loman. 2017 Nat Rev Genomics. www.ncbi.nlm.nih.gov/pmc/articles/PMC7097748/external icon
- Scientists have a powerful new tool for controlling the coronavirus: Its own genetic code. Washington Post, 2020. www.washingtonpost.com/graphics/2020/health/coronavirus-genetic-code/external icon
This module describes the basics of microbial genomes, with specific refence to the SARS-CoV-2 genome.
Presenter: Shatavia S. Morrison, PhD
Bioinformatics Unit Lead, CDC
- How Coronavirus Mutates and Spreads. New York Times, 2020. www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.htmlexternal icon
- SARS-CoV-2 Sequencing Data: The Devil is in the Genomic Details. Hemarajata 2020 ASM.org asm.org/Articles/2020/October/SARS-CoV-2-Sequencing-Data-The-Devil-Is-in-the-Genexternal icon
- Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Alm et al. 2020 Euro Surveill. www.ncbi.nlm.nih.gov/pmc/articles/PMC7427299/external icon
- SARS-CoV-2 Sequencing Resources. Github.com/CDCgov. github.com/CDCgov/SARS-CoV-2_Sequencingexternal icon
This module describes the anatomy of phylogenetic trees and how to interpret them in the context of transmission.
Presenter: Michael Weigand, PhD
- How to read a phylogenetic tree. ARTIC Network. artic.network/how-to-read-a-tree.htmlexternal icon
- Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Deng et al. 2020 Science. www.ncbi.nlm.nih.gov/pmc/articles/PMC7286545/external icon
- Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Munnink et al. 2020 Nature Medicine. www.nature.com/articles/s41591-020-0997-yexternal icon
- Cryptic transmission revealed by genomic epidemiology. Trevor Bedford 2020. bedford.io/blog/ncov-cryptic-transmission/external icon
- How to interpret phylogenetic trees. Nextstrain.org. nextstrain.org/narratives/trees-backgroundexternal icon
- Genomic epidemiology playbook — a primer on uses and interpretation. Sidney Bell. Nextstrain.org. nextstrain.org/community/narratives/czbiohub/covidtracker/pawnee-interpretation-examplesexternal icon
This module introduces basic concepts relevant to the emergence of new SARS-CoV-2 variants and the role of sequencing in their detection and definition.
Presenter: Michael Weigand, PhD
- The coronavirus is evolving before our eyes. The Atlantic, 2021. www.theatlantic.com/health/archive/2021/01/coronavirus-mutations-variants/617694/external icon
- Coronavirus variants and mutations. New York Times, 2021. www.nytimes.com/interactive/2021/health/coronavirus-variant-tracker.htmlexternal icon
- Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Hodcroft et al. 2020 MedRxiv. www.medrxiv.org/content/10.1101/2020.10.25.20219063v2external icon
- Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Korber et al. 2021 Cell. www.sciencedirect.com/science/article/pii/S0092867420308205external icon
- Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Rambaut et al. 2020 Virological. www.virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563external icon
- Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Washington et al. 2021 MedRxiv. www.medrxiv.org/content/10.1101/2021.02.06.21251159v1external icon
- Emergence of SARS-CoV-2 B.1.1.7 lineage — United States, December 29, 2020–January 12, 2021. Galloway et al. 2021 MMWR. www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm
- About variants of the virus that causes COVID-19. www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html
- Genomic surveillance for SARS-CoV-2 variants. www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html
- Why S-gene sequencing is key for SARS-CoV-2 surveillance. ThermoFisher. www.thermofisher.com/blog/behindthebench/why-s-gene-sequencing-is-key-for-sars-cov-2-surveillance/external icon
- PANGO lineage global reports. cov-lineages.org/global_report.htmlexternal icon
- CoVariants.org. covariants.orgexternal icon
- SARS-CoV-2 mutation situation reports. Scripps Research. outbreak.info/situation-reports/external icon
- Pangolin COVID-19 lineage assigner. pangolin.cog-uk.io/external icon
- Nextclade clade assignment, mutation calling. clades.nextstrain.org/external icon
This module provides insight into how SARS-CoV-2 sequencing is used to describe the genomic epidemiology of a state and as an investigative tool in COVID-19 outbreak settings.
Presenter: Hayley Yaglom, MS, MPH
Genomic Epidemiologist, Translational Genomics Research Institute
- An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. Ladner et al. 2020 American Society for Microbiology. mbio.asm.org/content/11/5/e02107-20external icon
- AZ-Strain: Genomic Epidemiology of SARS-CoV-2 in Arizona nextstrain.org/community/narratives/tgennorth/arizona-covid-19/ external icon
This module provides insight into two separate outbreaks at long-term care settings, and how sequencing helped clarify the pattern of transmission in these settings.
Presenter: Nicholas Lehnertz, MD MPH MHS
Physician and Epidemiologist, Minnesota Department of Health
- Serial testing for SARS-CoV-2 and virus whole-genome sequencing. Taylor et al. 2020 MMWR. www.cdc.gov/mmwr/volumes/69/wr/mm6937a3.htm
Further Reading for Case Studies
- Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. Arons et al. 2020 NEJM. www.ncbi.nlm.nih.gov/pmc/articles/PMC7200056/external icon
- COVID-19 outbreak associated with a 10-day motorcycle rally in a neighboring state. Firestone et al. 2020 MMWR. www.cdc.gov/mmwr/volumes/69/wr/mm6947e1.htm?s_cid=mm6947e1_w
- Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. Lemieux et al. 2020 MedRxiv. www.medrxiv.org/content/10.1101/2020.08.23.20178236v1external icon
- The emergence of SARS-CoV-2 in Europe and North America. Worobey et al. 2020 Science. science.sciencemag.org/content/370/6516/564external icon
- Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa. Richmond et al. 2020 MedRxiv. www.medrxiv.org/content/10.1101/2020.06.08.20125534v1external icon
- SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations. Richmond et al. 2020 MedRxiv. www.medrxiv.org/content/10.1101/2020.10.12.20210294v1external icon
This module gives an introduction to Nextstrain, a powerful tool for interactive tree visualization.
Presenter: Michael Weigand, PhD
Bioinformatician , CDC
- Nextstrain: Real-time tracking of pathogen evolution. Hadfield et al. 2018. Bioinformatics. academic.oup.com/bioinformatics/article/34/23/4121/5001388 external icon
- Nextstrain documentation docs.nextstrain.orgexternal icon
- A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2 docs.nextstrain.org/en/latest/tutorials/SARS-CoV-2/steps/index.html#a-getting-started-guide-to-the-genomic-epidemiology-of-sars-cov-2external icon
- Interacting with auspice, the visualization web application neherlab.org/201901_krisp_auspice.htmlexternal icon
- SPHERES state builds nextstrain.org/groups/spheresexternal icon