Pathogen Genomics

The Emerging Role of Pathogen Genomics in Public Health.
CDC Public Health Grand Rounds, January 21, 2020.

Pathogen Genomics in Public Health.
Armstrong GL, MacCannell DR, Taylor J, Carleton HA, Neuhaus EB, Bradbury RS, Posey JE, Gwinn M.
New Engl J Med, December26, 2019.

Next-Generation Sequencing of Infectious Pathogens.
Gwinn M, MacCannell D, Armstrong GK.
JAMA, February 14, 2019.

The Centers for Disease Control and Prevention (CDC) is well known for its work in monitoring, investigating, and controlling infectious diseases in the United States and worldwide. Genetic information from viruses, bacteria, and other infectious organisms has long played a crucial role in these efforts.

Advances in molecular technologies and bioinformatics have made it possible to examine pathogen genomes in much greater detail. Now, falling costs and turnaround times are bringing high-throughput genetic sequencing within reach for use by clinical and public health investigators. CDC’s Office of Advanced Molecular Detection (OAMD) works with infectious disease programs to leverage these tools against a variety of pathogens at national, state, and local levels.

Public health applications of pathogen genomics include:

SARS-CoV-2 genomics and the COVID-19 pandemic

Analysis of SARS-CoV-2 genome sequences is central to the global public health response to COVID-19. CDC, state and local health departments, and other public health organizations nationwide contribute to genomic surveillance of SARS-CoV-2. CDC’s Office of Advanced Molecular Detection (OAMD) conducts several activities to support these efforts, including:

SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)

OAMD established SPHERES as an open consortium of scientists from clinical and public health laboratories, academic institutions, and the private sector to coordinate SARS-CoV-2 sequencing in the US. As part of this initiative, CDC has made 29 awards to academic and research organizations to fill knowledge gaps and promote innovation.

COVID-19 Genomic Epidemiology Toolkit

OAMD recruited a group of scientists from CDC and state and local health departments to develop the COVID-19 Genomic Epidemiology Toolkit. Specifically tailored to epidemiologists, the Toolkit is a practical introduction to using SARS-CoV-2 genomics to investigate and control COVID-19.

OGPPH Resources

Check out the Weekly Advanced Molecular Detection Clips. Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions.

Search the  Pathogen Advanced Molecular Detection Database for information on genomic sequencing and diagnostic methods, evolution, antimicrobial resistance, outbreak investigation, and host-pathogen interactions.

Use the COVID-19 GPH portal to search for publications on emerging discoveries and applications of genomic, molecular, and other precision health tools in the investigation and control of COVID-19.

Recent OGPPH blog posts on infectious diseases and microbial genomics:

Page last reviewed: August 20, 2021