The COVID-19 pandemic has shone new light on the importance of genomic sequencing in understanding pathogens and controlling the spread of disease. Harnessing the transformative power of this technology, including in response to SARS-CoV-2, requires the active engagement from a broad spectrum of stakeholders, including ASM members working in research laboratories, academic medical centers, hospitals and clinical microbiology laboratories, industry partners and public health labs. Supporting and advancing pathogen genomics surveillance and sequencing, through initiatives like the CDC's Advanced Molecular Detection (AMD) program, is a top priority for ASM. 

ASM was awarded funding from CDC to develop deliver accredited training to educate the clinical microbiology workforce on NGS technology. Trainings will begin in early 2023

ASM' Advocates for Next-Gen Sequencing

Working with CDC

COVID-19 Variants and Next Steps for Pathogen Genomic Sequencing and Surveillance, with CDC's Greg Armstrong and former ASM President Susie Sharp

Previous Updates

World Microbe Forum Update (June 2021)
Feb 2021 Update
June 2020 Update

With $1.7 billion in multi-year funding from the American Rescue Plan Act of 2021, the AMD program is supporting state, local and territorial public health laboratories with more staff and resources to collect specimens for COVID-19 testing, sequence them to identify and track SARS-CoV-2 variants and share data. In addition to the current investments in state and local jurisdictions included in the data below, CDC has been supporting national SARS-CoV-2 sequencing capacity through contracts with large commercial diagnostic laboratories, which have received over $240 million to sequence specimens from across the United States. 

Why Invest in Genomic Sequencing?

Significantly boosting U.S. genetic surveillance and viral sequencing is key to moving beyond the current COVID-19 pandemic and effectively responding to future challenges, not only associated with novel and evolving infectious diseases, but also seasonal threats, antimicrobial resistance and food borne pathogens.


Estimates of SARS-CoV-2 Variant Prevalence in the U.S.

Data Visualization Source: CDC.

Hear From Experts


Dr. Charles Chiu discusses his research on metagenomic sequencing as a diagnostic tool that can identify all potential pathogens in a given patient sample.

Dr. Joe DeRisi talks about how genomics helped solve the mystery of dying leopard sharks in San Francisco bay, how a “virochip” array helped identify the SARS virus, how genomics can help identify unknown causes of encephalitis, how the sewer may hold the key to predicting infectious disease outbreaks and how computational capabilities represent the current bottleneck to global benefit from genomics technologies.

The entire TWiV team assembles to discuss resurgence of COVID-19 in Manaus, Brazil, discovery of SARS-CoV-2 related viruses in bats in Southeast Asia and increased Ct values after administration of mRNA vaccine.


Next generation sequencing (NGS) to identify the etiology of infectious disease has the potential to assist physicians in provided faster, pathogen-targeted antimicrobial therapy. ASM hosted a symposium on clinical metagenomics for infectious disease at World Microbe Forum 2021.

Network with Experts

The ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines taking place October 2022 in Baltimore, Md. will feature leading experts on topics including sequencing in clinical and public health microbiology, bioinformatic tools, data integration and more. 

Register to Attend

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