U.S. flag An official website of the United States government
  1. Home
  2. Food
  3. Science & Research (Food)
  4. Whole Genome Sequencing (WGS) Program
  5. Wastewater Surveillance for SARS-CoV-2 Variants
  1. Whole Genome Sequencing (WGS) Program

Wastewater Surveillance for SARS-CoV-2 Variants

Studies have shown that SARS-CoV-2 (COVID-19) variants of concern from wastewater can be identified 1-2 weeks prior to being detected in clinical samples from the same area, making wastewater surveillance useful for detecting and monitoring SARS-CoV-2 at the population scale. Accordingly, FDA has developed the capacity to sequence SARS-CoV-2 RNA from wastewater samples. By monitoring for both known and unknown variants of the virus, GenomeTrakr labs are providing information about the evolution of the virus, which is critical to evaluating the effectiveness of FDA-regulated COVID-19 vaccines, therapeutics, and diagnostics. Geographic regions with high percentages of agricultural and food facility workers, whose health is critical for stability of the U.S. food supply chain, are of interest.  Resulting sequence data are being submitted in real time to public repositories where active monitoring for circulating variants of concern takes place.

Beyond the COVID-19 application, the project provides the participating laboratories with experience extracting genomic information from wastewater samples and working with a broader network of laboratories in response to a national emergency. 


Up-to-date genomic information and associated metadata from the project are available via the National Center for Biotechnology Information (NCBI), at GenomeTrakr Umbrella for SARS-CoV-2 Wastewater Data.

Participating Laboratories

  • Arizona Department of Health Services with the Translational Genomics Research Institute
  • California Department of Public Health
  • Indiana State Department of Health
  • Kentucky Cabinet for Health and Family Services
  • Massachusetts State Public Health Laboratory
  • Nevada Department of Health and Human Services with the University of Nevada - Reno
  • New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory
  • New Jersey Department of Health and Senior Services
  • New Mexico State University, Food Safety Laboratory
  • North Carolina State University, College of Veterinary Medicine
  • Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture
  • Pennsylvania Department of Health with Pennsylvania State University
  • Rhode Island Department of Health
  • South Carolina Department of Health and Environmental Control
  • South Dakota Department of Health with South Dakota State University
  • Texas Department of State Health Services
  • Virginia Department of Health
  • Washington State Department of Agriculture
  • Washington State Department of Health Public Health Laboratories
  • West Virginia Department of Agriculture
  • FDA-CFSAN Gulf Coast Seafood Laboratory
Back to Top