Wastewater Surveillance for SARS-CoV-2 Variants

President Biden declared May 11, 2023, the end of the COVID-19 public health emergency. FDA is working to conclude its work on the Wastewater Surveillance for SARS-CoV-2 Variants project, as well. Although the work to identify COVID-19 variants in wastewater is ending, FDA will continue to apply the methods developed for the wastewater surveillance project to foodborne pathogen surveillance. FDA thanks all participating laboratories for their contributions to this project. Links to publications with our findings will be added to this page once available.

NOTE: As of June 30th, 2023, FDA will no longer update the COVID-19 wastewater dashboard. However, all underlying data will remain publicly available through links at this site and through our BioProject at the National Center for Biotechnology Information (NCBI).

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 in the population. Accordingly, through the American Rescue Plan Act of 2021, Congress provided temporary funding for FDA to develop the capacity to sequence SARS-CoV-2 RNA from wastewater samples and to conduct a sampling and sequencing project through 2022. By monitoring population-level variants over time, 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.

The software FDA developed to analyze sequences obtained from wastewater samples has been adopted by other public health partners, including the CDC. FDA will continue its SARS-CoV-2 wastewater sequencing efforts, including further developing its sequencing methods and analysis tools, and updating public repositories of genomic information, until the funding for the project expires.

Status

To facilitate the sharing of information about progress on this sequencing effort, FDA has developed a dashboard that graphically presents information from and about the project. Individuals can make selections on the dashboard to display: the number of samples collected and the number of samples sequenced, both nationwide and by individual laboratories in each state; the names of the states from which the samples were collected; the names of the labs that conducted the sequencing; and the changes in the relative abundance of variants and their sublineages detected over time. Sequencing records generated during pilot testing of the methods and sequencing records with data insufficient for variant detection have been omitted from the dashboard.

Wastewater Surveillance for SARS-CoV-2 Variants: Laboratory Data Submitted to NCBI Project PRJNA757291

^{† For assistance with keyboard navigation and instructions for acquiring data in a format that can be read by a screen reader, please navigate to: https://help.tableau.com/current/pro/desktop/en-us/access_keyboard_navigation.htm. Individuals using assistive technology may still have difficulty fully accessing the information in the interactive dashboard and may gain alternative access to the information by visiting NCBI’s SRA Run Selector page, entering PRJNA757291 in the accession search box at the top of the page, and clicking the search button. Once the search results display, scroll to the “Select” section of the page, and in the “Download” column click on “Metadata.” The metadata will download to your computer. This data is not confidential and is free for public use. Individuals with disabilities who require further assistance may contact covidtrakr@fda.hhs.gov.}

^{‡ For assistance with keyboard navigation and instructions for acquiring data in a format that can be read by a screen reader, please navigate to: https://help.tableau.com/current/pro/desktop/en-us/access_keyboard_navigation.htm. Individuals using assistive technology may still have difficulty fully accessing the information in the interactive dashboard and may gain alternate access to the information by downloading it here. This data is not confidential and is free for public use. Individuals with disabilities who require further assistance may contact covidtrakr@fda.hhs.gov.}

Additional Resources

The following resources contain information related to the SARS-CoV-2 project, including protocols and analysis software developed by FDA’s Center for Food Safety and Applied Nutrition and utilized by the labs sequencing SARS-CoV-2 variants from wastewater samples.

GenomeTrakr Umbrella for SARS-CoV-2 Wastewater Data – Genomic information and associated metadata collected as part of this project
SARS-CoV-2 Wastewater Protocols – Protocols developed and/or optimized for this project covering methods for collecting and testing wastewater samples, sequencing SARs-CoV-2 from the samples, and submitting the sequence data and associated metadata for public access
CFSAN Wastewater Analysis Pipeline (C-WAP) Tool – Developed for analyzing SARS-CoV-2 sequence data obtained from wastewater samples

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