SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38819130", "kind": "science-record", "revision": 3, "content_hash": "sha256:4e7ad5a21ade701c8d66d5bb404dade091a1b723db8c2b667c29caeb321ad1ee", "created_at": "2026-11-01T19:20:46Z", "updated_at": "2026-11-01T21:33:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.", "doi": "10.1128/msystems.01415-23", "pmid": "38819130", "authors": ["Ruth E Timme", "Jacquelina Woods", "Jessica L Jones", "Kevin R Calci", "Rachel Rodriguez", "Candace Barnes", "Elizabeth Leard", "Mark Craven", "Haifeng Chen", "Cameron Boerner", "Christopher Grim", "Amanda M Windsor", "Padmini Ramachandran", "Tim Muruvanda", "Hugh Rand", "Bereket Tesfaldet", "Jasmine Amirzadegan", "Tunc Kayikcioglu", "Tamara Walsky", "Marc Allard", "Maria Balkey", "C Hope Bias", "Eric Brown", "Kathryn Judy", "Tina Pfefer", "Sandra M Tallent", "Maria Hoffmann", "James Pettengill"], "journal": "mSystems", "year": 2024, "abstract": "Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA's GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA.\nIMPORTANCE: This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA's laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.", "claims": [{"id": "claim-method", "statement": "New sequence submissions under the BioProject PRJNA757291 were downloaded daily and analyzed with CFSAN’s Wastewater Analysis Pipeline (C-WAP) (34) for both QC metrics and to infer relative abundances of SARS-CoV-2 lineages in each sample, computed using the Freyja method (8).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38819130", "locator": "sections[7] \"Data flow and visualization\" paragraph 3", "quote": "New sequence submissions under the BioProject PRJNA757291 were downloaded daily and analyzed with CFSAN’s Wastewater Analysis Pipeline (C-WAP) (34) for both QC metrics and to infer relative abundances of SARS-CoV-2 lineages in each sample, computed using the Freyja method (8)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data for the dashboard are available for download here: https://github.com/CFSAN-Biostatistics/WW-SC2-variant-estimations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38819130", "locator": "sections[7] \"Data flow and visualization\" paragraph 4", "quote": "Raw data for the dashboard are available for download here: https://github.com/CFSAN-Biostatistics/WW-SC2-variant-estimations."}], "state": "complete"}, {"id": "claim-target-result", "statement": "From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38819130", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38819130"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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