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

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.

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training

“…The GenomeTrakr network conducted a pilot study utilizing PHA4GE QC tags, tailored specifically for targeted amplicon sequencing of SARS-CoV-2 in wastewater samples [ 26 ]. The pilot study involved 19 GenomeTrakr laboratories plus FDA-CFSAN laboratories (combination of federal and state laboratories).…”

“…PHA4GE’s quality control (QC) tags were piloted by the FDA’s GenomeTrakr network [ 24 25 ] during its pandemic expansion into metagenomic wastewater surveillance for COVID-19 [ 26 ], enabling transparent sharing of early-stage data at the US National Centre for Biotechnology Information (NCBI). Many datasets, especially early on, were flagged as lower quality with these tags, allowing a federal agency to comfortably share pandemic data while clearly communicating confidence levels.…”

Outbreak-associatedSalmonellaBaildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance

“…Wastewater-based surveillance detects SARS-CoV-2 RNA before the peak of clinical cases and has been shown to identify variants of concern prior to presentation in patients (10)(11). Emergency appropriations in 2021 expanded wastewater-based surveillance efforts for COVID-19 through the US Food and Drug Administration GenomeTrakr program which has been focused on foodborne pathogens (12).…”