SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network
Authors: Timme Ruth E. , Woods Jacquelina , Jones Jessica L. , Calci Kevin R. , Rodriguez Rachel , Barnes Candace , Leard Elizabeth , Craven Mark , Chen Haifeng , Boerner Cameron , Grim Christopher , Windsor Amanda M. , Ramachandran Padmini , Muruvanda Tim , Rand Hugh , Tesfaldet Bereket , Amirzadegan Jasmine , Kayikcioglu Tunc , Walsky Tamara , Allard Marc , Balkey Maria , Bias C. Hope , Brown Eric , Judy Kathryn , Pfefer Tina , Tallent Sandra M. , Hoffmann Maria ,   The GenomeTrakr Laboratory consortium, Pettengill James , Jacox Ward , Engelthaler Dave , Valentine Michael , Hepp Crystal , Kiang David , Li Zhirong , Gentry Ryan , Hagerman Mary Ann , Robinson Mary , Knibbs Jesse , Asbell Madi , Johnson Beth , Burns Logan , Aurand-Cravens Ashley , Stacy Joshua , Stiles Tracy , Fortes Esther , Doucette Matthew , Sabina Brandon , Gagne Luc , Binns Kelly , Pandori Mark , Gorzalski Andrew , Massic Lauryn , Dasgupta Sarmila , Patil Amar , Panyi Apryle , Acheampong Edward , Kirn Thomas , Palmateer Nicholas , Fedio Willis , Preciado Yatziri , Paladugu Srikanth , Thakur Siddhartha , Harden-Plumley Lyndy , Raymond Luke , Prarat Melanie , Sawyer Ashley , Perkins Jonah , Dudley Edward , Kovac Jasna , M’ikanatha Nkuchia M. , Nawrocki Erin M. , Fu Yezhi , Mbogo Nyduta , Carpenter-Azevedo Kristin , Huard Richard C. , Sierra-Patev Sean , Davis Megan , Lane Laura M. , Jeffcoat Christy A. , Goodwin Gregory , Godfrey Gabrielle , Smith Andrew , Aroh Chukwuemika N. , Gilmore Kirsti R. , Freeman Jessica , Scaria Joy , Hennings Jane , Nelson Eric , Sun Yan , Oh Bonnie , Jost Michael , Brooks Bryan , Langan Laura , Turner Lauren , Cruz Stephanie Dela , Maitland Jessica , Bennett Shelby , Fink Logan , Toothman Mary , Moon Hyunsook , Liu Yong , Hendrickson Mychal , Lucas Darren , Dykema Phillip , Meek Roxanne , Melly Geoff , Sickles Paige , McArdle Breanna , Jansen Anneke , Young Megan , Arbaugh Josh , Kuhl Zachary , King Ewa 
Published: May 2024

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.

IMPORTANCE

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.