[저자] 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, The GenomeTrakr Laboratory consortiumJacoxWard1EngelthalerDave1ValentineMichael1HeppCrystal1KiangDavid2LiZhirong2GentryRyan3HagermanMary Ann3RobinsonMary3KnibbsJesse3AsbellMadi3JohnsonBeth4BurnsLogan4Aurand-CravensAshley4StacyJoshua4StilesTracy5FortesEsther5DoucetteMatthew5SabinaBrandon5GagneLuc5BinnsKelly5PandoriMark6GorzalskiAndrew6MassicLauryn6DasguptaSarmila7PatilAmar7PanyiApryle7AcheampongEdward8KirnThomas8PalmateerNicholas8FedioWillis9PreciadoYatziri9PaladuguSrikanth10ThakurSiddhartha11Harden-PlumleyLyndy11RaymondLuke11PraratMelanie12SawyerAshley12PerkinsJonah12DudleyEdward13KovacJasna13M’ikanathaNkuchia M.13NawrockiErin M.13FuYezhi13MbogoNyduta13Carpenter-AzevedoKristin14HuardRichard C.14Sierra-PatevSean14DavisMegan15LaneLaura M.15JeffcoatChristy A.15GoodwinGregory15GodfreyGabrielle15SmithAndrew15ArohChukwuemika N.15GilmoreKirsti R.15FreemanJessica15ScariaJoy16HenningsJane16NelsonEric16SunYan17OhBonnie17JostMichael17BrooksBryan18LanganLaura18TurnerLauren19CruzStephanie Dela19MaitlandJessica19BennettShelby19FinkLogan19ToothmanMary19MoonHyunsook19LiuYong20HendricksonMychal20LucasDarren21DykemaPhillip21MeekRoxanne21MellyGeoff21SicklesPaige21McArdleBreanna21JansenAnneke21YoungMegan22ArbaughJosh22KuhlZachary22KingEwa23Arizona
State Department of Health Services and TGen
North, Phoenix,
Arizona, USACalifornia Department of
Public Health, Richmond,
California, USAIndiana
Department of Health,
Indianapolis, Indiana,
USAKentucky
State Cabinet for Health and Family
Services, Frankfort,
Kentucky, USAMassachusetts Department
of Public Health, Jamaica
Plain, Massachusetts, USANevada
State Public Health Laboratory,
Reno, Nevada, USAAnimal
Health Diagnostic Laboratory, New Jersey Department of
Agriculture, Ewing,
New Jersey, USANew
Jersey State Department of Health,
Ewing, New Jersey, USANew
Mexico State University-Las Cruces,
Las Cruces, New Mexico,
USANew
Mexico Department of Health,
Albuquerque, New Mexico,
USACollege of Veterinary
Medicine, North Carolina State
University, Raleigh,
North Carolina, USAAnimal
Diseases Diagnostic Laboratory (ADDL), Ohio Department of
Agriculture, Reynoldsburg,
Ohio, USAThe
Pennsylvania State University,
University Park, Pennsylvania,
USAState
Health Laboratory, Rhode Island Department of
Health, Providence,
Rhode Island, USASouth
Carolina Department of Health and Environmental
Control, Columbia,
South Carolina, USADepartment of
Veterinary & Biomedical Sciences, South Dakota State
University, Brookings,
South Dakota, USATexas
Department of State Health Services,
Austin, Texas, USABaylor
University, Waco,
Texas, USAVirginia Division of
Consolidated Laboratory Services,
Richmond, Virginia, USAWashington State
Department of Agriculture,
Olympia, Washington,
USAWashington State
Department of Health,
Shoreline, Washington,
USAWest
Virginia Department of Agriculture,
Charleston, West Virginia,
USAAssociation of Public
Health Laboratories,
Bethesda, Maryland, USAInvestigationMethodologyWriting – review and editing, James Pettengill
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. 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.
All Keywords
【저자키워드】 COVID-19, SARS-CoV-2, wastewater surveillance, data standards, wastewater based epidemiology, FAIR data, data structures, GenomeTrakr, pathogen genomic surveillance,