Development of NYC DEP’s SARS-CoV2 RNA Environmental Monitoring Program

SARS CoV-2 Wastewater Testing - State of the Science (Session 2)
Oral Presentation

Prepared by F. Chauvin1, M. Trujillo2, C. Hoar3, A. Silverman3, A. Clare4, D. Smyth5, J. Dennehy6
1 - NYC Environmental Protection - Bureau of Wastewater Treatment, 59-17 Junction Blvd, 2nd Floor, Flushing, New York, 11373, United States
2 - Department of Biology, Queensborough Community College, The City University of New York, New York, , , United States
3 - Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, , ,
4 - NYC Environmental Protection - Bureau of Wastewater Treatment, , ,
5 - Department of Natural Sciences and Mathematics, Eugene Lang College of Liberal Arts at The New School, New York, , ,
6 - Biology Department, Queens College, The City University of New York, New York; The Graduate Center, The City University of New York, New York, , ,

Contact Information: [email protected]; 347-633-0832


When the COVID-19 pandemic started,New York City’s Department of Environmental Protection (NYC DEP) did not have an active molecular biology program. Recognizing the benefits of the rapidly evolving tools of wastewater-based epidemiology, DEP acted swiftly to establish its COVID-19 Environmental Monitoring Program, and to develop its relationship with New York City’s Department of Health and Mental Hygiene (NYC DOHMH).

This presentation will outline how NYC DEP’s collaboration with two teams of academic researchers, NYU and CUNY, allowed the development of a full-fledged program of SARS-CoV-2 tracking in the influent wastewater streams from our 14 Wastewater Resource Recovery Facilities, including:

1 - Implementation of quantitative Reverse Transcription-Polymerase Chain Reaction (RT-qPCR) of the SARS-CoV-2 RNA signal in wastewater. The RNA signal correlates well with the presence, and eventually, prevalence of COVID-19 clinical cases in the communities served within DEP sewersheds. Our method optimization, analytical variability minimization and normalization approaches will be outlined.

2 - Development and implementation of sequencing capabilities to identify mutations in wastewater samples, and to provide some measure of quantitation of virus mutant prevalence. This presentation will describe both targeted sequencing and whole genome sequencing and will summarize the optimization of sample processing and sequencing methodology to improve SARS-CoV-2 genome coverage and depth.

3 - Optimization of the sampling program to better balance sampling and analytical capabilities with the needs for city-wide data gathering as well as localized information collection.

This presentation will emphasize the development of our relationship with NYC DOHMH and our efforts as to how best to provide NYC DOHMH with timely and actionable data and to comply with the local laws.