Monitoring SARS-CoV-2 in wastewater during New York City's second wave of COVID-19: Sewershed-level trends and relationships to publicly available clinical testing data

New York Citys ongoing wastewater monitoring program tracked trends in sewershed-level SARS-CoV-2 loads starting in the fall of 2020, just before the start of the Citys second wave of the COVID-19 outbreak. During a five-month study period, from November 8, 2020 to April 11, 2021, viral loads in influent wastewater from each of New York Citys 14 wastewater treatment plants were measured and compared to new laboratory-confirmed COVID-19 cases for the populations in each corresponding sewershed, estimated from publicly available clinical testing data. We found significant positive correlations between viral loads in wastewater and new COVID-19 cases. The strength of the correlations varied depending on the sewershed, with Spearmans rank correlation coefficients ranging between 0.38 and 0.81 (mean = 0.55). Based on a linear regression analysis of a combined data set for New York City, we found that a 1 log10 change in the SARS-CoV-2 viral load in wastewater corresponded to a 0.6 log10 change in the number of new laboratory-confirmed COVID-19 cases/day in a sewershed. An estimated minimum detectable case rate between 2 - 8 cases/day/100,000 people was associated with the method limit of detection in wastewater. This work offers a preliminary assessment of the relationship between wastewater monitoring data and clinical testing data in New York City. While routine monitoring and method optimization continue, information on the development of New York Citys ongoing wastewater monitoring program may provide insights for similar wastewater-based epidemiology efforts in the future.

Protocol for Safe, Affordable, and Reproducible Isolation and Quantitation of SARS-CoV-2 RNA from Wastewater

The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps in the process. This protocol is one of the safest, cheapest, and most reproducible approaches for the detection of SARS-CoV-2 RNA in wastewater. Furthermore, the RNA obtained using this protocol, minus the pasteurization step, can be sequenced both using a targeted approach sequencing specific regions or the whole genome. The protocol was adopted by the New York City Department of Environmental Protection in August 2020 to support their efforts in monitoring SARS-CoV-2 prevalence in wastewater in all five boroughs of the city. Owing to a pasteurization step, it is safe for use in a BSL1+ facility. This step also increases the genetic signal of the virus while making the protocol safe for the personnel involved. This protocol could be used to isolate a variety of other clinically relevant viruses from wastewater and serve as a foundation of a wastewater surveillance strategy for monitoring community spread of known and emerging viral pathogens.