Searched and Found: A Wastewater Based Epidemiology program at Loma Linda University as a surveillance method for the COVID-19 pandemic

Sinclair R, Leal R, Cisneros S, Dhillon J, NaseryGonzales P.

Introduction

Wastewater can be used as a surveillance tool to detect the occurrence of pathogens in a community. Wastewater can be used as anearly detection warning tool for use of biological weapons, an early detection tool for managing infectious disease outbreaks, or a tool to indicate vaccine coverage.On the LLU campus, Wastewater Based Epidemiology (WBE) is an alternative approach for a pooled COVID-19 surveillance mechanism.Wastewater Based Epidemiology (WBE) tests wastewaterfor the SARS CoV-2 signal from a defined area and it can represent our entire campus. The WBE system has been shown to give a 4-10 day early warning on impending COVID-19 outbreaks.

Objectives

This project is investigating the most cost-effective methodsfor use in the laboratory using available sampling, concentration and extraction technologies that can produce a product to be tested with RT-qPCR. Specifically, we are determining:

Sampling: Can a field deployable sterile swab replace the use of an expensive auto sampler.

Concentration: Can a skim milk and centrifugation method replace the time intensive filter process while also representing larger sample volumes?

Extraction: Can a simple enzyme 2-step extraction kit be used in substitution for the current 14-step kit?Extraction: Can a magnet separation based DNA extractionprocess be usedwith a semi-automated 3d printing technology?

Methods

The above research questions are investigated through qPCR by processing aliquots of 100ml raw wastewater samples through 0.45um Millipore Membrane filters on the day of receipt. Samples are stored in bead tubes and a bead beater was used in combination with an RNA extraction kit to produce 100ul of genetic material that represents 100ml of wastewater. A RT-qPCR analysis followed the CDC standard RUO protocol and used standard curves for concentration estimates. The process analyzed wastewater for the RNA targets of N1 and N2 in order to quantify. All samples were processed in duplicate filters and triplicate aliquots of 5ul were processed for each N target on the RT-qPCR. Results are given in number of gene copies per liter of wastewater (GC/L).

Results

The project was successful in continuing the monitoring at the San Bernardino wastewater treatment plant from October 2020 through February 2021 and obtaining similar values to that of the previous commercial labs that processed data before the LLU SPH project. During the course of this pandemic, the occurrences of infections within confined populations on campus and in private elementary schools were higher (1x107GC/Liter) than the concentrations that occurred in the larger wastewater treatment plants (1x106GC/Liter). This was due to a lower water volume in the confined population and the dilution from the varied water source at the WWTP.

Conclusion

This method shows utility for monitoring all phases of the pandemic including: the exponential infectionrate increase, the continued monitoring and will help evaluate the overall vaccine coverage. The LLU campus benefits from:

  1. Detection of the first occurrence of a COVID-19 outbreak and routine monitoring of confined populations (e.g. dorms).
  2. Monitoring to validate complete vaccination coverage.

In the early response, the LLU developed a WBE response committee to decide on communication strategies for the results that were found with this method.

Contact: rsinclair@llu.edu