Cartridge Based qPCR. The New Gold Standard for Wastewater Epidemiology.

Wastewater Surveillance - State of the Science
Poster Presentation

Prepared by J. Harbridge, D. Kroll
Hach, Hach, 5600 Lindbergh Drive, Loveland, Colorado, 80539, United States

Contact Information: [email protected]; 970-281-2268


Wastewater based epidemiology has been proven to be effective for monitoring SARS-CoV-19 (Leading indicator vs. lagging Clinical methods) in sewers with results up to 5-10 days before clinical detection. However, broad adoption has been hindered by several hurdles, all which are as result of how difficult and time consuming it is to perform a SARS CoV-2 extraction in wastewater. Because the extractions are complex, costly, and highly variable it has led to almost no in-house testing at wastewater treatment plants, high outsourcing costs, delayed data, and lack in confidence in actionability of the results.
To this end, Cepheid’s GeneXpert technology has been demonstrated to easily and reliably perform SARS-CoV-2 analyses in wastewater. The technology fully automates the capture, lysis, and measurement of SARS-CoV-2 viral RNA in wastewater in a single self-contained cartridge (using real-time reverse transcriptase PCR as the measurement approach). The cartridge contains all the reagents, primers, probes, buffers, and filtration required to isolate, lyse, and extract viral RNA as well as perform the real-time RT PCR analysis, which occurs in an optical reaction tube/extension (Figure 1), Each cartridge also contains an internal control to help ensure the nucleic acid extraction process and amplification are valid and return quality results.
The GeneXpert cartridge technology has been used in clinical applications for over fifteen years and now has been proven to be a successful methodology for applications in wastewater analysis. The PCR instrumentation has the capacity to test 1, 2, 3 or 4 samples at a time. Each PCR analysis takes approximately 35-40 minutes with 1-2 minutes of hands-on time to prepare each sample. The SARS CoV-2 methodology measures the Nucleocapsid (N2), Envelope (E) and RNA dependent RNA (RdRP) polymerase gene targets. The system also has the capability to measure Flu, RSV, Antibiotic resistant bacteria and norovirus in wastewater, all with 1-step preparation.
In this paper we will describe how the GeneXpert technology works and show analytical performance data compared against traditional viral extraction methodologies used in wastewater and present a 2-year case study monitoring SARS CoV-2 in a community in Colorado.