SARS-CoV-2 Quantification and Variants Detection in Wastewater Samples: Lessons Learned from Analyzing Geographically Diverse Samples

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

Prepared by A. Quintero1, J. Carpenter2, M. Waud2, M. Hargreaves3, A. Edupuganti1, D. Gramajo1, J. Boswell1
1 - Source Molecular/ LuminUltra Technologies, 15280 NW 79th Ct, Ste 107, Miami Lakes, FL, 33016, United States
2 - LuminUltra Technologies, 520 King Street, Fredericton, NB, E3B 6G3, Canada
3 - LuminUltra Technologies, 1448 South Rolling Road, Ste 212, Baltimore, MD, 21227, United States

Contact Information: [email protected]; 603-277-0354


SARS-CoV-2 testing in wastewater samples has provided invaluable information to the public since the start of COVID-19 pandemic in January 2020. The quantitative RT-qPCR and RT-ddPCR analysis supplements clinical testing on specific populations in large municipalities as well as small academic institutes. Next generation sequencing (NGS) of whole SARS-CoV-2 genome in wastewater samples also aids in viral variants surveillance. However, the complex nature of wastewater samples presents great challenges in the accuracy of viral quantification and sensitivity of mutant detection. In this study, we characterized 30 wastewater samples from 10 geographically diverse sites from the United States. We evaluated the impact of salinity, pH, total dissolved solid (TDS), and human fecal load on SARS-CoV-2 workflow recovery percentage and whole genome sequencing coverage rates. Our study yielded critical references for analytical labs to select the most suitable sample processing methods based on specific wastewater sample types, to achieve more accurate and sensitive results.