An evaluation of a new rapid qPCR test for the detection of 2019-novel coronavirus nucleocapsid (N1) gene in wastewater in Roanoke and Salem VA sewersheds

• Published in: Journal of water and health 2024-08, Vol.22 (8), p.1419-1428
• Main Authors: Lehrer, Lia Willow, Lewis, Anna Marie, Tolliver, Susan, Degen, Marcia, Singh, Rekha, Houser, Sara, Rao, Jayasimha
• Format: Article
• Language: English
• Subjects: Coronavirus Nucleocapsid Proteins - genetics; Coronaviruses; Cost analysis; COVID-19; COVID-19 - virology; Epidemiology; Genes; Genomes; Glycoproteins; Health surveillance; Humans; Medical laboratories; Nucleic acids; Nucleocapsids; Nucleotide sequence; Pandemics; PCR; Phosphoproteins; Polymerase chain reaction; Proteins; Public concern; Public health; Real-Time Polymerase Chain Reaction - methods; RNA, Viral - analysis; RNA, Viral - genetics; Sample preparation; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity analysis; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Sewage - virology; Software; Target detection; Thermal cycling; Viral diseases; Wastewater; Wastewater - virology; Water sampling
• ISSN: 1477-8920; 1996-7829
• DOI: 10.2166/wh.2024.085

The COVID-19 pandemic initiated public interest in wastewater-based epidemiology (WBE). Public and private entities responded to the need to produce timely and accurate data. LuminUltra and Hach partnered to provide a rapid, field-based quantitative polymerase chain reaction (qPCR) test for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. This study evaluates the Hach GeneCount SARS-CoV-2 Wastewater RT-qPCR Assay Kit and LuminUltra GeneCount Q-16 RT-PCR instrument. The Hach LuminUltra methods were compared to the Promega Wizard Enviro Total Nucleic Acid kit and Bio-Rad CFX Opus 96 Real-time PCR Detection System. Over a 12-week period, wastewater samples were collected weekly from seven locations in the Roanoke/Salem, VA sewersheds. Concentration and extraction of the viral RNA were followed by qPCR analysis. The target gene for detection was the nucleocapsid gene (N1) of the SARS-CoV-2 virus. Costs, ease of use, time to produce results, sample preparation, and data comparisons were considered. The comparison determined that the Hach LuminUltra method and instrument were more affordable, consumed less time, and required less technical expertise. While the new method was specific, it had low sensitivity. This evaluation suggests the Hach LuminUltra method should be reserved for limited situations requiring onsite field analysis where data accuracy is not essential.