Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests

• Published in: Environmental science & technology 2022-06, Vol.56 (12), p.8875-8884
• Main Authors: Xu, Xiaoqing, Deng, Yu, Zheng, Xiawan, Li, Shuxian, Ding, Jiahui, Yang, Yu, On, Hei Yin, Yang, Rong, Chui, Ho-Kwong, Yau, Chung In, Tun, Hein Min, Chin, Alex W. H., Poon, Leo L. M., Peiris, Malik, Leung, Gabriel M., Zhang, Tong
• Format: Article
• Language: English
• Subjects: Clinical trials; Coronaviruses; COVID-19; Health surveillance; Pandemics; Performance evaluation; Public health; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Sewage; Surveillance; Treatment and Resource Recovery; Viral diseases
• ISSN: 0013-936X; 1520-5851
• DOI: 10.1021/acs.est.2c00974

Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per μL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2–10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.