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Journal Article Ppublish 28 citations

PubMed: 35679788 DOI: 10.1016/j.watres.2022.118686

Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance.

Water Res 220:118686

Authors: Xiaoqing Xu, Yu Deng, Jiahui Ding, Xiawan Zheng, Shuxian Li, Lei Liu, Ho-Kwong Chui, Leo L M Poon, Tong Zhang

Affiliations

  • Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
  • Environmental Protection Department, The Government of Hong Kong SAR, Tamar, Hong Kong SAR, China.
  • School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China.
  • Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.

Abstract

To effectively control the ongoing outbreaks of fast-spreading SARS-CoV-2 variants, there is an urgent need to add rapid variant detection and discrimination methods to the existing sewage surveillance systems established worldwide. We designed eight assays based on allele-specific RT-qPCR for real-time allelic discrimination of eight SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Omicron, Lambda, Mu, and Kappa) in sewage. In silico analysis of the designed assays for identifying SARS-CoV-2 variants using more than four million SARS-CoV-2 variant sequences yielded ∼100% specificity and >90% sensitivity. All assays could sensitively discriminate and quantify target variants at levels as low as 10 viral RNA copy/µL with minimal cross-reactivity to the corresponding nontarget genotypes, even for sewage samples containing mixtures of SARS-CoV-2 variants with differential abundances. Integration of this method into the routine sewage surveillance in Hong Kong successfully identified the Beta variant in a community sewage. Complete concordance was observed between the results of viral whole-genome sequencing and those of our novel assays in sewage samples that contained exclusively the Delta variant discharged by a clinically diagnosed COVID-19 patient living in a quarantine hotel. Our assays in this method also provided real-time discrimination of the newly emerging Omicron variant in sewage two days prior to clinical test results in another quarantine hotel in Hong Kong. These novel allelic discrimination assays offer a rapid, sensitive, and specific way for detecting multiple SARS-CoV-2 variants in sewage and can be directly integrated into the existing sewage surveillance systems.

MeSH

Sars-Cov-2, Water Pollution, Sewage, Quarantine, Severe Acute Respiratory Syndrome-Related Coronavirus

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