Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 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, China.
Sci Total Environ. 2023 Dec 15;904:166300. doi: 10.1016/j.scitotenv.2023.166300. Epub 2023 Aug 15.
Sewage surveillance has proven to be an essential complementary tool to clinical diagnosis in combating the COVID-19 pandemic by tracking the spread of the SARS-CoV-2 virus and evaluating infection levels in populations. With the striking spreading and continuous evolution of SARS-CoV-2 Omicron VOC that characterized with higher transmissibility and potential immune evasion, there is an urgent need for the rapid surveillance of this prevalent strain and its sub-lineages in sewage. In this study, based on three multiplex allele-specific (AS) RT-qPCR assays, we established a rapid and high-throughput detection workflow for the simultaneous discrimination of Omicron sub-lineages BA.2.2, BA.2.12.1, BA.4 and BA.5 (hereafter referred to as BA.4/BA.5) to track their community circulation in Hong Kong. All primer-probe sets in the multiplex assays could correctly discriminate and quantitate their target genotypes with high sensitivity and specificity, even when multiple variants co-existed in the sewage samples. Using the established multiplex assays, the trends of SARS-CoV-2 total viral load and variant dynamics in influent samples collected from 11 wastewater treatment plants (WWTPs) during June 2022 and September 2022, aligned with the clinical data, successfully unveiling the swift emergence and predominance of Omicron BA.4/BA.5 in Hong Kong. The study highlights the feasibility and applicability of multiplex RT-qPCR assays for monitoring epidemic trends and tracking variant displacement dynamics in sewage samples, providing a more rapid, high-throughput and cost-effective alternative to enhance the current sewage surveillance system.
污水监测已被证明是对抗 COVID-19 大流行的临床诊断的重要补充手段，通过追踪 SARS-CoV-2 病毒的传播和评估人群中的感染水平。随着 SARS-CoV-2 奥密克戎变异株的惊人传播和持续进化，其具有更高的传染性和潜在的免疫逃避能力，因此迫切需要对这种流行株及其在污水中的亚系进行快速监测。在这项研究中，我们基于三种多重等位基因特异性（AS）RT-qPCR 检测方法，建立了一种快速高通量的检测工作流程，用于同时区分奥密克戎亚系 BA.2.2、BA.2.12.1、BA.4 和 BA.5（以下简称 BA.4/BA.5），以追踪它们在香港的社区传播。多重检测中的所有引物探针组都可以正确区分和定量其目标基因型，具有高灵敏度和特异性，即使在污水样本中存在多种变体时也是如此。使用建立的多重检测方法，从 2022 年 6 月和 2022 年 9 月收集的 11 个污水处理厂（WWTP）的进水样本中，SARS-CoV-2 总病毒载量和变异动态的趋势与临床数据一致，成功揭示了奥密克戎 BA.4/BA.5 在香港的迅速出现和主导地位。该研究强调了多重 RT-qPCR 检测方法在监测污水样本中流行趋势和追踪变异替代动态方面的可行性和适用性，为增强当前污水监测系统提供了一种更快速、高通量和具有成本效益的替代方法。
