Lott Megan E J, Norfolk William A, Dailey Cody A, Foley Amelia M, Melendez-Declet Carolina, Robertson Megan J, Rathbun Stephen L, Lipp Erin K
Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States.
Department of Epidemiology and Biostatistics, University of Georgia, 101 Buck Road, Athens, GA 30606, United States.
FEMS Microbes. 2023 Jan 12;4:xtad004. doi: 10.1093/femsmc/xtad004. eCollection 2023.
Wastewater surveillance has proven to be an effective tool to monitor the transmission and emergence of infectious agents at a community scale. Workflows for wastewater surveillance generally rely on concentration steps to increase the probability of detection of low-abundance targets, but preconcentration can substantially increase the time and cost of analyses while also introducing additional loss of target during processing. To address some of these issues, we conducted a longitudinal study implementing a simplified workflow for SARS-CoV-2 detection from wastewater, using a direct column-based extraction approach. Composite influent wastewater samples were collected weekly for 1 year between June 2020 and June 2021 in Athens-Clarke County, Georgia, USA. Bypassing any concentration step, low volumes (280 µl) of influent wastewater were extracted using a commercial kit, and immediately analyzed by RT-qPCR for the SARS-CoV-2 N1 and N2 gene targets. SARS-CoV-2 viral RNA was detected in 76% (193/254) of influent samples, and the recovery of the surrogate bovine coronavirus was 42% (IQR: 28%, 59%). N1 and N2 assay positivity, viral concentration, and flow-adjusted daily viral load correlated significantly with per-capita case reports of COVID-19 at the county-level (ρ = 0.69-0.82). To compensate for the method's high limit of detection (approximately 10-10 copies l in wastewater), we extracted multiple small-volume replicates of each wastewater sample. With this approach, we detected as few as five cases of COVID-19 per 100 000 individuals. These results indicate that a direct-extraction-based workflow for SARS-CoV-2 wastewater surveillance can provide informative and actionable results.
废水监测已被证明是在社区层面监测传染病原体传播和出现的有效工具。废水监测工作流程通常依赖浓缩步骤来提高低丰度目标物的检测概率，但预浓缩会大幅增加分析时间和成本，同时在处理过程中还会导致目标物额外损失。为解决其中一些问题，我们开展了一项纵向研究，采用基于柱的直接提取方法，实施了一种简化的从废水中检测严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的工作流程。2020年6月至2021年6月期间，在美国佐治亚州雅典-克拉克县每周采集混合进水废水样本，为期1年。绕过任何浓缩步骤，使用商业试剂盒提取少量（280微升）进水废水，并立即通过逆转录定量聚合酶链反应（RT-qPCR）分析SARS-CoV-2 N1和N2基因靶点。在76%（193/254）的进水样本中检测到了SARS-CoV-2病毒RNA，替代牛冠状病毒的回收率为42%（四分位距：28%，59%）。N1和N2检测阳性率、病毒浓度以及流量调整后的每日病毒载量与县级COVID-19的人均病例报告显著相关（ρ = 0.69 - 0.82）。为弥补该方法较高的检测限（废水中约为10-10拷贝/升），我们对每个废水样本提取多个小体积重复样本。通过这种方法，我们检测到每10万人中低至5例COVID-19病例。这些结果表明，基于直接提取的SARS-CoV-2废水监测工作流程能够提供信息丰富且可采取行动的结果。
