Wilder Maxwell L, Middleton Frank, Larsen David A, Du Qian, Fenty Ariana, Zeng Teng, Insaf Tabassum, Kilaru Pruthvi, Collins Mary, Kmush Brittany, Green Hyatt C
Department of Environmental and Forest Biology, SUNY-ESF, Syracuse, NY 13210.
Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY 13210.
Water Res X. 2021 May 1;11:100100. doi: 10.1016/j.wroa.2021.100100. Epub 2021 Apr 6.
Wastewater surveillance of SARS-CoV-2 RNA is increasingly being incorporated into public health efforts to respond to the COVID-19 pandemic. In order to obtain the maximum benefit from these efforts, approaches to wastewater monitoring need to be rapid, sensitive, and relatable to relevant epidemiological parameters. In this study, we present an ultracentrifugation-based method for the concentration of SARS-CoV-2 wastewater RNA and use crAssphage, a bacteriophage specific to the human gut, to help account for RNA loss during transit in the wastewater system and sample processing. With these methods, we were able to detect, and sometimes quantify, SARS-CoV-2 RNA from 20 mL wastewater samples within as little as 4.5 hours. Using known concentrations of bovine coronavirus RNA and deactivated SARS-CoV-2, we estimate recovery rates of approximately 7-12% of viral RNA using our method. Results from 24 sewersheds across Upstate New York during the spring and summer of 2020 suggested that stronger signals of SARS-CoV-2 RNA from wastewater may be indicative of greater COVID-19 incidence in the represented service area approximately one week in advance. SARS-CoV-2 wastewater RNA was quantifiable in some service areas with daily positives tests of less than 1 per 10,000 people or when weekly positive test rates within a sewershed were as low as 1.7%. crAssphage DNA concentrations were significantly lower during periods of high flow in almost all areas studied. After accounting for flow rate and population served, crAssphage levels per capita were estimated to be about 1.35 × 10 and 2.42 × 10 genome copies per day for DNA and RNA, respectively. A negative relationship between per capita crAssphage RNA and service area size was also observed likely reflecting degradation of RNA over long transit times. Our results reinforce the potential for wastewater surveillance to be used as a tool to supplement understanding of infectious disease transmission obtained by traditional testing and highlight the potential for crAssphage co-detection to improve interpretations of wastewater surveillance data.
对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）RNA的废水监测正越来越多地纳入应对2019冠状病毒病（COVID-19）大流行的公共卫生工作中。为了从这些工作中获得最大收益，废水监测方法需要快速、灵敏，并且与相关流行病学参数相关。在本研究中，我们提出了一种基于超速离心的方法来浓缩SARS-CoV-2废水RNA，并使用人肠道特异性噬菌体crAssphage来帮助解释废水系统运输和样品处理过程中的RNA损失。通过这些方法，我们能够在短短4.5小时内从20毫升废水样本中检测到，有时还能定量检测到SARS-CoV-2 RNA。使用已知浓度的牛冠状病毒RNA和灭活的SARS-CoV-2，我们估计使用我们的方法病毒RNA的回收率约为7%-12%。2020年春夏期间纽约州北部24个排水区域的结果表明，废水中SARS-CoV-2 RNA的更强信号可能提前约一周表明所代表的服务区中COVID-19发病率更高。在一些服务区，当每日阳性检测率低于万分之一或排水区域内每周阳性检测率低至1.7%时，SARS-CoV-2废水RNA是可定量的。在几乎所有研究区域，高流量期间crAssphage DNA浓度显著降低。在考虑流速和服务人口后，估计人均crAssphage水平，DNA和RNA分别约为每天1.35×10和2.42×10基因组拷贝。还观察到人均crAssphage RNA与服务区面积之间呈负相关，这可能反映了RNA在长时间运输过程中的降解。我们的结果强化了废水监测作为一种工具来补充通过传统检测获得的对传染病传播理解的潜力，并突出了crAssphage共同检测改善废水监测数据解释的潜力。
