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Development and Validation of the Skimmed Milk Pellet Extraction Protocol for SARS-CoV-2 Wastewater Surveillance
Food and Environmental Virology ( IF 3.4 ) Pub Date : 2022-02-10 , DOI: 10.1007/s12560-022-09512-5
Sarah E Philo 1 , Angelo Q W Ong 1 , Erika K Keim 1 , Rachael Swanstrom 1 , Alexandra L Kossik 1 , Nicolette A Zhou 1 , Nicola K Beck 1 , John Scott Meschke 1
Affiliation  

Wastewater surveillance for SARS-CoV-2 may serve as a useful source of data for public health departments as the virus is shed in the stool of infected individuals. However, for wastewater data to be actionable, wastewater must be collected, concentrated, and analyzed in a timely manner. This manuscript presents modifications on a skimmed milk concentration protocol to reduce processing time, increase the number of samples that can be processed at once, and enable use in resource-limited settings. Wastewater seeded with Human coronavirus OC43 (OC43) was concentrated using a skimmed milk flocculation protocol, and then pellets were directly extracted with the QIAamp Viral RNA Mini kit. This protocol has a higher average effective volume assayed (6.35 mL) than skimmed milk concentration methods, with and without Vertrel XF™, which involve resuspension of the pellets in PBS extraction prior to nucleic acid extraction (1.28 mL, 1.44 mL, respectively). OC43 was selected as a recovery control organism because both it and SARS-CoV-2 are enveloped respiratory viruses that primarily infect humans resulting in respiratory symptoms. The OC43 percent recovery for the direct extraction protocol (3.4%) is comparable to that of skimmed milk concentration with and without Vertrel XF™ extraction (4.0%, 2.6%, respectively). When comparing SARS-CoV-2 detection using McNemar’s chi-square test, the pellet extraction method is not statistically different from skimmed milk concentration, with and without Vertrel XF™ extraction. This suggests that the method performs equally as well as existing methods. Added benefits include reduced time spent per sample and the ability to process more samples at a single time. Direct extraction of skimmed milk pellets is a viable method for quick turnaround of wastewater data for public health interventions.



中文翻译:

用于 SARS-CoV-2 废水监测的脱脂牛奶颗粒提取方案的开发和验证

SARS-CoV-2 的废水监测可作为公共卫生部门的有用数据来源,因为该病毒会散布在受感染者的粪便中。然而,要使废水数据具有可操作性,必须及时收集、浓缩和分析废水。本手稿介绍了对脱脂牛奶浓缩方案的修改,以减少处理时间,增加可一次处理的样品数量,并能够在资源有限的环境中使用。使用脱脂牛奶絮凝方案浓缩接种了人类冠状病毒 OC43 (OC43) 的废水,然后使用 QIAamp Viral RNA Mini 试剂盒直接提取沉淀。该方案的平均有效体积测定值 (6.35 mL) 高于脱脂牛奶浓缩方法,无论是否使用 Vertrel XF™,这涉及在核酸提取之前在 PBS 提取中重新悬浮颗粒(分别为 1.28 mL、1.44 mL)。OC43 被选为恢复控制生物体,因为它和 SARS-CoV-2 都是包膜呼吸道病毒,主要感染人类,导致呼吸道症状。直接提取方案的 OC43 百分比回收率 (3.4%) 与使用和不使用 Vertrel XF™ 提取的脱脂牛奶浓度(分别为 4.0%、2.6%)相当。在使用 McNemar 卡方检验比较 SARS-CoV-2 检测时,无论是否使用 Vertrel XF™ 提取,颗粒提取方法与脱脂牛奶浓度在统计学上没有差异。这表明该方法的性能与现有方法一样好。额外的好处包括减少每个样本花费的时间以及一次处理更多样本的能力。直接提取脱脂牛奶颗粒是一种快速周转废水数据以进行公共卫生干预的可行方法。

更新日期:2022-02-10
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