Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage

• DOI: 10.1016/j.scitotenv.2022.161101
• Publication Date: 2022-12-27T00:34:08Z
• Authors: Gyuhyon Cha; Katherine E. Graham; Kevin J. Zhu; Gouthami Rao; Blake G. Lindner; Kumru Kocaman; Seongwook Woo; Isabelle D'amico; Lilia R. Bingham; Jamie M. Fischer; Camryn I. Flores; John W. Spencer; Pranav Yathiraj; Hayong Chung; Shweta Biliya; Naima Djeddar; Liza J. Burton; Samantha J. Mascuch; Joe Brown; Anton Bryksin; Ameet Pinto; Janet K. Hatt; Konstantinos T. K...
• Keywords: 0301 basic medicine; Feces; 03 medical and health sciences; Sewage; SARS-CoV-2; Humans; COVID-19; Pandemics; Article; 6. Clean water; 3. Good health

Wastewater-based epidemiology during the COVID-19 pandemic has proven useful for public health decision-making but is often hampered by sampling methodology constraints, particularly at the building- or neighborhood-level. Time-weighted composite samples are commonly used; however, autosamplers are expensive and can be affected by intermittent flows in sub-sewershed contexts. In this study, we compared time-weighted composite, grab, and passive sampling via Moore swabs, at four locations across a college campus to understand the utility of passive sampling. After optimizing the methods for sample handling and processing for viral RNA extraction, we quantified SARS-CoV-2 N1 and N2, as well as a fecal strength indicator, PMMoV, by ddRT-PCR and applied tiled amplicon sequencing of the SARS-CoV-2 genome. Passive samples compared favorably with composite samples in our study area: for samples collected concurrently, 42 % of the samples agreed between Moore swab and composite samples and 58 % of the samples were positive for SARS-CoV-2 using Moore swabs while composite samples were below the limit of detection. Variant profiles from Moore swabs showed a shift from variant BA.1 to BA.2, consistent with in-person saliva samples. These data have implications for the broader implementation of sewage surveillance without advanced sampling technologies and for the utilization of passive sampling approaches for other emerging pathogens.