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

Highlights

• Passive sampling for SARS-CoV-2 sewage surveillance has advantages and limitations relative to composite sampling approaches.

• We conducted a wastewater sampling campaign on a college campus utilizing passive (Moore swab), composite, and grab sampling and directly compared three using ddRT-PCR and tiled amplicon sequencing.

• Moore swabs were the most sensitive of the sampling approaches and were accurate in identifying a shift in viral variants, confirmed by individual saliva testing.

• These findings reveal that Moore swabs can provide robust information for wastewater-based epidemiology (WBE) within small, campus-like communities.

Abstract

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.