Significance of Wastewater Surveillance in Detecting the Prevalence of SARS-CoV-2 Variants and Other Respiratory Viruses in the Community – A Multi-Site Evaluation

ABSTRACT Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2’s broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring. HIGHLIGHTS/KEY FINDINGS WBE better represents regional virus prevalence under declining testing and clinical reporting rates. SARS-CoV-2 virus was present throughout the year compared to a seasonal prevalence of other respiratory viral pathogens. SARS-CoV-2 variant monitoring via WBE can provide insights into regionally co-circulating respiratory viruses, causing flu-like symptoms. WBE-AMR gene monitoring is feasible and provides valuable insight into regional AMRs. Our workflow enables the estimation of the relative proportion of different variants in any pooled samples. GRAPHICAL ABSTRACT