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 could 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 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.

Evaluation of the impact of concentration and extraction methods on the targeted sequencing of human viruses from wastewater

“…This differentiation was observed consistently across all four methods. These temporal shifts in virus composition may suggest a temporally variable metavirome composition in wastewater, potentially influenced by changes in circulating viruses 8, 48, 49 and changing wastewater conditions, such as flow rate, total suspended solids (TSS), total organic compounds (TOC), and the abundance of antagonistic microorganisms 50, 51 .…”

“…Finally, the choice of probe panel likely also impacts the sensitivity of virus detection in probe-capture sequencing. When using the RVOP probe set (which contains fewer virus targets than the VSP probe set) several studies found remarkably high coverages of SARS-CoV-2, surpassing that of other human viruses included in the RVOP panel 14, 15, 49 . However, in the present study and other studies using broad virus capture panels 23, 48 , sequence data were dominated by enteric viruses such as mamastrovirus, with limited detection of SARS-CoV-2.…”

“…This differentiation was observed consistently across all four methods. These tempora shifts in virus composition may suggest a temporally variable metavirome composition in wastewater, potentially influenced by changes in circulating viruses 8,48,49 and changing wastewater conditions, such as flow rate, total suspended solids (TSS), total organic compounds (TOC), and the abundance of antagonistic microorganisms 50,51 . 3.3 Human virus species richness and composition PMG and IP methods yielded higher species-level richness of total viruses detected with >10 reads (241 and 176 viruses, respectively) and human viruses (20 and 26 respectively) compared to NT and Solids (Figure S3a), although total read depth was similar for all samples (Figure 1b, p = 0.44).…”

Tomato Brown Rugose Fruit Virus (ToBRFV): A Better Indicator of Viral Load and Treatment Efficacy of Wastewater Treatment.

“…This study included 7 local sub-sewershed and 3 WRF sites, ranging from the Southern Truckee Meadows region to the Northern Reno-Stead region. 13,14 Collectively, these sites represent in uent from over 450,000 residents. The largest sample site is the Truckee Meadows WRF (TMWRF).…”

Detección de variantes del SARS-CoV-2 en aguas residuales de hospitales en Perú, 2022

“…De forma complementaria a la detección clínica, la vigilancia ambiental de los virus, especialmente los relacionados con la viabilidad y la potencial infectividad como el SARS-CoV-2, podría actuar como una herramienta útil para predecir brotes oportunos de enfermedades y emitir una alerta rápida por parte de las autoridades sanitarias (12,13) . En ese sentido, las muestras de aguas residuales son una fuente de información no invasiva y económica para investigar la propagación de diferentes variantes genéticas del SARS-CoV-2 dentro de una comunidad (14,15) . La secuenciación masiva y el análisis metagenómico nos permitirían detectar el virus e identificar las variantes circulantes del SARS CoV-2 al mismo tiempo.…”