Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE)

Abstract

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical RSV surveillance and the lack of predictable RSV seasonal dynamics and limits the public health response. Wastewater-based epidemiology (WBE) has the capacity to determine levels of health-associated biomarkers and has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community. However, the application of genomic WBE for the surveillance of other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, using RT-qPCR and partial sequencing of the G gene to monitor RSV levels and variants in the community across 2 years encompassing two periods of high RSV clinical positivity in Northern Ireland. We report increasing detection of RSV in wastewater concomitant with increasing numbers of RSV positive clinical cases. Furthermore, analysis of wastewater-derived RSV sequences permitted subtyping, genotyping, and identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance efforts and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

“…The representative identification of SARS-CoV-2 lineages in wastewater provides a foundation for applying similar genomic techniques to characterize other pathogens present in wastewater, as has been recently demonstrated for polioviruses [15], RSV [37], and influenza [38]. This methodological approach not only reinforces the utility of WBE for SARS-CoV-2 surveillance but also underscores its potential for broader pathogen detection and characterization [39], offering a scalable and non-invasive tool for public health monitoring and response planning.…”

Spatial and temporal variation in respiratory syncytial virus (RSV) subtype RNA in wastewater, and relation to clinical specimens

“…Wastewater has recently emerged as a tool for monitoring the disease levels of a community contributing to it, as concentrations of viral genetic material in wastewater have been shown to correlate with positivity rates or clinical case rates for a number of different viruses [24][25][26][27] . Several studies have measured RSV RNA wastewater concentrations 25,[28][29][30][31][32][33][34][35] , with only three of them measuring RSV subtypes using PCR-methods 25,29,30 , and one using a sequence-based methods 32 . Overall, there is limited research investigating the variability of RSV subtype predominance in wastewater.…”

Spatial and temporal variation in respiratory syncytial virus (RSV) subtype RNA in wastewater and relation to clinical specimens

“…Wastewater has recently emerged as a tool for monitoring the disease levels of a community contributing to it, as concentrations of viral genetic material in wastewater have been shown to correlate with positivity rates or clinical case rates for a number of different viruses ( 24 – 27 ). Several studies have measured RSV RNA wastewater concentrations ( 25 , 28 – 35 ), with only three of them measuring RSV subtypes using PCR methods ( 25 , 29 , 30 ) and one using sequence-based methods ( 32 ). Overall, there is limited research investigating the variability of RSV subtype predominance in wastewater.…”