Wastewater-based SARS-CoV-2 surveillance and sequencing

Abstract

Though most often associated with poliovirus surveillance, wastewater-based surveillance (WBS) can be employed for viruses shed in human excreta (faeces, urine, skin, sputum, blood) that may enter the wastewater system, including SARS-CoV-2. WBS has been widely adopted during the COVID-19 pandemic, to complement clinical surveillance in monitoring community burden and implementing timely public health interventions. As wastewater is a non-biased, composite sample, it can provide population-level health information in near real-time, in a cost-effective manner compared to similarly scaled clinical surveillance. In many instances, data gathered from wastewater, including viral loads (quantified by RT-qPCR) and variant detections (determined through partial or whole genome sequencing), have been predictive of what is observed eventually in clinical cases. Newly emergent lineages, including the recent BA.2.86 variant, can and have been detected in wastewater samples prior to their detection in clinical specimens. There remain many challenges to wastewater genomic analysis including the presence of RT-qPCR inhibitors, degraded nucleic acid and the lack of consistent or standardised methodology between reporting labs. The wide adoption of WBS practices provides an excellent opportunity to expand this method for surveillance of other pathogens of public health importance. Herein, a broad overview of the WBS field will be provided including discussion on its advantages and applications, challenges, and how it is being utilised to characterise circulating SARS-CoV-2 lineages through sequencing.