Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations

SARS-CoV-2 is a new type of coronavirus that is capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing enormous impacts across the whole Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in urine and feces samples. Thus, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a tool to monitor the virus spread in the communities. The surveillance, frequently used to elaborate economical non-invasive diagnoses about the circulation of chemicals and pollutants in populations, could be used as a quick alert about emerging and reemerging COVID-19 epidemics, improve the predictions concerning the SARS-CoV-2 dissemination and promote the development of better viral containment measures. Along that, the approach could be used to construct more accurately epidemiological models, foment better practices to coordinate resources an administer the vaccines, assess the propagation of SARS-CoV-2 variants across temporal and geographic scales, evaluate environmental risks and also the effectiveness of disinfection systems. In this review, it was addressed early reports regarding SARS-CoV-2 detections in wastewater and the importance of this valuable approach in the application of faster and more effective interventions from public health authorities, either towards the COVID-19 or any other epidemic disease in the future.

Laboratory-based wastewater surveillance for SARS-CoV-2, the causative agent of the ongoing COVD-19 pandemic, can be conducted using RT-qPCR-based screening of municipal wastewater samples. Although it provides rapid viral detection and can inform SARS-CoV-2 abundance in wastewater, this approach lacks the resolution required for viral genotyping and does not support tracking of viral genome evolution. The recent emergence of several variants of concern, a result of mutations across the genome including the accrual of important mutations within the viral spike glycoprotein, has highlighted the need for a method capable of detecting the cohort of mutations associated with these and newly emerging genotypes. Here we provide an innovative methodology for the recovery of a near-complete SARS-CoV-2 sequence from a wastewater sample collected from across Canadian municipalities including one that experienced a significant outbreak attributable to the SARS-CoV-2 B.1.1.7 variant of concern. Our results demonstrate that a combined interrogation of genome consensus-level sequences and alternative alleles enables the identification of a SARS-CoV-2 variant of concern and the detection of a new allele within a viral accessory gene that may be representative of a recently evolved B.1.1.7 sublineage.

Wastewater-based epidemiology (WBE) is expected to become a powerful tool to monitor the dissemination of SARS-CoV-2 at the community level, which has attracted the attention of scholars all over the world. However, there is not yet a standard protocol to guide its implementation. In this paper, we proposed a comprehensive technical and theoretical framework of relative quantification via qPCR for determining the virus abundance in wastewater and estimating the infection ratio in corresponding communities, which is expected to achieve horizontal and vertical comparability of the data using a human-specific biomarker as the internal reference. Critical factors affecting the virus detectability and the estimation of infection ratio include virus concentration methods, lag-period, per capita virus shedding amount, sewage generation rate, temperature-related decay kinetics of virus/biomarker in wastewater, and hydraulic retention time (HRT), etc. Theoretical simulation shows that the main factors affecting the detectability of virus in sewage are per capita virus shedding amount and sewage generation rate. While the decay of SARS-CoV-2 RNA in sewage is a relatively slow process, which may have limited impact on its detection. Under the ideal condition of high per capita virus shedding amount and low sewage generation rate, it is expected to detect a single infected person within 400,000 people.