Detection of SARS-CoV-2 in Wastewater: Community Variability, Temporal Dynamics, and Genotype Diversity

Abstract

A systematic investigation of SARS-CoV-2 genome concentrations in nine Southern California wastewater treatment plants (WWTPs) was carried out. The goal was to compare the variability of the viral concentration among different WWTPs that serve different communities and to correlate the concentration of virus in wastewater with the community level COVID-19 epidemic. The results showed that there were significant differences in viral concentration detected in different plants. However, the variability of SARS-CoV-2 concentration cannot easily be explained by the COVID-19 case reports because a large number of sewer-shed characteristics have important influences on the quantifiable viral concentration in the sewage samples. The results from year-long tracking of SARS-CoV-2 concentration in two large WWTPs, however, matched fairly well with the county level COVID-19 case reports. This suggests continuous monitoring of SARS-CoV-2 in the same treatment plant can offer insights into community level trends of COVID-19 and can serve as an alert for a possible resurgence of the disease. Amplicon-based sequencing targeting two SARS-CoV-2 single nucleotide polymorphism (SNP) mutations was shown as a proof-of-concept for identifying SARS-CoV-2 variants in wastewater. The outcomes of this research contribute to the advancement of wastewater-based epidemiology for COVID-19 and other infectious diseases.

Relationships between SARS-CoV-2 in Wastewater and COVID-19 Clinical Cases and Hospitalizations, with and without Normalization against Indicators of Human Waste

“…Community-based clinical COVID case surveillance is the global standard for evaluating the state of the pandemic. − However, clinical data has its limitations, which include restricted clinical testing capacity and access to testing . The efficacy of clinical tracking has been diminished due to widespread vaccinations against COVID-19 resulting in more asymptomatic or mild cases for which individuals will not seek testing. ,, In contrast, wastewater-based epidemiology (WBE), also known as wastewater surveillance, has been shown to be a useful tool to predict potential outbreaks. − In addition to saliva and nasal discharges, studies have shown that the RNA of the virus that causes COVID-19, SARS-CoV-2, can be found in feces and urine of both symptomatic and asymptomatic individuals. − This phenomenon is like with other viruses, such as poliovirusone of the initial focuses of WBE. − Studies have shown that RNA within excreted SARS-CoV-2 viral particles can be reliably detected after sample collection and processing. , A study in Brisbane indicated that wastewater SARS-CoV-2 RNA detection could predict COVID-19 outbreaks about a week before it was observed in clinical records . This forewarning can be used to initiate mitigation measures earlier to minimize disease transmission and to prepare communities for increases in hospitalization rates.…”

“… 3 , 5 , 6 In contrast, wastewater-based epidemiology (WBE), also known as wastewater surveillance, has been shown to be a useful tool to predict potential outbreaks. 7 − 15 In addition to saliva and nasal discharges, studies have shown that the RNA of the virus that causes COVID-19, SARS-CoV-2, can be found in feces and urine of both symptomatic and asymptomatic individuals. 13 − 17 This phenomenon is like with other viruses, such as poliovirus—one of the initial focuses of WBE.…”

RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern

“… 1 − 6 SARS-CoV-2 WS is a promising tool for early warning, trending, and predicting outbreaks and detecting major circulating lineages in sewersheds. 7 − 14 Accurate and precise quantification of viral RNA loads in wastewater is critical for the generation of reliable information to help decision-making in public health. Until now, there have been no standardized protocols available for SARS-COV-2 WS.…”

“…Wastewater surveillance (WS) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has been applied globally to complement traditional clinical testing of individuals. − SARS-CoV-2 WS is a promising tool for early warning, trending, and predicting outbreaks and detecting major circulating lineages in sewersheds. − Accurate and precise quantification of viral RNA loads in wastewater is critical for the generation of reliable information to help decision-making in public health. Until now, there have been no standardized protocols available for SARS-COV-2 WS …”

Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification

“…Since the start of the COVID-19 outbreak in December of 2019, there was a quick response for developing human health surveillance and wastewater-based surveillance (WBS) processes. [1], [2],[3], [4], [5], [6], [7], [8], [9] Collected wastewater has a unique capability of assimilating human health markers of the specific community contributing to a sampling point. [3], [10] For severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), WBS has been pivotal to addressing its impact on communities worldwide, with its correlative power for clinical cases and hospitalizations [4], [6], [7],[9], [11], [12],[13],[14], [15], [16] as well as for realizing SARS-CoV-2's evolution with emerging variants.…”