Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater

Abstract

<jats:p>SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 52-day time course. We show that changes in SARS-CoV-2 RNA concentrations correlate with local COVID-19 epidemiological data (R2=0.9), though detection in wastewater trails symptom onset dates by 5-8 days. We determine a near-complete (98.5%) SARS-CoV-2 genome sequence from the wastewater and use phylogenic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for high-resolution genotyping of the predominant strains circulating in a community.</jats:p>

Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds

“…These results suggest that the increase in case counts may occur concurrently with or even precede the increase in SARS-CoV-2 RNA in wastewater, while the decline in SARS-CoV-2 RNA in wastewater may lag the decline in case counts. This temporal variation in RNA in wastewater versus case counts has been suggested by others 24,25,28,34 . Further, the long term shedding of the SARS-CoV-2 after negative nasopharyngeal swabs may account for the detection of RNA in wastewater after the decline in case counts 35 .…”

“…Three wastewater treatment plants (WWTPs) in France were sampled over a 7-week period and reported data that correlated with the country's nationwide lockdown 24 . Attempts to detect SARS-CoV-2 RNA in wastewater were also successful in Italy 25,26 , the Netherlands 27 and the United States 28,29 , and in some cases were shown to correlate with COVID-19 case counts. The maximum SARS-CoV-2 RNA concentrations reported in wastewater influent ranged from 1.2x10 3 to 3.2x10 6 gene copies/L in wastewater influent 23,24,25,26,28,29 .…”

Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing

“…viral RNA yield for sequencing 29 animals such rabbits, minks, cats and ferrets [31][32][33][34][35] . The analysis of a consensus sequence genome from a wastewater sample may identify the predominant virus strain present in a population, which might be suitable for locations where only 1 or few introductions of closely related viruses have occurred, as it seems to be the case for 2 previous studies in Italy and USA 23,24 . Nonetheless, the consensus genome approach cannot reflect the diversity of the viruses circulating in a population with a high degree of viral diversity.…”

Highly predictive regression model of active cases of COVID-19 in a population by screening wastewater viral load

“…Previous studies have evaluated the presence in wastewater of several viruses [41][42][43][44][45] . Processes to monitor SARS-CoV-2 in wastewater were first developed in the Netherlands 35 , followed by the USA 46 , France 39 , Australia 36 , Italy 47 and Spain 37,48 . In the Netherlands, no viral RNA was detected 3 weeks before the first case was reported, but genetic material started to appear over time, as the number of cases of COVID-19 increased 35 .…”

“…In the present work, nonparametric and even simple parametric regression models have been shown to be useful tools to construct prediction models for the real number of COVID-19 active cases as a function of the viral load. This is a pioneering approach in the context of the SARS-CoV-2 pandemic since, to our knowledge, WBE studies available are still limited to reporting the occurrence of SARS-CoV-2 RNA in WWTPs and sewer networks, in order to establish a direct comparison with declared COVID-19 cases35,37,[46][47][48] . The only precedent52 combines computational analysis and modelling with a theoretical approach in order to identify useful variables and confirm the feasibility and cost-effectiveness of WBE as a prediction tool.…”