Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states
TL;DR: This work describes a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states from February 18 to June 2, 2020, and finds that a national wastewater-based approach to disease surveillance may be feasible and effective.
Abstract: Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.
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Commonwealth Scientific and Industrial Research Organisation1, University of Notre Dame2, University of Melbourne3, University of Barcelona4, Instituto Nacional de Saúde Dr. Ricardo Jorge5, University of Queensland6, Queensland Health7, University of North Carolina at Chapel Hill8, University of South Australia9, Michigan State University10, University of Health Sciences Antigua11, Vienna University of Technology12, Southern Nevada Water Authority13, Southern California Coastal Water Research Project14, Drexel University15, Arizona State University16, National Environment Agency17, University of South Florida18, International Centre for Diarrhoeal Disease Research, Bangladesh19, University of New South Wales20, Stellenbosch University21, Hokkaido University22, United States Environmental Protection Agency23, Istituto Superiore di Sanità24, University of Georgia25, University of Wisconsin–Milwaukee26, University College Dublin27, University of Guelph28, University of California, Merced29, Griffith University30, National Institute for Health and Welfare31, University of Helsinki32, National University of Salta33, Spanish National Research Council34, Tulane University35, Chulabhorn Research Institute36, National University of Singapore37, Tohoku University38, Nanyang Technological University39, University of Minnesota40
TL;DR: A technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors.
116 citations
Cites background from "Wastewater Surveillance of SARS-CoV..."
...…in many states within the United States still exceeded 5% in early 2021 (CDC, 2021a; https://www.cdc.gov/coronavirus/2019-ncov/covid-data/ covidview/index.html), leading to more consistent detection of SARSCoV-2 RNA in wastewater (Gonzalez et al., 2020; Gerrity et al., 2021; Wu et al., 2021)....
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...html), leading to more consistent detection of SARSCoV-2 RNA in wastewater (Gonzalez et al., 2020; Gerrity et al., 2021; Wu et al., 2021)....
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TL;DR: This work paves the way for AS RT-qPCR as a method for rapid inexpensive surveillance of SARS-CoV-2 variants in wastewater, targeting spike protein mutations at three independent genomic loci that are highly predictive of B.1.1 .1.7 variant.
Abstract: The critical need for surveillance of SARS-CoV-2 variants of concern has prompted the development of methods that can track variants in wastewater. Here, we develop and present an open-source method based on allele-specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci that are highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions down to 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track the occurrence of B.1.1.7 over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-type sequences quantified by our assays matches SARS-CoV-2 levels indicated by the U.S. CDC N1 and N2 assays. This work paves the way for AS RT-qPCR as a method for rapid inexpensive surveillance of SARS-CoV-2 variants in wastewater. © 2021 The Authors. Published by American Chemical Society.
62 citations
TL;DR: In this paper , the authors demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater copy numbers of SARS-CoV-2 gene fragments and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and Clinical case curves.
54 citations
01 Aug 2021
TL;DR: In this article, the concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical test data.
Abstract: Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.
42 citations
TL;DR: In this paper, a vector autoregression (VAR) model with different data forms was fitted on this data from April 29, 2020 through January 27, 2021, and the performance in three weeks ahead forecasting (February 3, 10, and 17) were compared with measures of Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAPE).
30 citations
References
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TL;DR: The results support current proposals for the length of quarantine or active monitoring of persons potentially exposed to SARS-CoV-2, although longer monitoring periods might be justified in extreme cases.
Abstract: Using news reports and press releases from provinces, regions, and countries outside Wuhan, Hubei province, China, this analysis estimates the length of the incubation period of COVID-19 and its pu...
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TL;DR: This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
Abstract: An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. We report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient's initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
4,970 citations
"Wastewater Surveillance of SARS-CoV..." refers background in this paper
...2 Fuqing Wu(1,2)†; Amy Xiao(1,2)†; Jianbo Zhang(1,2); Katya Moniz(1,2); Noriko 3 Endo(3); Federica Armas(4,5); Mary Bushman(6); Peter R Chai(7,8); Claire 4 Duvallet(3); Timothy B Erickson(7,9,10); Katelyn Foppe(3); Newsha Ghaeli(3); 5 Xiaoqiong Gu(4,5); William P Hanage(6); Katherine H Huang(11); Wei Lin 6...
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TL;DR: The quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE) and highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities.
1,325 citations
TL;DR: The detection of the virus RNA in sewage, even when the CO VID-19 prevalence is low, and the correlation between concentration in sewage and reported prevalence of COVID-19, indicate that sewage surveillance could be a sensitive tool to monitor the circulation of theirus in the population.
Abstract: In the current COVID-19 pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To determine if SARS-CoV-2 RNA was present in sewage during the emergence...
1,075 citations
"Wastewater Surveillance of SARS-CoV..." refers background in this paper
...Lee(4,5); Mariana Matus(3); Kyle A McElroy(3); Steven F Rhode(12); Stefan 7 Wuertz (5,13,14); Janelle Thompson(5,13,15); Eric J Alm(1,2,4,5,11)* 8 9 1: Department of Biological Engineering, Massachusetts Institute of Technology 10 2: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute 11 of Technology 12 3: Biobot Analytics, Inc....
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TL;DR: The data show the utility of viral RNA monitoring in municipal wastewater for SARS-CoV-2 infection surveillance at a population-wide level and in communities facing a delay between specimen collection and the reporting of test results, immediate wastewater results can provide considerable advance notice of infection dynamics.
Abstract: We measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in primary sewage sludge in the New Haven, Connecticut, USA, metropolitan area during the Coronavirus Disease 2019 (COVID-19) outbreak in Spring 2020. SARS-CoV-2 RNA was detected throughout the more than 10-week study and, when adjusted for time lags, tracked the rise and fall of cases seen in SARS-CoV-2 clinical test results and local COVID-19 hospital admissions. Relative to these indicators, SARS-CoV-2 RNA concentrations in sludge were 0–2 d ahead of SARS-CoV-2 positive test results by date of specimen collection, 0–2 d ahead of the percentage of positive tests by date of specimen collection, 1–4 d ahead of local hospital admissions and 6–8 d ahead of SARS-CoV-2 positive test results by reporting date. Our data show the utility of viral RNA monitoring in municipal wastewater for SARS-CoV-2 infection surveillance at a population-wide level. In communities facing a delay between specimen collection and the reporting of test results, immediate wastewater results can provide considerable advance notice of infection dynamics. Testing sewage for the novel coronavirus reveals epidemiological trends.
672 citations