Research

15 pages, 2840 KiB

Open AccessArticle

The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

by Eric C. Rouchka, Julia H. Chariker, Kumar Saurabh, Sabine Waigel, Wolfgang Zacharias, Mei Zhang, Daymond Talley, Ian Santisteban, Madeline Puccio, Sarah Moyer, Rochelle H. Holm, Ray A. Yeager, Kevin J. Sokoloski, Joshua Fuqua, Aruni Bhatnagar and Ted Smith

Pathogens 2021, 10(10), 1271; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10101271 - 01 Oct 2021

Cited by 13 | Viewed by 2825

Abstract

Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater [...] Read more.

Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest/concern through next-generation sequencing has enhanced the understanding of the SARS-CoV-2 outbreak. In this report, we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern/Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. Importantly, these efforts confirm that regional emergence and spread of variants of interest/concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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14 pages, 1892 KiB

Open AccessArticle

Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France

by Nathalie Wurtz, Océane Revol, Priscilla Jardot, Audrey Giraud-Gatineau, Linda Houhamdi, Christophe Soumagnac, Alexandre Annessi, Alexandre Lacoste, Philippe Colson, Sarah Aherfi and Bernard La Scola

Pathogens 2021, 10(8), 1042; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10081042 - 17 Aug 2021

Cited by 18 | Viewed by 3692

Abstract

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to [...] Read more.

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the “UK variant” in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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9 pages, 245 KiB

Open AccessEditor’s ChoiceArticle

Occurrence of SARS-CoV-2 RNA in Six Municipal Wastewater Treatment Plants at the Early Stage of COVID-19 Pandemic in The United States

by Samendra P. Sherchan, Shalina Shahin, Jeenal Patel, Lauren M. Ward, Sarmila Tandukar, Sital Uprety, Bradley W. Schmitz, Warish Ahmed, Stuart Simpson and Pradip Gyawali

Pathogens 2021, 10(7), 798; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10070798 - 23 Jun 2021

Cited by 22 | Viewed by 4378

Abstract

In this study, we investigated the occurrence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) RNA in primary influent (n = 42), secondary effluent (n = 24) and tertiary treated effluent (n = 34) collected from six wastewater treatment plants (WWTPs [...] Read more.

In this study, we investigated the occurrence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) RNA in primary influent (n = 42), secondary effluent (n = 24) and tertiary treated effluent (n = 34) collected from six wastewater treatment plants (WWTPs A–F) in Virginia (WWTP A), Florida (WWTPs B, C, and D), and Georgia (WWTPs E and F) in the United States during April–July 2020. Of the 100 wastewater samples analyzed, eight (19%) untreated wastewater samples collected from the primary influents contained SARS-CoV-2 RNA as measured by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays. SARS-CoV-2 RNA were detected in influent wastewater samples collected from WWTP A (Virginia), WWTPs E and F (Georgia) and WWTP D (Florida). Secondary and tertiary effluent samples were not positive for SARS-CoV-2 RNA indicating the treatment processes in these WWTPs potentially removed SARS-CoV-2 RNA during the secondary and tertiary treatment processes. However, further studies are needed to understand the log removal values (LRVs) and transmission risks of SARS-CoV-2 RNA through analyzing wastewater samples from a wider range of WWTPs. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

10 pages, 1676 KiB

Open AccessFeature PaperArticle

Seasonal Stability of SARS-CoV-2 in Biological Fluids

by Taeyong Kwon, Natasha N. Gaudreault and Juergen A. Richt

Pathogens 2021, 10(5), 540; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10050540 - 30 Apr 2021

Cited by 23 | Viewed by 3408

Abstract

The transmission of SARS-CoV-2 occurs by close contact with infected persons through droplets, the inhalation of infectious aerosols, and the exposure to contaminated surfaces. Previously, we determined the virus stability on different types of surfaces under indoor and seasonal climatic conditions. SARS-CoV-2 survived [...] Read more.

The transmission of SARS-CoV-2 occurs by close contact with infected persons through droplets, the inhalation of infectious aerosols, and the exposure to contaminated surfaces. Previously, we determined the virus stability on different types of surfaces under indoor and seasonal climatic conditions. SARS-CoV-2 survived the longest on surfaces under winter conditions, followed by spring/fall and summer conditions, suggesting the seasonal pattern of stability on surfaces. However, under natural conditions, the virus is secreted in various biological fluids from infected humans. In this respect, it remains unclear how long the virus survives in various types of biological fluids. This study explores SARS-CoV-2 stability in virus-spiked human biological fluids under different environmental conditions by determining the virus half-life. The virus was stable for up to 21 days in nasal mucus, sputum, saliva, tear, urine, blood, and semen; it remained infectious significantly longer under winter and spring/fall conditions than under summer conditions. In contrast, the virus was only stable up to 24 h in feces and breast milk. These findings demonstrate the potential risk of infectious biological fluids in SARS-CoV-2 transmission and have implications for its seasonality. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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12 pages, 5641 KiB

Open AccessArticle

Microscopic Observation of SARS-Like Particles in RT-qPCR SARS-CoV-2 Positive Sewage Samples

by Djamal Brahim Belhaouari, Nathalie Wurtz, Clio Grimaldier, Alexandre Lacoste, Gabriel Augusto Pires de Souza, Gwilherm Penant, Sihem Hannat, Jean-Pierre Baudoin and Bernard La Scola

Pathogens 2021, 10(5), 516; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10050516 - 24 Apr 2021

Cited by 11 | Viewed by 4018

Abstract

The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from [...] Read more.

The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from the faeces and urine of infected patients, which can then enter the wastewater system. The currently available evidence indicates that the viral RNA present in wastewater may become a potential source of epidemiological data. However, to investigate whether wastewater may present a risk to humans such as sewage workers, we investigated whether intact particles of SARS-CoV-2 were observable and whether it was possible to isolate the virus in wastewater. Using a correlative strategy of light microscopy and electron microscopy (CLEM), we demonstrated the presence of intact and degraded SARS-like particles in RT-qPCR SARS-CoV-2-positive sewage sample collected in the city of Marseille. However, the viral infectivity assessment of SARS-CoV-2 in the wastewater was inconclusive, due to the presence of other viruses known to be highly resistant in the environment such as enteroviruses, rhinoviruses, and adenoviruses. Although the survival and the infectious risk of SARS-CoV-2 in wastewater cannot be excluded from our study, additional work may be required to investigate the stability, viability, fate, and decay mechanisms of SARS-CoV-2 thoroughly in wastewater. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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7 pages, 346 KiB

Open AccessCommunication

Evaluation of Two Methods to Concentrate SARS-CoV-2 from Untreated Wastewater

by Roger Dumke, Magali de la Cruz Barron, Reinhard Oertel, Björn Helm, Rene Kallies, Thomas U. Berendonk and Alexander Dalpke

Pathogens 2021, 10(2), 195; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10020195 - 12 Feb 2021

Cited by 25 | Viewed by 3922

Abstract

Use of wastewater-based epidemiology as a tool to record and manage the course of SARS-CoV-2 infections in human populations requires information about the efficiency of methods to concentrate the virus from wastewater. In the present study, we spiked untreated wastewater with quantified SARS-CoV-2 [...] Read more.

Use of wastewater-based epidemiology as a tool to record and manage the course of SARS-CoV-2 infections in human populations requires information about the efficiency of methods to concentrate the virus from wastewater. In the present study, we spiked untreated wastewater with quantified SARS-CoV-2 positive clinical material and enriched the virus by polyethylene glycol precipitation and ultrafiltration with Vivaspin 10 kDa MWCO columns. SARS-CoV-2 was detected and quantified by reverse transcription quantitative PCR (E- and S-gene) and droplet digital PCR. The concentration of virus with precipitation resulted in mean recoveries between 59.4% and 63.7% whereas rates from 33.0% to 42.6% after ultrafiltration of samples were demonstrated. The results suggest that the use of both methods allows an effective and practicable enrichment of SARS-CoV-2 from raw wastewater. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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Review

Jump to: Research, Other

27 pages, 2602 KiB

Open AccessReview

Wastewater Based Epidemiology Perspective as a Faster Protocol for Detecting Coronavirus RNA in Human Populations: A Review with Specific Reference to SARS-CoV-2 Virus

by Milad Mousazadeh, Razieh Ashoori, Biswaranjan Paital, Işık Kabdaşlı, Zacharias Frontistis, Marjan Hashemi, Miguel A. Sandoval, Samendra Sherchan, Kabita Das and Mohammad Mahdi Emamjomeh

Pathogens 2021, 10(8), 1008; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10081008 - 10 Aug 2021

Cited by 27 | Viewed by 5947

Abstract

Wastewater-based epidemiology (WBE) has a long history of identifying a variety of viruses from poliovirus to coronaviruses, including novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The presence and detection of SARS-CoV-2 in human feces and its passage into the water bodies are [...] Read more.

Wastewater-based epidemiology (WBE) has a long history of identifying a variety of viruses from poliovirus to coronaviruses, including novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The presence and detection of SARS-CoV-2 in human feces and its passage into the water bodies are significant public health challenges. Hence, the hot issue of WBE of SARS-CoV-2 in the coronavirus respiratory disease (COVID-19) pandemic is a matter of utmost importance (e.g., SARS-CoV-1). The present review discusses the background, state of the art, actual status, and prospects of WBE, as well as the detection and quantification protocols of SARS-CoV-2 in wastewater. The SARS-CoV-2 detection studies have been performed in different water matrixes such as influent and effluent of wastewater treatment plants, suburban pumping stations, hospital wastewater, and sewer networks around the globe except for Antarctica. The findings revealed that all WBE studies were in accordance with clinical and epidemiological data, which correlates the presence of SARS-CoV-2 ribonucleic acid (RNA) with the number of new daily positive cases officially reported. This last was confirmed via Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) testing which unfortunately is not suitable for real-time surveillance. In addition, WBE concept may act as a faster protocol to alert the public health authorities to take administrative orders (possible re-emerging infections) due to the impracticality of testing all citizens in a short time with limited diagnostic facilities. A comprehensive and integrated review covering all steps starting from sampling to molecular detection of SARS-CoV-2 in wastewater has been made to guide for the development well-defined and reliable protocols. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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28 pages, 501 KiB

Open AccessReview

COVID-19 Crisis Creates Opportunity towards Global Monitoring & Surveillance

by Ahmed Donia, Sammer-ul Hassan, Xunli Zhang, Lamiaa Al-Madboly and Habib Bokhari

Pathogens 2021, 10(3), 256; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10030256 - 24 Feb 2021

Cited by 12 | Viewed by 5651

Abstract

The spectrum of emerging new diseases as well as re-emerging old diseases is broadening as infectious agents evolve, adapt, and spread at enormous speeds in response to changing ecosystems. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recent phenomenon and may take [...] Read more.

The spectrum of emerging new diseases as well as re-emerging old diseases is broadening as infectious agents evolve, adapt, and spread at enormous speeds in response to changing ecosystems. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recent phenomenon and may take a while to understand its transmission routes from less traveled territories, ranging from fomite exposure routes to wastewater transmission. The critical challenge is how to negotiate with such catastrophic pandemics in high-income countries (HICs ~20% of the global population) and low-and middle-income countries (LMICs ~ 80% of the global population) with a total global population size of approximately eight billion, where practical mass testing and tracing is only a remote possibility, particularly in low-and middle-income countries (LMICs). Keeping in mind the population distribution disparities of high-income countries (HICs) and LMICs and urbanisation trends over recent years, traditional wastewater-based surveillance such as that used to combat polio may help in addressing this challenge. The COVID-19 era differs from any previous pandemics or global health challenges in the sense that there is a great deal of curiosity within the global community to find out everything about this virus, ranging from diagnostics, potential vaccines/therapeutics, and possible routes of transmission. In this regard, the fact that the gut is the common niche for both poliovirus and SARS-CoV-2, and due to the shedding of the virus through faecal material into sewerage systems, the need for long-term wastewater surveillance and developing early warning systems for better preparedness at local and global levels is increasingly apparent. This paper aims to provide an insight into the ongoing COVID-19 crisis, how it can be managed, and what measures are required to deal with a current global international public health concern. Additionally, it shed light on the importance of using wastewater surveillance strategy as an early warning practical tool suitable for massive passive screening, as well as the urgent need for microfluidic technology as a rapid and cost-effective approach tracking SARS-CoV-2 in wastewater. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

Other

Jump to: Research, Review

4 pages, 509 KiB

Open AccessBrief Report

Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature

by Rudolf Markt, Markus Mayr, Evelyn Peer, Andreas O. Wagner, Nina Lackner and Heribert Insam

Pathogens 2021, 10(9), 1215; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10091215 - 18 Sep 2021

Cited by 20 | Viewed by 2629

Abstract

SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at −20 °C led to [...] Read more.

SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at −20 °C led to a significant reduction in gene copy numbers. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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