Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Girón-Guzmán, Inés; Díaz-Reolid, Azahara; Cuevas-Ferrando, Enric; Falcó, Irene; Cano-Jiménez, Pablo; Comas, Iñaki; Pérez-Cataluña, Alba; Sánchez, Glòria

doi:10.1016/j.scitotenv.2022.160914

Cited by 13 publications

(16 citation statements)

References 37 publications

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“…In fact, Giron-Guzman et al 2023 found that the Enviro Wastewater TNA concentration kit was more effective at recovering non-enveloped viruses from wastewater as compared to an aluminum-based adsorption-precipitation method. The opposite was true for enveloped viruses (Girón-Guzmán et al, 2023). This makes direct extraction a plausible approach to circumvent such challenges.…”

Section: Targeted Metagenomics With Electronegative Membrane Filtrati...mentioning

confidence: 99%

“…Membrane filtration is a common concentration method used, either as a stand-alone method or in conjunction with other methods, in wastewater metagenomic studies (McCall et al 2019). Although concentration can improve virus detection, it can impose bias during sample processing depending on several factors such as the method used and virus morphology (Hjelmsø et al, 2017, Girón-Guzmán et al, 2023). More studies are needed to explore the impact of concentration biases on virus detection in metagenomic datasets.…”

Section: Introductionmentioning

confidence: 99%

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Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

McCall

Elworth

Wylie

et al. 2023

Preprint

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Viruses of concern for quantitative wastewater monitoring are usually selected as a result of an outbreak and subsequent detection in wastewater. However, targeted metagenomics could proactively identify viruses of concern when used as an initial screening tool. To evaluate the utility of targeted metagenomics for wastewater screening, we used ViroCap, a panel of probes designed to target all known vertebrate viruses. Untreated wastewater was collected from wastewater treatment plants (WWTPs) and building-level manholes associated with vulnerable populations in Houston, TX. We evaluated differences in vertebrate virus detection between WWTP and building-level samples, classified human viruses in wastewater, and performed phylogenetic analysis on astrovirus sequencing reads to evaluate targeted metagenomics for subspecies level classification. Vertebrate viruses varied widely across building-level samples. Rarely detected and abundant viruses were identified in WWTP and building-level samples, including enteric, respiratory, and bloodborne viruses. Furthermore, full length genomes were assembled from astrovirus reads and two human astrovirus serotypes were classified in wastewater samples. This study demonstrates the utility of targeted metagenomics as an initial screening step for public health surveillance.

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Section: Targeted Metagenomics With Electronegative Membrane Filtrati...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

McCall

Elworth

Wylie

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Molecular methods have demonstrated superior performance in terms of sensitivity, specificity, reliability, and speed and are therefore being used more frequently in wastewater monitoring studies. The classical technique of PCR is more suitable for quantification, so the use of large-scale sequencing techniques that can be used qualitatively to detect viruses in the environment is being increased (Girón-Guzmán et al 2023 ). Finally, many new and innovative approaches are using the unique properties of nanomaterials to enable the detection of infectious pathogens.…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

Yang

Guo

Møhlenberg

et al. 2023

Environ Sci Pollut Res

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The novel coronavirus SARS-CoV-2 has spread at an unprecedented rate since late 2019, leading to the global COVID-19 pandemic. During the pandemic, being able to detect SARS-CoV-2 in human populations with high coverage quickly is a huge challenge. As SARS-CoV-2 is excreted in human excreta and thus exposed to the aqueous environment through sewers, the goal is to develop an ideal, non-invasive, cost-effective epidemiological method for detecting SARS-CoV-2. Wastewater surveillance has gained widespread interest and is increasingly being investigated as an effective early warning tool for monitoring the spread and evolution of the virus. This review emphasizes important findings on SARS-CoV-2 wastewater-based epidemiology (WBE) in different continents and techniques used to detect SARS-CoV-2 in wastewater during the period 2020–2022. The results show that WBE is a valuable population-level method for monitoring SARS-CoV-2 and is a valuable early warning alert. It can assist policymakers in formulating relevant policies to avoid the negative impacts of early or delayed action. Such strategy can also help avoid unnecessary wastage of medical resources, rationalize vaccine distribution, assist early detection, and contain large-scale outbreaks.

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“…VOI Zeta (P.2), a descendant of the B.1.1.28 strain, was first described in December 2020 in the state of Rio de Janeiro, Brazil, and rapidly spread across the country (Voloch et al 2021 ). Different SARS-CoV-2 variants have been detected in wastewater, and since then, different methods have been compared for virus sequencing (Cha et al 2023 ; Girón-Guzmán et al 2023 ). Recent studies suggest a combination of centralized and decentralized WBE implementation in high-, middle-, and low-income countries for genomic surveillance (Amin et al 2023 ; Gonçalves et al 2022 ; Jarvie et al 2023 ; Prado et al 2023 ).…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil

Lanzarini

Mannarino

Ribeiro

et al. 2023

Environ Sci Pollut Res

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Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log 10 100 mL −1 . The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies. Graphical Abstract

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Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Cited by 13 publications

References 37 publications

Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil

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