Efficient wastewater sample filtration improves the detection of SARS-CoV-2 variants: An extensive analysis based on sequencing parameters DOI Creative Commons
Angelo Robotto, Carlotta Olivero, Elisa Pozzi

и другие.

PLoS ONE, Год журнала: 2024, Номер 19(5), С. e0304158 - e0304158

Опубликована: Май 24, 2024

During the SARS-CoV-2 pandemic, many countries established wastewater (WW) surveillance to objectively monitor level of infection within population. As new variants continue emerge, it has become clear that WW is an essential tool for early detection variants. The EU Commission published a recommendation suggesting approach establish and its in WW, besides specifying methodology concentration RNA extraction. Therefore, different groups have approached issue with strategies, mainly focusing on methods, but only few highlighted importance prefiltering samples and/or purification samples. Aiming obtain high-quality sequencing data allowing detection, we compared four experimental conditions generated from treatment of: i) by filtration ii) extracted DNase treatment, RNA. To evaluate best condition, results were assessed several parameters, as outcome crucial variant detection. Overall, result was obtained filtering sample. Moreover, present study provides overview some parameters consider when optimizing method monitoring samples, which can also be applied any sample preparation methodology.

Язык: Английский

A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges DOI Creative Commons
Surabhi Singh,

Amina Ismail Ahmed,

Sumayya Almansoori

и другие.

Frontiers in Public Health, Год журнала: 2024, Номер 12

Опубликована: Июль 30, 2024

The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used track water-borne or fecal-orally transmitted pathogens, providing a sensitive means monitoring within community. This technique offers comprehensive, real-time, cost-effective approach disease surveillance, especially for diseases that are difficult monitor through individual clinical screenings.

Язык: Английский

Процитировано

12
Comparative assessment of Nanotrap and polyethylene glycol-based virus concentration in wastewater samples DOI Creative Commons
Kata Farkas, Jessica L. Kevill, Rachel C. Williams

и другие.

FEMS Microbes, Год журнала: 2024, Номер 5

Опубликована: Янв. 1, 2024

Abstract Wastewater-based epidemiology is now widely used in many countries for the routine monitoring of SARS-CoV-2 and other viruses at a community level. However, efficient sample processing technologies are still under investigation. In this study, we compared performance novel Nanotrap® Microbiome Particles (NMP) concentration method to commonly polyethylene glycol (PEG) precipitation concentrating from wastewater their subsequent quantification sequencing. For this, first spiked with SARS-CoV-2, influenza measles norovirus found that NMP recovered 0.4%–21% them depending on virus type, providing consistent reproducible results. Using PEG methods, monitored A B viruses, RSV, enteroviruses GI GII crAssphage using quantitative PCR (qPCR)-based methods next-generation Good viral recoveries were observed highly abundant both methods; however, was more successful recovery low-abundance present wastewater. Furthermore, samples processed successfully sequenced than those method. Virus enhanced by high volumes when applied. Overall, our results suggest rapid easy targets wastewater, whereas may be suited analysis next generation

Язык: Английский

Процитировано

6
Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater DOI Creative Commons
Jesmin Akter, Wendy Smith, Yawen Liu

и другие.

The Science of The Total Environment, Год журнала: 2023, Номер 908, С. 167966 - 167966

Опубликована: Окт. 28, 2023

The lack of standardized methods and large differences in virus concentration extraction workflows have hampered severe acute respiratory syndrome (SARS-CoV-2) wastewater surveillance data reporting practices. Numerous studies shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence recovered concentrations target DNA/RNA, including membrane types, homogenization instruments, speed duration, lysis buffer. In this study, 42 different varied these were compared to determine by quantifying endogenous SARS-CoV-2, human adenovirus (HAdV 40/41) a bacterial marker gene fecal pollution (Bacteroides HF183). Our findings suggest certain selected workflow had significant impact on SARS-CoV-2 concentrations, whereas it minimal HF183 no effect HAdV 40/41 concentrations. When comparing individual workflow, such as type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm) instruments (Precellys 24 homogenizer Vortex-Genie®-2), we found they 40/41, This suggests at least some consumables equipment are interchangeable. Buffer PM1 + TRIzol based yielded higher than other workflows. without chloroform. Similarly, speeds (5000-10,000 rpm) led increased but 40/41. indicate minor enhancements can improve recovery viruses bacteria from wastewater, leading outcomes efforts.

Язык: Английский

Процитировано

9
High-resolution and real-time wastewater viral surveillance by Nanopore sequencing DOI
Xiaoqing Xu, Yu Deng, Jiahui Ding

и другие.

Water Research, Год журнала: 2024, Номер 256, С. 121623 - 121623

Опубликована: Апрель 16, 2024

Язык: Английский

Процитировано

3
20-Month monitoring of SARS-CoV-2 in wastewater of Curitiba, in Southern Brazil DOI Open Access
Ricardo Belmonte-Lopes, Carlos Eduardo Rodrigues Barquilha, Caroline Kozak

и другие.

Environmental Science and Pollution Research, Год журнала: 2023, Номер 30(31), С. 76687 - 76701

Опубликована: Май 27, 2023

Язык: Английский

Процитировано

8
Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area DOI Creative Commons
Dennis Schmiege, Ivana Kraiselburd, Timo Haselhoff

и другие.

The Science of The Total Environment, Год журнала: 2023, Номер 898, С. 165458 - 165458

Опубликована: Июль 14, 2023

Wastewater surveillance of SARS-CoV-2 proved useful, including for identifying the local appearance newly identified virus variants. Previous studies focused on wastewater treatment plants (WWTP) with sewersheds several hundred thousand people or at single building level, representing only a small number people. Both approaches may prove inadequate small-scale intra-urban inferences early detection emerging novel Our study aims (i) to analyze nucleotide variants (SNVs) in sub-sewersheds and WWTP using whole genome sequencing order (ii) investigate potential known concern (VOC) within metropolitan system. We selected three sub-sewershed sampling sites, based estimated population- built environment-related indicators, inlet receiving Ruhr region, Germany. Untreated was sampled weekly between October December 2021, total 22 samples collected. RNA analyzed by RT-qPCR sequencing. For all samples, sequences were obtained, while 13 positive RT-qPCR. multiple specific SNVs WWTP. Identified reflected dominance VOC Delta time sampling. Interestingly, we could identify an Omicron-specific SNV one sub-sewershed. A concurrent same detected Omicron week later. observations suggest that approach particularly useful description spatially confined existing circulating populations. Future applying strategies taking into account features system will be temporal spatial variance more detail.

Язык: Английский

Процитировано

7
Correlation of wastewater surveillance data with traditional influenza surveillance measures in Cook County, Illinois, October 2022–April 2023 DOI
Emily A. Groene, Deniz Yüce,

Colin Korban

и другие.

The Science of The Total Environment, Год журнала: 2023, Номер 912, С. 169551 - 169551

Опубликована: Дек. 20, 2023

Язык: Английский

Процитировано

6
A Gold Standard Dataset for Lineage Abundance Estimation from Wastewater DOI Creative Commons
Jannatul Ferdous, Samuel Kunkleman, W. A. Taylor

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 17, 2024

Abstract During the SARS-CoV-2 pandemic, genome-based wastewater surveillance sequencing has been a powerful tool for public health to monitor circulating and emerging viral variants. As medium, is very complex because of its mixed matrix nature, which makes deconvolution samples more difficult. Here we introduce gold standard dataset constructed from synthetic control mixtures known composition, spiked into RNA sequenced on Oxford Nanopore Technologies platform. We compare performance eight most commonly used tools in identifying variants present these mixtures. The software evaluated was primarily chosen relevance CDC reporting protocol, until recently employed pipeline that incorporates results four methods: Freyja, kallisto, Kraken2/Bracken, LCS. also tested Lollipop, method by Swiss SARS-CoV2 Sequencing Consortium, three recently-published lineagespot, Alcov, VaQuERo. found Freyja outperformed other correct identification lineages mixtures, newer VaQuERo similarly accurate, with minor differences ability two methods avoid false negatives suppress positives. These provide insight effect tiling primer scheme extract data outcomes. Highlights Generation Comparative evaluation relative abundance estimation Evaluation CFSAN’s CWAP

Язык: Английский

Процитировано

2
Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification DOI Open Access
Kristina M. Babler,

Mark Sharkey,

Ayaaz Amirali

и другие.

Journal of Biomolecular Techniques JBT, Год журнала: 2023, Номер 34(4), С. 3fc1f5fe.dfa8d906 - 3fc1f5fe.dfa8d906

Опубликована: Дек. 20, 2023

Wastewater-based surveillance (WBS) is a noninvasive, epidemiological strategy for assessing the spread of COVID-19 in communities. This was based upon wastewater RNA measurements viral target, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The utility WBS has motivated research to measure targets beyond SARS-CoV-2, including pathogens containing DNA. objective this study establish necessary steps isolating DNA from by modifying long-standing RNA-specific extraction workflow optimized SARS-CoV-2 detection. Modifications were made sample concentration process and included an evaluation bead bashing prior either or RNA. Results showed that reduced detection but improved recovery as assessed quantitative polymerase chain reaction (qPCR). Bead therefore not recommended quantification viruses using qPCR. Whereas Mycobacterium bacterial isolation, improving qPCR quantification. Overall, we recommend 2 separate workflows, one does include other microbes use isolation. experimentation done here shows current-standing program methodologies need be modified reoptimized allow alternative readily detected monitored, expanding its tool public health assessment.

Язык: Английский

Процитировано

4
Definition of a concentration and RNA extraction protocol for optimal whole genome sequencing of SARS-CoV-2 in wastewater (ANRS0160) DOI Creative Commons

Ahlam Chaqroun,

Ghina El Soufi, Zuzana Gerber

и другие.

The Science of The Total Environment, Год журнала: 2024, Номер 952, С. 175823 - 175823

Опубликована: Авг. 26, 2024

Monitoring the presence of RNA from emerging pathogenic viruses, such as SARS-CoV-2, in wastewater (WW) samples requires suitable methods to ensure an effective response. Genome sequencing WW is one crucial methods, but it high-quality sufficient quantities, especially for monitoring variants. Consequently, viral concentration and extraction have be optimized before sequencing. The purpose this study was achieve high coverage (≥ 90 %) depth (at least ≥200×) even low initial concentrations (< 10

Язык: Английский

Процитировано

1