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

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

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The first detection of SARS-CoV-2 RNA in the wastewater of Bucharest, Romania

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Сен. 17, 2024

Wastewater-based epidemiology (WBE) has been previously used as a tool for pathogen identification within communities. After the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) outbreak, in 2020, Daughton proposed implementation of wastewater surveillance strategy that could determine incidence COVID-19 (coronavirus disease 2019) nationally. Individuals various stages infection, including presymptomatic, asymptomatic and symptomatic patients, can be identified carriers virus their urine, saliva, stool other bodily secretions. Studies using this method were conducted to monitor prevalence high-density populations, such cities but also smaller communities, schools college campuses. The aim pilot study was assess feasibility effectiveness Bucharest, Romania, samples collected weekly from seven locations between July September 2023. RNA (ribonucleic acid) extraction, followed by dPCR (digital polymerase chain reaction) analysis, performed detect viral genetic material. Additionally, NGS (next generation sequencing) technology identify circulating variants Romania. Preliminary results indicate successful detection wastewater, providing valuable insights into circulation community.

Язык: Английский

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Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater

Journal of Infection, Год журнала: 2024, Номер 89(5), С. 106284 - 106284

Опубликована: Сен. 26, 2024

Rapid evolution of SARS-CoV-2 has resulted in the emergence numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, limitations capturing full epidemiological dynamics circulating variants general population. This study aimed monitor variant community and using receptor-binding domain (RBD) amplicon sequencing wastewater samples.

Язык: Английский

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Quantitative analysis of SARS-CoV-2 RNA in wastewater and evaluation of sampling frequency during the downward period of a COVID-19 wave in Japan

The Science of The Total Environment, Год журнала: 2023, Номер 906, С. 166526 - 166526

Опубликована: Авг. 29, 2023

Wastewater-based epidemiology (WBE) is a practical approach for detecting the presence of SARS-CoV-2 infections and assessing epidemic trend coronavirus disease 2019 (COVID-19). The purpose this study was to evaluate minimum sampling frequency required properly identify COVID-19 during downward period when using highly sensitive RNA detection method. WBE conducted Efficient Practical virus Identification System with ENhanced Sensitivity Solids (EPISENS-S), method, at nine neighboring wastewater treatment plants (WWTPs). These WWTPs were in same prefecture Japan, they had different sewer types, methods, frequencies. overall rate 97.8 % entire geometric means new cases per 100,000 inhabitants between 3.3 7.7 each WWTP. maximum concentration 2.14 × 104 copies/L, which corresponded pepper mild mottle (PMMoV)-normalized concentrations 6.54 10-3. We evaluated effect frequencies on probability significant correlation number newly reported by hypothetically reducing dataset. When occurred 5, 3, 2, 1 times week, these results exhibited correlations 100 (5/5), 89 (8/9), 85 (23/27), 48 (13/27), respectively. To achieve high over %, twice week required, even if methods types are different. EPISENS-S method more than can be used monitor wave trends, periods.

Язык: Английский

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Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 21, 2023

Abstract Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity which can be used to identify viral lineages (including variants concern) that are circulating in local population. Capturing sequencing not trivial, as samples often contain diverse mixture with real mutations errors, must deconvoluted computationally short reads. In this study we assess nine different computational tools have recently been developed address challenge. We simulated 100 sequence consisting BA.1, BA.2, Delta lineages, various mixtures, well Delta-Omicron recombinant synthetic “novel” lineage. Most performed identifying true present their relative abundances, were generally robust variation depth read length. While many identified down 1% frequency, results more reliable above 5% threshold. The presence unknown lineage, represents unclassified increases error abundance estimates other but magnitude effect was small most tools. also varied how they labelled novel recombinants. our dataset just one possible use cases these methods, hope it helps users understand potential sources noise bias data appreciate commonalities differences methods.

Язык: Английский

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Hyperplex PCR enables the next-generation of wastewater-based surveillance systems: long-term SARS-CoV-2 variant surveillance in Sweden as a case study

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

Опубликована: Июнь 11, 2024

Abstract Wastewater-based epidemiology aims at measuring pathogens in wastewater as a means of deriving unbiased epidemiological information population scale, ranging from buildings and aircrafts to entire cities or countries. After gaining significant mainstream attention during the SARS-CoV-2 pandemic, field holds promise continuous monitoring early warning system tracking emerging viral variants new with pandemic potential. To expand current toolbox analytical techniques for analysis, we explored use Hyperplex PCR (hpPCR) analyse mutations samples collected weekly up 22 sites across Sweden between October 2022 December 2023. Approximately 900 were tested using dynamic probe panel multiplexity 10-to 18-plex, continuously adapted within 1-2 weeks quantify relevant concern over time. The simultaneously covered deletions, single nucleotide substitutions, well variable regions resorting degeneracy. By analysing all parallel gold standard methods including qPCR two different NGS technologies, performance hpPCR is herein shown bridge gap these by providing (1) systematic sensitivity simple design, (2) high without re-optimization requirements (3) 4-5-week earlier mutation detection compared excellent quantitative linearity good correlation frequency (r=0.88). Based on demonstrated performance, authors propose combined routine discovery high-frequency key pathogens/variants potential alternative analysis paradigm.

Язык: Английский

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