Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Wastewater genomic sequencing for SARS-CoV-2 variants surveillance in wastewater-based epidemiology applications

PROVIDER: PRJNA1004046 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25593000_1.fastq.gz	Fastqsanger.gz
	SRR25593000_2.fastq.gz	Fastqsanger.gz
	SRR25593001_1.fastq.gz	Fastqsanger.gz
	SRR25593001_2.fastq.gz	Fastqsanger.gz
	SRR25593002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 152

Similar Datasets

Diagnostic Microbiology & Infectious Disease Rapid and sensitive detection of Sars-CoV-2 variants in nasopharyngeal swabs and wastewaters

Project description:The SARS-CoV-2 virus is continuously evolving, with appearance of new variants characterized by multiple genomic mutations, some of which can affect functional properties, including infectivity, interactions with host immunity, and disease severity. The rapid spread of new SARS-CoV-2 variants has highlighted the urgency to trace the virus evolution, to help limit its diffusion, and to assess effectiveness of containment strategies. We propose here a PCR-based rapid, sensitive and low-cost allelic discrimination assay panel for the identification of SARS-CoV-2 genotypes, useful for detection in different sample types, such as nasopharyngeal swabs and wastewater. The tests carried out demonstrate that this in-house assay, whose results were confirmed by SARS-CoV-2 whole-genome sequencing, can detect variations in up to 10 viral genome positions at once and is specific and highly sensitive for identification of all tested SARS-CoV-2 clades, even in the case of samples very diluted and of poor quality, particularly difficult to analyze.

2022-06-03 | E-MTAB-11261 | biostudies-arrayexpress

FIRST DETECTION OF SARS-COV-2 PROTEINS IN WASTEWATER SAMPLES BY MASS SPECTROMETRY

Project description:On March 12, 2020, the World Health Organization (WHO) declared COVID-19 as a global pandemic. COVID-19 is produced by a novel β-coronavirus known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) [1]. Several studies have detected SARS-CoV-2 RNA in urine, feces, and other biofluids from both symptomatic and asymptomatic people with COVID-19 [2], suggesting that SARS-CoV-2 RNA could be detected in human wastewater [3]. Thus, wastewater-based epidemiology (WBE) is now used as an approach to monitor COVID-19 prevalence in many different places around the world [4-10] . Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most common SARS-CoV-2 detection method in WBE, but there are other methods for viral biomolecule detection that could work as well. The aim of this study was to evaluate the presence of SARS-CoV-2 proteins in untreated wastewater (WW) influents collected from six wastewater treatment plants (WWTPs), from Durham Region, Ontario, Canada, using a LC-MS/MS-based proteomics approach. We identified many SARS-CoV-2 proteins in these wastewater samples, with peptides from pp1ab being the most consistently detected and with consistent abundance.

2022-03-31 | PXD026412 | Pride

wastewater metagenome

Project description:SARS-CoV-2 Wastewater-based Genomic Epidemiology (WGE) in Japan

| PRJDB19812 | ENA

Project description:Wastewater based SARS-CoV-2 genomic surveillance in Ethiopia

| PRJNA1225690 | ENA

SARS-CoV-2: wastewater surveillance

Project description:SARS-CoV-2 wastewater surveillance in central Arkansas, USA

2025-03-24 | PRJEB87405 | EVA

Project description:Wastewater based genomic surveillance of SARS-CoV-2 throughout Germany

| PRJNA1283912 | ENA

Swiss SARS-CoV-2 Wastewater Surveillance

Project description:Surveillance of SARS-CoV-2 genomic variants in wastewater in Switzerland

| PRJEB44932 | ENA

Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance

Project description:Wastewater-based surveillance (WBS) is a proven tool for monitoring population-level infection events. Wastewater contains high concentrations of inhibitors, which contaminate total nucleic acids (TNA) extracted from these samples. We found that TNA extracts from raw influent of Berlin wastewater treatment plants contained highly variable amounts of inhibitors that impaired molecular analyses like dPCR and next-generation sequencing (NGS). By using dilutions, we were able to detect inhibitory effects. To enhance WBS sensitivity and stability, we applied a combination of PCR inhibitor removal and TNA dilution (PIR+D). This approach led to a 26-fold increase in measured SARS-CoV-2 concentrations, practically reducing the detection limit. Additionally, we observed a substantial increase in stability of the time series. We define suitable stability as a mean absolute error (MAE) below 0.1 log10 copies/l and a geometric mean relative absolute error (GMRAE) below 26%. Using PIR+D, the MAE could be reduced from 0.219 to 0.097 and the GMRAE from 65.5% to 26.0% and even further in real-world WBS. Furthermore, PIR+D improved SARS-CoV-2 genome alignment and coverage in amplicon-based NGS for low to medium concentrations. In conclusion, we strongly recommend both the monitoring and removal of inhibitors from samples for WBS.

2024-11-27 | GSE283001 | GEO

Project description:Wastewater-based surveillance and molecular epidemiology of SARS-CoV-2 in northern South Africa

| PRJNA980445 | ENA

SARS-CoV-2 Surveillance in Minas Gerais, Brazil

Project description:SARS-CoV-2 variants surveillance

| PRJEB49204 | ENA