SAMN48961743
External Id
Queen's University Belfast
INSDC center name
2025-06-10T00:00:00Z
INSDC first public
2025-06-10T11:06:03.090Z
INSDC last update
SRS25323390
INSDC secondary accession
live
INSDC status
SARS-CoV-2: wastewater surveillance
NCBI submission model
SARS-CoV-2.wwsurv.1.0
NCBI submission package
SRS25323390
SRA accession
Andrew J. Lee, Marina I. Reyne, and Danielle M. Allen
collected_by
2022-08-11
collection_date
sequencing protocol: see https://doi.org/10.1186/s12967-022-03307-9 & https://doi.org/10.17504/protocols.io.bvntn5en; for additional details, please see https://doi.org/10.1016/j.watres.2025.123953.
description
United Kingdom: Northern Ireland, Mid Ulster; Dungannon
geo_loc_name
municipal wastewater, influent
isolation_source
wastewater metagenome
http://purl.obolibrary.org/obo/NCBITaxon_527639
organism
public health surveillance community-level
purpose_of_ww_sampling
genomic surveillance of SARS-CoV-2 in wastewater to assess mutation diversity and estimate circulating variant proportions using depth-weighted demixing
purpose_of_ww_sequencing
Marina I. Reyne, Danielle M. Allen, Andrew J. Lee, Clara H. Radulescu, and Stephen J. Bridgett
sequenced_by
SARS-CoV-2 wastewater treatment plant sample collected in Dungannon on 11-Aug-2022 and sequenced with Mini-XT ARTIC amplicon protocol
title
18079
ww_population
census blocks clipped to wastewater service area polygon
ww_population_source
centrifugation for supernatant clarification
ww_pre_treatment
Composite wastewater samples from municipal wastewater treatment plants were collected over a 24-hour period using an Isco Glacier autosampler. All samples were cold chain delivered (i.e. chilled and processed immediately or placed temporarily in the fridge). After centrifugation and concentration, nucleic acids were extracted and purified using the Roche MagNA Pure 96 Instrument. SARS-CoV-2 RNA was detected by RT-qPCR with AgPath-ID™ One-Step Reagents (ThermoFisher) and N1 + N2 Assay Kits (Qiagen). Whole-genome amplification was performed using ARTIC Network primer schemes, followed by Illumina sequencing using the Mini-XT protocol (https://doi.org/10.1186/s12967-022-03307-9) with ARTIC Network primer schemes. For full methodology, please refer to the accompanying publication (https://doi.org/10.1016/j.watres.2025.123953)
ww_processing_protocol
24
ww_sample_duration
raw wastewater
ww_sample_matrix
composite
ww_sample_type
Mid Ulster
ww_surv_jurisdiction
DNG110822_S98_L001
ww_surv_system_sample_id
SARS-CoV-2
ww_surv_target_1
N1 and N2 genes, combined assay (QIAGEN N.V. ID 222015)
ww_surv_target_1_gene
yes
ww_surv_target_1_known_present
absolute quantification of viral target via RT-qPCR standard curve generated using an external standard
ww_surv_target_1_protocol
4
ww_temperature