Dataset Information

SARS-CoV2 variant analysis in wastewater in six Swedish cities from 2021-2022

ABSTRACT: SARS-CoV-2 genome can be detected in faeces samples from COVID-19 patients using molecular methods. Therefore, monitoring SARS CoV-2 in wastewater could provide early surveillance of disease prevalence at a population-wide level, referred to as wastewater-based epidemiology. High-throughput sequencing of SARS-CoV2 in wastewater can provide information on SARS-CoV2 variants circulating in the population and act as an early warning system for the introduction of new variants of concern. The data presented here were generated by the two wastewater laboratories of SEEC (The Swedish Environmental Epidemiology Center): * SEEC-SLU: Samples from Uppsala, Örebro, Umeå, and Kalmar are analysed at the Swedish University of Agricultural Sciences (SLU) node led by associate professor Anna J. Székely (anna.szekely@slu.se) and associate professor Maja Malmberg (maja.malmberg@slu.se). * SEEC-KTH: Samples from Stockholm and Malmö are analysed at the KTH Royal Institute of Technology (KTH) node led by associate professor Zeynep Cetecioglu Gurol (zeynepcg@kth.se). The Swedish Environmental Epidemiology Center is part of the Pandemic Laboratory Preparedness network of SciLifeLab, Science for Life Laboratory, an institution for the advancement of molecular biosciences in Sweden. For all places, untreated wastewater samples representative of a single day (24 hours) is collected weekly by flow compensated samplers. All measurements represent only 1 day except for Uppsala, where the measurements represent 1 week as samples are collected each day and then combined flow-proportionally into 1 composite weekly sample. The samples were processed according to standard methods. Briefly, the viral genomic material is concentrated and extracted by the direct capture method using the Maxwell RSC Enviro TNA kit (Promega). Sequencing libraries were made using Ion AmpliSeq SARS-CoV-2 Insight Research Assay (ThermoFisher) and sequenced on IonS5 at the National Genomic Infrastructure (NGI) at SciLifeLab in Uppsala, Sweden. The data was analysed using the SARS-CoV-2 analysis tools available from the Torrent Suite Software. In publications based on this data, the authors must acknowledge SciLifeLab and NGI with the following sentences: “Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala. The facility is part of the National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory. The SNP&SEQ Platform is also supported by the Swedish Research Council and the Knut and Alice Wallenberg Foundation.”

ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 SARS-CoV-2

SUBMITTER:

PROVIDER: S-BSST1185 | biostudies-other |

SECONDARY ACCESSION(S): PRJEB60156

REPOSITORIES: biostudies-other

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Project description:Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA's GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA.ImportanceThis paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA's laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

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SARS-CoV2 variant analysis in wastewater in six Swedish cities from 2021-2022

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