SARS-CoV2 variant analysis in Swedish wastewater samples collected in 2023

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 at the Swedish University of Agricultural Sciences (SLU) by the 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 ([e-mail]) and associate professor Maja Malmberg ([e-mail]). 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 was performed either by generating libraries 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, or using the Illumina COVIDSeq Assay kit and sequenced on the Illumina Miseq platform using the MiSeq Reagent Kit v3 (150-cycle) at the Functional Microbial Ecology Lab (FUME) within the Swedish University of Agriculture. 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.”