Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland.

Autor: Lipponen A; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland. anssi.lipponen@thl.fi.; Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland. anssi.lipponen@thl.fi., Kolehmainen A; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland., Oikarinen S; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland., Hokajärvi AM; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland., Lehto KM; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland., Heikinheimo A; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.; Microbiology Unit, Laboratory and Research Division, Finnish Food Authority, Helsinki, Finland., Halkilahti J; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Juutinen A; Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Luomala O; Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Smura T; Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Liitsola K; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Blomqvist S; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Savolainen-Kopra C; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland., Pitkänen T; Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland.; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2024 Apr 02; Vol. 14 (1), pp. 7751. Date of Electronic Publication: 2024 Apr 02.
DOI: 10.1038/s41598-024-58113-8
Abstrakt: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating the importance of variant detection at the population level. Wastewater-based surveillance of SARS-CoV-2 RNA fragments has been shown to be an effective way to monitor the COVID-19 pandemic at the population level. Wastewater is a complex sample matrix affected by environmental factors and PCR inhibitors, causing insufficient coverage in sequencing, for example. Subsequently, results where part of the genome does not have sufficient coverage are not uncommon. To identify variants and their proportions in wastewater over time, we utilized next-generation sequencing with the ARTIC Network's primer set and bioinformatics pipeline to evaluate the presence of variants in partial genome data. Based on the wastewater data from November 2021 to February 2022, the Delta variant was dominant until mid-December in Helsinki, Finland's capital, and thereafter in late December 2022 Omicron became the most common variant. At the same time, the Omicron variant of SARS-CoV-2 outcompeted the previous Delta variant in Finland in new COVID-19 cases. The SARS-CoV-2 variant findings from wastewater are in agreement with the variant information obtained from the patient samples when visually comparing trends in the sewerage network area. This indicates that the sequencing of wastewater is an effective way to monitor temporal and spatial trends of SARS-CoV-2 variants at the population level.
(© 2024. The Author(s).)
Databáze: MEDLINE
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