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

Authors :
Anssi Lipponen
Aleksi Kolehmainen
Sami Oikarinen
Anna-Maria Hokajärvi
Kirsi-Maarit Lehto
Annamari Heikinheimo
Jani Halkilahti
Aapo Juutinen
Oskari Luomala
Teemu Smura
Kirsi Liitsola
Soile Blomqvist
Carita Savolainen-Kopra
Tarja Pitkänen
WastPan Study Group
Source :
Scientific Reports, Vol 14, Iss 1, Pp 1-13 (2024)
Publication Year :
2024
Publisher :
Nature Portfolio, 2024.

Abstract

Abstract 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.

Subjects

Subjects :
Medicine
Science

Details

Language :
English
ISSN :
20452322
Volume :
14
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Scientific Reports
Publication Type :
Academic Journal
Accession number :
edsdoj.6281527677244848b45fb2bda219b9a4
Document Type :
article
Full Text :
https://doi.org/10.1038/s41598-024-58113-8