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

Author:

Lipponen Anssi,Kolehmainen Aleksi,Oikarinen Sami,Hokajärvi Anna-Maria,Lehto Kirsi-Maarit,Heikinheimo Annamari,Halkilahti Jani,Juutinen Aapo,Luomala Oskari,Smura Teemu,Liitsola Kirsi,Blomqvist Soile,Savolainen-Kopra Carita,Pitkänen Tarja, ,Länsivaara Annika,Hyder Rafiqul,Janhonen Erja,Heikinheimo Annamari,Heljanko Viivi,Johansson Venla,Kurittu Paula,Tiwari Ananda,Al-Mustapha Ahmad,Sarekoski Anniina,Möttönen Teemu,Räisänen Kati,Savolainen-Kopra Carita

Abstract

AbstractSevere 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.

Publisher

Springer Science and Business Media LLC

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