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Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater

Wilhelm, Alexander ; Agrawal, Shelesh ; Schoth, Jens ; Meinert-Berning, Christina ; Bastian, Daniel ; Orschler, Laura ; Ciesek, Sandra ; Teichgräber, Burkhard ; Wintgens, Thomas ; Lackner, Susanne ; Weber, Frank-Andreas ; Widera, Marek (2022):
Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater. (Publisher's Version)
In: Viruses, 14 (9), MDPI, e-ISSN 1999-4915,
DOI: 10.26083/tuprints-00022326,
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Item Type: Article
Origin: Secondary publication DeepGreen
Status: Publisher's Version
Title: Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater
Language: English
Abstract:

Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due to the severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required to assess and implement countermeasures in time. In this study, we monitored the prevalence of SARS-CoV-2 BA.4/BA.5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability for detecting BA.4/BA.5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022, and the presence of BA.4/BA.5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V and NGS sequencing. Finally, the mutant fractions were quantitatively monitored by digital PCR, confirming BA.4/BA.5 as the majority variant by 5 June 2022. In conclusion, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variants spreading independently of individual test capacities.

Journal or Publication Title: Viruses
Volume of the journal: 14
Issue Number: 9
Place of Publication: Darmstadt
Publisher: MDPI
Collation: 15 Seiten
Uncontrolled Keywords: COVID-19 surveillance, SARS-CoV-2 monitoring, wastewater-based epidemiology (WBE), Omicron, BA.4, BA.5, variant of concern
Classification DDC: 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin, Gesundheit
600 Technik, Medizin, angewandte Wissenschaften > 620 Ingenieurwissenschaften
Divisions: 13 Department of Civil and Environmental Engineering Sciences > Institute IWAR > Water and Environmental Biotechnology
Date Deposited: 31 Oct 2022 14:29
Last Modified: 31 Oct 2022 14:29
DOI: 10.26083/tuprints-00022326
Corresponding Links:
URN: urn:nbn:de:tuda-tuprints-223265
Additional Information:

This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2

SWORD Depositor: Deep Green
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/22326
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