Early detection of SARS-CoV-2 Omicron BA.4/5 in German wastewater

  • Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. Omicron sub-variants BA.4/5 have spread globally displacing the predeceasing variants. Due to the severe transmissibility and immune escape potential of BA.4/5, early monitoring was required to asses and implement countermeasures in time. In this study, we monitored the prevalence of SARS-CoV-2 BA.4/5 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 to detect BA.4/5. 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.4/5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V. Finally, the mutant fractions were quantitatively monitored by digital PCR confirming BA.4/5 as the majority variant by 5th June 2022. In conclusions, 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 variant spreading independent of individual test capacities.

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Author:Alexander WilhelmORCiDGND, Jens SchothGND, Christina Meinert-BerningGND, Daniel BastianORCiDGND, Sandra CiesekORCiDGND, Burkhard TeichgräberGND, Thomas WintgensORCiDGND, Frank-Andreas WeberGND, Marek WideraORCiDGND
Parent Title (English):medRxiv
Document Type:Preprint
Date of Publication (online):2022/07/29
Date of first Publication:2022/07/29
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/08/08
Issue:2022.07.27.22278003 Version 1
Edition:Version 1
Page Number:12
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Licence (German):License LogoCreative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International