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

medRxiv

Abstract

Abstract 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.

Authors 9

1. Alexander Wilhelm

   University Hospital Frankfurt · Goethe University Frankfurt

   Affiliation as printed

   Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany

2. Jens Schoth

   Emschergenossenschaft

   Affiliation as printed

   Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany

   Emschergenossenschaft/Lippeverband, Kronprinzenstraße 4, D-4518 Essen, Germany

3. Christina Meinert‐Berning

   Ruhrverband (Germany)

   Affiliation as printed

   Ruhrverband, Kronprinzenstraße 37, D-45128 Essen, Germany

   Ruhrverband, Kronprinzenstraße 7, D-45128 Essen, Germany

4. Daniel Bastian Aachen FiW e.V Research Institute for Water Management and Climate Future

   RWTH Aachen University

   Affiliation as printed

   FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany

5. Sandra Ciesek

   German Center for Infection Research · University Hospital Frankfurt · Goethe University Frankfurt · Fraunhofer Institute for Translational Medicine and Pharmacology

   Affiliation as printed

   Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, D 60595 Frankfurt am Main, Germany

   German Center for Infection Research (DZIF), 38124 Braunschweig, Germany

   Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany

   Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, D 0595 Frankfurt am Main, Germany

6. Burkhard Teichgräber

   Emschergenossenschaft

   Affiliation as printed

   Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany

   Emschergenossenschaft/Lippeverband, Kronprinzenstraße 4, D-4518 Essen, Germany

7. Thomas Wintgens Aachen Institute of Environmental Engineering FiW e.V Research Institute for Water Management and Climate Future

   RWTH Aachen University

   Affiliation as printed

   FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany

   Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074, Aachen, Germany

   Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-5204, Aachen, Germany

8. Frank‐Andreas Weber Aachen FiW e.V Research Institute for Water Management and Climate Future

   RWTH Aachen University

   Affiliation as printed

   FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany

9. Marek Widera corresponding

   University Hospital Frankfurt · Goethe University Frankfurt

   Affiliation as printed

   Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany