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

Autor: Widera, Alexander Wilhelm, Shelesh Agrawal, Jens Schoth, Christina Meinert-Berning, Daniel Bastian, Laura Orschler, Sandra Ciesek, Burkhard Teichgräber, Thomas Wintgens, Susanne Lackner, Frank-Andreas Weber, Marek
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Viruses; Volume 14; Issue 9; Pages: 1876
ISSN: 1999-4915
DOI: 10.3390/v14091876
Popis: 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.
Databáze: OpenAIRE
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