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- Title
Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater.
- Authors
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
- 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.
- Subjects
NORTH Rhine-Westphalia (Germany); SARS-CoV-2 Omicron variant; SARS-CoV-2; SEWAGE disposal plants; SINGLE nucleotide polymorphisms; SEWAGE
- Publication
Viruses (1999-4915), 2022, Vol 14, Issue 9, p1876
- ISSN
1999-4915
- Publication type
Article
- DOI
10.3390/v14091876