Wastewater surveillance allows early detection of SARS-CoV-2 omicron in North Rhine-Westphalia, Germany

  • Wastewater-based epidemiology (WBE) has demonstrated its importance to support SARS-CoV-2 epidemiology complementing individual testing strategies. Due to their immune-evasive potential and the resulting significance for public health, close monitoring of SARS-CoV-2 variants of concern (VoC) is required to evaluate the regulation of early local countermeasures. In this study, we demonstrate a rapid workflow for wastewater-based early detection and monitoring of the newly emerging SARS-CoV-2 VoCs Omicron in the end of 2021 at the municipal wastewater treatment plant (WWTP) Emschermuendung (KLEM) in the Federal State of North-Rhine-Westphalia (NRW, Germany). Initially, available primers detecting Omicron-related mutations were rapidly validated in a central laboratory. Subsequently, RT-qPCR analysis of purified SARS-CoV-2 RNA was performed in a decentral PCR laboratory in close proximity to KLEM. This decentralized approach enabled the early detection of K417N present in Omicron in samples collected on 8th December 2021 and the detection of further mutations (N501Y, Δ69/70) in subsequent biweekly sampling campaigns. The presence of Omicron in wastewater was confirmed by next generation sequencing (NGS) in a central laboratory with samples obtained on 14th December 2021. Moreover, the relative increase of the mutant fraction of Omicron was quantitatively monitored over time by dPCR in a central PCR laboratory starting on 12th December 2021 confirming Omicron as the dominant variant by the end of 2021. In conclusions, WBE plays a crucial role in surveillance of SARS-CoV-2 variants and is suitable as an early warning system to identify variant emergence. In particular, the successive workflow using RT-qPCR, RT-dPCR and NGS demonstrates the strength of WBE as a versatile tool to monitor variant spreading.

Download full text files

Export metadata

Additional Services

Share in Twitter Search Google Scholar
Author:Alexander WilhelmORCiDGND, Jens SchothGND, Christina Meinert-BerningGND, Shelesh AgrawalORCiDGND, Daniel BastianORCiDGND, Laura OrschlerORCiDGND, Sandra CiesekORCiDGND, Burkhard TeichgräberGND, Thomas WintgensORCiDGND, Susanne LacknerORCiDGND, Frank-Andreas WeberGND, Marek WideraORCiDGND
Parent Title (English):Science of the total environment
Place of publication:Amsterdam
Document Type:Article
Date of Publication (online):2022/07/20
Date of first Publication:2022/07/16
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/11/10
Tag:B.1.1.529; COVID-19 surveillance; Detection workflow; Omicron; SARS-CoV-2 monitoring; Variant of concern; Wastewater-based epidemiology (WBE)
Article Number:157375
Page Number:8
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