SARS-CoV-2 has genetically changed since the first infections. The quick adaption of the virus to the new host led to mutations in the binding sites of the spike protein, which is known to increase the infectivity of the virus (Korber et al., 2020). The genome sequencing of wastewater has developed into an additional tool for better assessment of the infection situation.
This case study shows the dynamics of SARS-CoV-2 and its variants in wastewater samples of a city in Germany with roughly 300.000 inhabitants from April to June. We monitored the SARS-CoV-2 concentration and the abundance of the alpha variant (B.1.1.7) by RT-qPCR. Additionally, we used genome sequencing to screen the samples for the known variants of concern (VOCs). We used the Ion AmpliSeq SARS-CoV-2 research panel (Thermo Fisher Scientific) consisting of 237 primer pairs, resulting in an amplicon length range of 125 to 275 bp and covering the nearly full genome of SARS-CoV-2. RT-qPCR was performed as published in Agrawal et al. (2020).
We saw a steady decline in SARS-CoV-2 concentrations and loads over the course of the monitored 8 weeks, confirming local incidence values. The alpha variant was dominant with numbers of constantly > 90% abundance. Genome-sequencing confirmed that B.1.1.7 was the dominant VOC, but the delta variant (B.1.617.2.) started to appear starting mid of May reaching values of around 60% total VOC abundance. We were able to detect a trend in SARS-CoV 2 RNA over the period to be examined using qPCR, as well as a successful genome analysis using NGS. The potential benefit of wastewater-based SARS-CoV-2 monitoring is a reliable prediction of the overall condition of a given catchment area with much less effort than clinical monitoring.
