Wastewater surveillance has proven its worth as a strategy for researching community-scale information about SARS-CoV-2 prevalence. Measuring titers of SARS-CoV-2 genetic material in wastewater offers a window into current and future infection rates at the level of whole municipalities, providing clues that can guide community-based public health initiatives faster than testing individual samples. This approach has important limitations.
Typical wastewater surveillance measures overall viral levels, which is important for predicting when local healthcare systems might become overwhelmed. However, this measurement cannot distinguish between strains. The enduring, global nature of the SARS-CoV-2 outbreak means that knowing more detail on circulating strains and how virus composition changes is more valuable than ever. The world is deeply connected. Local and regional events, such as the appearance of new or previously absent variants of concern (VOCs) in a particular place, inform mitigation strategies worldwide. Agrawal et al. set out to prove that this level of surveillance could be done with wastewater as part of the European Union Sewage Sentinel System for SARS-CoV-2.
The team studied SARS-CoV-2 genetic material from wastewater in 54 municipalities from 20 European countries using an Ion Torrent 530™ chip on an Ion GeneStudio S5™ System. Thanks to the system’s extremely high sensitivity (with a detection limit as low as 20 copies), Agrawal et al. were able to not only quantify overall SARS-CoV-2 titers in their samples but also distinguish and identify 711 different mutations, of which 633 were associated with VOCs. The mutations and variants they discovered corresponded to those seen in the above-mentioned countries during routine individual testing. For example, the 25 A220V mutation appeared only in wastewater samples from Lithuania, matching similar reports from Lithuanian clinical patient samples taken at the same time. Such complete genomic profiles from wastewater enabled researchers to address questions previously only answerable with other data sources, including which strains were prevalent throughout a given country versus which ones were only locally abundant. This shows consistency with the available clinical screening data.
Agrawal et al.’s study shows that wastewater-based epidemiology is up to the task of quantifying not just overall SARS-CoV-2 titers, but separate titers for VOCs, thanks to the sensitivity and ease of use of the Ion Torrent platform. With detailed sequencing data from NGS-based surveillance, community spread of new variants will be easier to track and measure. Wastewater surveillance cannot replace testing individuals, but it can supplement it by providing community-level information on viral genome sequences.
Agrawal et al.’s study is available as a preprint on MedRxiv.
Learn about the Ion AmpliSeq™ SARS-CoV-2 Insight Research Assay for research-based viral typing, discovery and epidemiological investigation using next-generation sequencing (NGS). Discover the Ion Torrent targeted NGS portfolio for SARS-CoV-2 research.
For research use only. Not for use in diagnostic procedures.