As the SARS-CoV-2 genome evolves, its genetic mutations can give rise to new variants of concern (VOCs) that are more deadly, infectious, or difficult to treat. Surveillance solutions can identify, detect, and confirm these high-risk variants. However, to effectively control their spread, timing is key – the sooner VOCs are detected, the sooner measures can be put in place to limit their transmission.
Wastewater-based surveillance may provide an early warning of rising SARS-CoV-2 transmission by detecting viral RNA in sewage samples before outbreaks appear. When combined with next-generation sequencing (NGS), wastewater surveillance can provide detailed genetic mutation data to distinguish between variants. For example, a pan-European study identified 633 mutations associated with VOCs across 54 municipalities and 20 countries using the Ion Torrent platform. Wastewater surveillance with NGS can also help us monitor the spread of SARS-CoV-2 variants within a population over time.
Now, a recent preprint by Joshi et al. describes early wastewater detection of the Delta variant weeks before any clinically confirmed cases in Ahmedabad, India, highlighting the value of wastewater-based NGS surveillance for high-risk variants.
Joshi et al. collected four samples: freshwater and untreated wastewater samples in late 2020 during India’s first wave and treated and untreated wastewater samples in February 2021 about a month before the second wave. A total of 35 spike protein mutations were detected across all four samples using an Ion Torrent 530™ chip on an Ion GeneStudio S5™ System. Mutations linked to the Delta variant were only present in the February 2021 samples. Importantly, these Delta variant mutations were detected in Ahmedabad’s wastewater more than a month before its first clinical case with the Delta variant in March 2021.
As noted by Joshi et al., an advantage of wastewater-based NGS surveillance is that requires fewer resources than sequencing multiple swab samples. It also represents a broader population, as most buildings are typically connected to municipal wastewater systems, whereas only some swab samples may be sequenced. But aside from its scale, what is most compelling about community-based wastewater surveillance is that it can potentially detect VOCs before they appear in individual samples. As SARS-CoV-2 variants continue to emerge and spread around the globe, wastewater surveillance with NGS may provide an early warning signal of high-risk variants, which could ultimately trigger rapid interventions to limit their spread.
Joshi et al.’s study is available as a preprint on MedRxiv.
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