Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

Sapoval et al. introduce QuaID, a bioinformatics tool for SARS-CoV-2 variant detection based on quasi-unique mutations. QuaID leverages all mutations, including insertions and deletions, and provides precise detection of variants early in their spread. As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).