Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Nicolae Sapoval, Yunxi Liu, Esther G. Lou, Loren Hopkins, Katherine B. Ensor, Rebecca Schneider, Lauren B. Stadler, Todd J. Treangen
Abstract
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).
Topics & Concepts
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Coronavirus disease 2019 (COVID-19)Wastewater2019-20 coronavirus outbreakComputational biologyComputer scienceBiologyBioinformaticsMedicineVirologyEnvironmental scienceEnvironmental engineeringInternal medicineInfectious disease (medical specialty)OutbreakDiseaseSARS-CoV-2 detection and testingAdvanced biosensing and bioanalysis techniquesSARS-CoV-2 and COVID-19 Research