SARS-CoV-2 variants of concern, Gamma (P.1) and Delta (B.1.617), sensitive detection and quantification in wastewater employing direct RT-qPCR

SARS-CoV-2 variants of concern present a worldwide threat. Demonstrating higher infection rate and durability to antibodies when compared to the original SARS-CoV-2 virus, the variants of concern are responsible for continuing global outbreaks. Prompt identification of the infecting SARS-CoV-2 variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive, time-consuming next generation sequencing. Rapid identification methodology for variants of concern is of great need and various variant-specific assays are being developed. Amongst the variants of concern that have recently appeared, the Gamma variant (P.1, Brazilian) and Delta variant (B.1.617, Indian) are the most prominent. Here we describe the development of a sensitive RT-qPCR assay for the quick direct detection of the Gamma and Delta variants as part of a methodical characterization and detection in municipal wastewater.