Detection of SARS-CoV-2 variants related mutations in wastewater using RT-qPCR and variant-specific probes in Porto Alegre, Southern Brazil

ABSTRACT The COVID-19 pandemic has underscored the significance of monitoring genetic variations in pathogenic viruses to manage its transmission and identify emerging variants. Nonetheless, sequencing every positive patient case is impractical for large-scale testing of the population. Here, we introduce a cost-effective tool for identifying SARS-CoV-2 mutations associated with variants in wastewater. This approach relies on a wastewater surveillance system and reverse transcription-quantitative polymerase chain reaction (RT-qPCR), utilizing mutation-specific probes. Wastewater samples were analyzed for SARS-CoV-2 mutations corresponding to variants under monitoring (VUM) (P.2, alpha, beta, gamma, delta, and omicron) as part of a wastewater-based SARS-CoV-2 monitoring program. Our findings validate the efficacy of this method in detecting SARS-CoV-2 mutations linked to variants in wastewater, facilitating early detection of emerging variants and informing decision-making on control measures.