Wastewater Treatment Plants (WWTPs) based on activated sludge (AS) processes have demonstrated moderate capacity to remove viruses from wastewater. However, few studies have systematically assessed viruses along water and sludge treatment lines and their associations with Antibiotic-Resistant Genes (ARGs). In this work, the fate, distribution and possible interactions of RNA from SARS-CoV-2 and coliphage MS2 with ARGs in a full-scale AS WWTP were investigated. Total reductions of SARS-CoV-2 and MS2 RNA (2.5 and 2.4 log10 units, respectively) were achieved mainly in the water treatment line. In contrast, lower total reductions (0.7–1.5 log10 units) of 16S rRNA, class 1 integron-integrase (intI1), sulfonamide-resistant dihydropteroate synthase (sul1) and tetracycline resistance protein (tetO) were mainly achieved during sludge treatment. In addition to the water treatment line, sludge stabilisation was a critical barrier to controlling viral RNA and ARGs in the outflows. Amplification of intI1 and sul1 seemed to occur in the AS reactors, potentially associated with bacteriophage presence in these units. Thus, the participation of bacteriophages in the amplification of ARGs in AS systems should not be ruled out. RNA viruses and ARGs should be more frequently determined in WWTPs to assess and prevent phage-mediated amplification of ARGs.
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