Metagenomes of SARS-CoV-2 in wastewater samples from a city in arid Patagonia

Wastewater samples were collected spanning epidemiological weeks 41-2020 (amid first COVID-19 wave in Argentina) and 1-2022 (third wave). The samples were processed by a high-purity multi-step virion enrichment protocol involving sequential filtration with decreasing pore sizes for clarification, tangential filtration for virus concentration, and dialfiltration to remove salts and enzymatic inhibitors. Daily samples from each epidemiological week were combined into composite pools, which were further concentrated by tangential filtration to achieve final nominal concentrations of 700X. After purifying viral RNA from the concentrates, cDNA was synthesized using random hexamers followed by SARS-CoV-2 enrichment by tiled PCR with ARTIC (v3) panel. Libraries were created by the QIASeq FX DNA Library kit (Qiagen), and paired end (2x150) sequenced in a NovaSeq 6000 Illumina platform.