ERX4624797 webin-reads-CoV_305_S65640 ERP123414 PRJEB39849 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio. Amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the 2100 Bioanalyzer system (Agilent). Amplicon concentrations were normalized, and sequencing libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (NewEngland Biolabs) according to manufacturer’s instructions. The library was sequenced in PE mode with 250 cycles. ERS5215842 SAMEA7457658 AMPLICON METATRANSCRIPTOMIC RT-PCR Illumina NovaSeq 6000