design: RNA of 100 L of each sample supernatant was extracted using TRIzol reagent (Invitrogen) following the manufacturers protocol. RNA was eluted in 30 L of nuclease-free water. After quantification using Quant-IT RNA assay kit (Thermo Fisher Scientific), viral RNA was enriched using polyA selection NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Libraries were prepared with NEBNext Ultra II RNA Library Prep Kit for Illumina. The quality of the libraries was verified using a High Sensitivity DNA Chip (Agilent) and quantified using the Quant-iT DNA assay kit (Thermo Fisher Scientific). Sequencing of the libraries was performed on a NextSeq 500 sequencer (Illumina) with a NextSeq Mid Output kit v2 (151 cycles).