Viral_DNA/cDNA
Viral nucleic acids were extracted using All Prep Power Viral DNA/RNA kit (Qiagen). Viral RNA was reverse transcribed into cDNA with Maxima h-minus double stranded cDNA synthesis kit (Thermo fisher scientific). Amplified DNA/cDNA was purified with GeneJet PCR Purification kit (Thermo Fisher Scientific). DNA was quantified using dsDNA HS Assay Kit (ThermoFisher Scientific) on a Qubit 3.0 instrument (Life Technologies) and processed for tagmentation and indexing using the Illumina Nextera XT Library prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer protocol. Libraries were then diluted and sequenced on Illumina Miseq platform using a V3-600 cycles chemistry.