PR8 virus (optimized RT-PCR protocol, RT-PCR products sheared with Covaris and sequenced on Illumina MiSeq)
To construct the library, 500 ng of the RT-PCR products was sheared with an M220 focused-ultrasonicator (Covaris) set to obtain peak fragment lengths of 300-400 bp. Next, the NEBNext Ultra DNA Library Preparation kit (New England Biolabs) was used to repair the ends and to add Illumina MiSeq-compatible barcode adapters to 100 ng of fragmented DNA. The resulting fragments were size-selected using Agencourt AMPure XP bead sizing (Beckman Coulter). Afterwards, indexes were added in a limited-cycle PCR (10 cycles), followed by purification on Agencourt AMpure XP beads.