Whole genome, deep sequencing of Hepacivirus C: UK retreatment patient
RNA was isolated from 200 microlitres of plasma using the RNAdvance Blood extraction kit (Beckman Coulter) and collected in 27 microlitres of water. Following conversion of RNA to double-stranded DNA, libraries were prepared for Illumina sequencing using the KAPA DNA LTP Library Preparation Kit (Roche), and NEBNext Multiplex Oligos for Illumina (NEB).  Libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution assessed using Agilent TapeStation with D1K High Sensitivity Kit (Agilent); libraries were normalised accordingly to viral load and mass. A 500ng aliquot of the pooled library was enriched using SeqCap EZ Developer Probes (Roche), following the manufacturer's protocol. Following a 14 cycle post-enrichment PCR, the cleaned pool was sequenced with 151-base paired-end reads on an Illumina NextSeq cartridge.