Multiplexed Illumina MiSeq of HIV: 87 weeks post-infection
Viral RNA was reverse transcribed to cDNA using Superscript III/IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 2 indexes and adapters. PCR products were purified using SPRIselect beads (Beckman Coulter).