title: 1HC2_Day0_FLEA_SMRT (2 technical replicates)
design: Three subjects were selected for SMRT sequencing analysis based on time of rebound, high viral load, and sample availability. Full-length HIV-1 env was amplified and sequenced on the Pacific Biosciences RS-II as described previously (http://ve.oxfordjournals.org/content/2/2/vew018) with two minor modifications. First, primers were designed specifically for sequenced subjects using available SGS sequences that spanned the primer regions. Primers used for amplification were 5’-GAGCAGARGACAGTGGCAATGA-3’ and 5’-GGAGAATAGCTCTACGAGCTCTTTG-3’ for 1HB3, 5’GAGCAGAAGACAGTGGCAATGA-3’51 and 5’TGACCATTTATTGCCCATCTTATAGC-3’ for 1HC2 and 5’-GAGCAGAAGACAGTGGCAATGA-3’51 and 5’-CCACTTGCCACCCATTTTATAGGA-3’ for 1HD1. Second, the more recent PacBio P6-C4 chemistry was used.