MiSeq of HIV-1 envelope V3
HIV RNA was extracted from plasma with QIAamp Viral RNA Mini Kit. cDNA was generated with SuperScript III using a custom cDNA primer targeting the envelope region, which also incorporated Unique Molecular Identifiers into each template. Final amplicons were generated with two rounds of PCR using custom primers, including MiSeq adapters, then subjected to MiSeq (V3, 600 cycles, paired-end).