Figure 1.

HIV-xGen strategy. 651 probes were selected to tile all HIV-1 and HIV-2 strains present in the phylogenetic tree at 1X coverage. Reverse transcription and second strand synthesis were performed by random priming with Superscript/Sequenase or by the HIV-SMART method. Nextera XT was used to convert cDNA to barcoded Illumina libraries consisting of both HIV (red inserts) and background (black) reads. Pooled libraries were hybridized to xGen probes (green) with 5′-biotin tags (gold) for a single capture and selected by magnetic bead separation. Multiplexed libraries were amplified by universal KAPA primers, sequenced on a MiSeq, and reads were parsed by barcode.