FIG 1.

The HIV-SMART protocol workflow. Benzonase treatment is required for clinical specimens prior to RNA extraction. The HIV-1 genome is shown with the locations of six HIV-SMART fusion primers that initiate reverse transcription of viral RNA. In the cDNA reaction, nontemplated bases (XX) are added to the ends of nascent cDNA, to which the SMART oligonucleotide anneals. The RT polymerase switches strands to transcribe the complement of the oligonucleotide, leaving the SMART adaptor at both ends of cDNA. Long-distance PCR with a single SMART primer amplifies libraries and is followed by fragmentation and addition of Illumina primer and barcode sequences with Nextera XT reagents.