UIS mapping and quantification of abundance. (A) Genomic DNA was extracted from PBMCs and sonicated. The end of the 3′-long terminal repeat and a fragment of genomic DNA were amplified by ligation-mediated PCR and the products sequenced on an Illumina Genome Analyser. (B) In this example, a genomic DNA sample contains 4 proviral copies from infected T-cell clone X and 1 copy from clone Y. Because the DNA shear site is random, the amplicon from each cell in clone X has a different shear site. The abundance of each UIS is quantified by counting the number of different shear sites for that UIS.