Fig. 3

PCR primers used in the amplification reaction, and their cognate substrates. We amplify both LTR/host junctions and the primers for both ends of the provirus are shown. Panel a. At the top is a drawing of the T-linker, and the first and second linker primers. The blocking group (NH3, C6) on the 3′ end of the short strand of the T-linker is shown, and the 5′ end of short strand is phosphorylated (P), to allow it to be ligated to the host DNA. The second linker primer is used to add the sequences needed for Illumina sequencing to one end of the amplified fragment. The first and second LTR primers used to amplify the 5′ LTR are shown in the drawing, with the linker primers used to amplify the host-virus DNA junction. The sequences needed for Illumina sequencing to the other end of the amplified fragments are added as part of the second LTR primer. Panel b shows the amplification of the 3′ LTR and the appended host sequences, together with the first and second LTR primers (see also Fig. 2). Panel c At the bottom of the drawing, are the corresponding primers used to amplify the 5′ LTR