Fig. 1

Overlapping fragment PCR strategy to assemble whole HTLV-1c genomes. A An overlapping PCR strategy was used to amplify the complete 9 kb HTLV-1c proviral genome from gDNA isolated from 22 infected participants. Five sets of oligonucleotides were used, each amplifying a region of the HTLV-1c genome: A (odp3100-odp3160, 1426nt); B (odp3161-odp3162, 2693nt); C (odp3163-odp3164, 1038nt); D (odp3165-odp3141, 2866nt) and E (odp3166-odp3101, 1108nt). The outer PCR fragments were then subjected to a nested PCR using overlapping primer pairs, followed by direct sequencing of the purified PCR products and assembly of the reads. B Representative agarose gel electrophoreses of PCR amplicons show intact sequences (MT2 cell line gDNA), a 5′ deletion and large internal deletions (HTLV-1c + gDNA). Asterisks (*) indicate amplicons with a smaller size than expected, which is likely derived from deleted proviruses