Fig. 1

Schematic of the mutations observed in defective HIV proviruses. The HIV genome is depicted on top, with underneath the large deletions and hypermutations (X, nucleotide substitution) that are found in 77–90% of defective proviruses in patients receiving therapy [3, 5, 13]. The bottom part represents a blow-up of the untranslated leader region of the HIV genome (RNA coordinates + 182/+ 338) that is affected in the MSD-Ѱ class of defective proviruses. We marked the position of several replication signals (PBS primer binding site, DIS dimerization initiation signal, AUG-Gag is the first start codon that is used for Gag translation). The deletions and mutations reported by Ho et al. [3] are schematically depicted, showing clustering around the MSD (shadowed)