Sequence features downstream of the primer-binding site of HIV type 1 subtype E shared by subtype G and a subset of subtype A

Two distinct sequence features downstream of the primer-binding site (PBS) were identified in a full-length HIV-1 subtype E clone amplified in this study. Both features are frequently found in HIV-1 subtypes A and G and in more than half of the full-length intersubtype recombinant clones. One of these is the absence of a trinucleotide sequence, which is located 14 nucleotides downstream of the PBS and found only in subtypes B, C, D, F, and H. The other is an insertion of 24 nucleotides immediately downstream of the PBS, which was previously reported as a sequence feature shared by subtypes A, E, and G. The analysis conducted here revealed that this 24-nucleotide insertion contained two sequence motifs duplicated in adjacent regions and was not found in all HIV-1 subtype A clones. Furthermore, our finding suggests that the PBS region of all known full-length subtype E clones, which are A/E intersubtype recombinants, is derived from the group of HIV-1 subtype A, which contains a similar insertion.