Characterization of a long terminal repeat region from an infectious Indian HIV type 2 isolate

An infectious Indian human immunodeficiency virus type 2 isolate from Mumbai, propagated in this laboratory, was found to bear an unusually short long terminal repeat (LTR) region. Complete sequencing of the 601 bp LTR indicated a loss of around 250 nucleotide pairs from the unique 3' (U3) region as compared to other well-characterized HIV-2 isolates. Phylogenetic analysis of this LTR shows closest relatedness to the Guinea-Bissau subtype A isolates HIV-2(CAM2) and HIV-2(ALI). The LTR from the biologically active infectious clone with the observed deletion contained all functionally relevant promoter and polyadenylation sequences.