vpu and env sequence variability of HIV-1 isolates from Tanzania.

The nucleotide sequences of an approximately 1400-base pair (bp) region spanning the vpu and env (V1-V3) genes of 9 HIV-1 isolates originating from Tanzania were determined. Peripheral blood lymphocyte (PBL) specimens were obtained in 1988 from urban patients with clinical signs of AIDS attending the Muhimbili Medical Center Dar es Salaam Tanzania. 9 samples (TZ005 TZ012 TZ016 TZ017 TZ023 TZ030 TZ053 TZ064 and TZ112) were randomly chosen for virus isolation by cocultivation with HIV-negative donor PBLs. Viral DNA sequences between the positions 5543 and 6956 were amplified by polymerase chain reaction (PCR) using 2 sets of primer pairs subcloned into a Bluescript vector and sequenced on both strands. Sequence analysis revealed vpu and env open reading frames (ORFs) for all clones except 2 that had a missense mutation in vpu (TZ016) or env (TZ017). The vpu sequences showed a high degree of homology among all isolates with TZ005 TZ016 and TZ030 having identical sequences. Phylogenetic tree analysis indicated that most of the isolates fell into the D subtype. The analysis of the deduced protein sequences of the V3 loop which contains the principal neutralizing domain (PND) revealed an amino acid pattern closely related but not identical to known African HIV isolates. The GSGQ motif was found in 4 isolates (TZ005 TZ030 TZ053 and TZ080) and the GPGQ motif was found in 2 cases (TZ016 and TZ017). The V3 variability of the HIV isolates was greater than previously reported for Tanzanian viruses. Although AIDS viruses are believed to have originated from Africa little is known about the sequence variability of African HIV-1 isolates compared to the information available on Euro-American viruses. The variability of East African HIV-1 isolates are consistent with the view that these are rapidly changing viruses for which further variants are likely to be discovered.