Genomic structure and nucleotide sequence analysis of a new HIV type 1 subtype A strain from Nigeria

We have isolated and characterized a new HIV-1 variant (IW-1(IbNg)) from the peripheral blood mononuclear cells (PBMCs) of an inhabitant of Nigeria, This virus is highly cytopathic to PBMCs in culture, replicates in primary human T cells and macrophages/monocytes as web as in established human T cell and monocytic cell lines (i.e., it has a wide host range), and it does not induce syncytia in MT-2 cells.(1) Because of these unusual infectivity parameters in vitro, we analyzed the genetic structure of the entire genome, Using cytoplasmic RNA from HIV-1(IbNg)-infected PBMCs, five overlapping DNA fragments were amplified by the reverse transcriptase-polymerase chain reaction (RT-PCR) technique and cloned into pBluescript II SK(+), DNA sequencing of these fragments indicated that the entire HN-1(IbNg) genome consisted of 9201 nucleotides and phylogenetic analysis of its env gene sequence revealed that this virus clustered with HIV-1 strains belonging to clade ''A'', In this article we present several genetic features unique to this virus, including (1) the presence of a 16-bp insert within the primer-binding site, (2) a large Rev open reading frame, (3) a Rev-responsive element that is predicted to form a different secondary structure than described for clade ''B'' viruses, (4) the potential to encode a heavily glycosylated Env protein, and (5) a frameshift, resulting in a stop codon, in the tat gene, This represents the first detailed analysis of the genetic structure of an HIV-I strain from Nigeria.