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 (HIV-1IbNg) 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 well 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-1IbNg-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 HIV-1IbNg 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-1 strain from Nigeria.
Laboratory of Viral Oncology, and AIDS Research, University of Southern California, School of Medicine, Los Angeles 90032-3626, USA.
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Howard
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Rasheed
D000328:Adult; D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry; D016679:Genome, Viral; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009549:Nigeria; D010802:Phylogeny
D004279:DNA, Viral