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

Abstract

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.

PIP: The authors isolated and characterized a new HIV-1 variant (HIV-1[IbNg]) from the peripheral blood mononuclear cells (PBMCs) of a person living in Nigeria. The 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, and it does not induce syncytia in MT-2 cells. Using cytoplasmic RNA from HIV-1[IbNg]-infected PBMCs, five overlapping DNA fragments were amplified through reverse transcriptase-polymerase chain reaction (RT-PCR) and cloned into pBluescript II SK(+). DNA sequencing of those fragments indicated that the entire HIV-1[IbNg] genome consists of 9201 nucleotides. Phylogenetic analysis of the variant's env gene sequence showed that the virus clustered with HIV-1 strains belonging to HIV-1 clade A. The following genetic features are unique to this virus: a 16-bp insert in the primer-binding site, a large Rev open reading frame, a Rev-responsive element which is predicted to form a different secondary structure than described for clade B viruses, the potential to encode a heavily glycosylated Env protein, and a frameshift resulting in a stop codon in the tat gene.