Sequence Analysis of the Glycoprotein 120 Coding Region of a New HIV Type 1 Subtype A Strain (HIV-1IbNg) from Nigeria

Abstract

A new subtype A strain of HIV-1, designated HIV-1 IbNg, was isolated from the peripheral blood mononuclear cells (PBMCs) of an HIV-seropositive, but healthy, 23-year-old blood donor from Ibadan, Nigeria. Analysis of the envelope-encoding sequences of HIV-1 strains isolated from the major centers of the AIDS pandemic has identified at least 9 distinct HIV-1 genetic clusters or clades, tentatively designated as A, B, C, D, E, F, G, H, and O. The gp120-coding region of HIV-1 IbNg was characterized. The env gene was amplified from viral RNA using the reverse transcriptase-polymerase chain reaction (RT-PCR) technique. RNA was prepared by cocultivations of PBMCs from the Nigerian subject with phytohemagglutinin-stimulated PBMCs from an HIV seronegative donor. The PCR products were cloned into pBluescriptIIsK(+) and sequenced by the dideoxy chain termination method. Nucleotide sequence data were used to generate a consensus nucleotide sequence of the entire gp120-coding region of HIV-l IbNg, using the Sequence Analysis Software Package. Alignment of the nucleotide sequences of the env gene of HIV-1 IbNg with those of other known HIV-1 strains indicated that this virus most closely clustered with HIV-1 strains belonging to the A subtype, which was in agreement with the observation that this subtype is most closely associated geographically with central and western Africa. DNA sequence analysis of the env genes of 4 additional HIV-1 strains (G3, G9, JV1083, and JP88) from Nigeria indicated that these strains clustered most closely with HIV-1 strains belonging to the G subgroup. Characterization of the entire genomic sequence of HIV-1 IbNg is important for identifying molecular structure(s) of viral gene(s) that may be involved in the pathogenesis of subtype A strains in Nigeria. Research is currently underway to obtain a complete sequence of the entire HIV-1 IbNg genome.