Full-length sequence of an ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C

Abstract

Genetic subtype C of the human immunodeficiency virus type-1 (HIV-1) has established foci of infection in India and in at least eight African countries, and is expected to contribute significantly to the global pandemic. Here we report the first almost full-length sequence of a subtype C HIV-1 from Ethiopia. Clone C2220, 9031 nt in length, was derived by long PCR amplification of proviral DNA from virus cultured on primary peripheral blood mononuclear cells, and contains all but 74 nt of the unique sequence information of the HIV-1 genome. This clone resembles HIV-1 isolates of subtypes A, B, and D in its genome organization with one notable exception: the core promoter contains not two, but three potential binding sites for the transcription factor NF-kB. The extra NF-kB site was found in all other Ethiopian strains analyzed, as well as in subtype C viruses from Zambia, suggesting it is typical for the C-subtype of HIV-1. The phylogenetic relationship of C2220 to other HIV-1 isolates is also presented. Subtype C viruses circulating in Ethiopia exhibit the low interisolate diversity typical of other, newly established HIV-1 epidemics, and C2220 is both representative of Ethiopian subtype C viruses and a suitable prototype for the development of vaccines against HIV-1 subtype C.

PIP: Foci of HIV-1 subtype C infection exist in India and at least eight African countries. HIV-1 subtype C will likely contribute significant numbers of cases to the global AIDS pandemic. The first almost full-length sequence of a subtype C HIV-1 from Ethiopia is presented. Clone C2220, 9031 nucleotides long, was derived by long polymerase chain reaction amplification of proviral DNA from virus cultured on primary peripheral blood mononuclear cells and contains all but 74 nucleotides of the unique sequence information of the HIV-1 genome. The clone's genome organization resembles HIV-1 isolates of subtypes A, B, and D except that its core promoter contains three rather than two potential binding sites for transcription factor NF-kB. The extra NF-kB site was found in all other Ethiopian strains analyzed, as well as in subtype C viruses from Zambia, suggesting that the configuration is typical for subtype C HIV-1. The phylogenetic relationship of C2220 to other HIV-1 isolates is also presented.