Sequence specificity of the human immunodeficiency virus type 2 (HIV-2) long terminal repeat U3 region in vivo allows subtyping of the principal HIV-2 viral subtypes A and B

Sequences from the nef/LTR overlap region of the human immunodeficiency vir us type 2 (HIV-2) genome were amplified from uncultured peripheral blood mo nonuclear cells (PBMCs) from 40 HIV-2-infected individuals in The Gambia, W est Africa. Additional sequences from the plasma of three blood donors were also derived. Analysis of HIV-2 U3 LTR transcription factor elements (PuB- 1, p-ets, PuB-2, peri-kappaB, and NF-kappaB sites) indicated a relatively h igh level of conservation in vivo. The region immediately 3' of the nef ter mination codon, which exhibits clade-dependent specificity, was targeted by PCR to differentiate HIV-2 subtype A from subtype B infections, the two pr incipal clinical HIV-2 subtypes. All clinical samples analyzed (n = 43) fro m The Gambia were identified as HIV-2 subtype A by a combination of LTR seq uence analysis and subtype-specific amplification of subtypes A and B. Diff erential PCR amplification of the HIV-2 U3 LTR region represents a rapid me ans of differentiating subtype A from subtype B infections, the two dominan t HIV-2 subtypes that are important in human disease.