title: 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.
abstract: Sequences from the nef/LTR overlap region of the human immunodeficiency virus type 2 (HIV-2) genome were amplified from uncultured peripheral blood mononuclear cells (PBMCs) from 40 HIV-2-infected individuals in The Gambia, West 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-kappa B, and NF-kappa B sites) indicated a relatively high level of conservation in vivo. The region immediately 3' of the nef termination codon, which exhibits clade-dependent specificity, was targeted by PCR to differentiate HIV-2 subtype A from subtype B infections, the two principal clinical HIV-2 subtypes. All clinical samples analyzed (n = 43) from The Gambia were identified as HIV-2 subtype A by a combination of LTR sequence analysis and subtype-specific amplification of subtypes A and B. Differential PCR amplification of the HIV-2 U3 LTR region represents a rapid means of differentiating subtype A from subtype B infections, the two dominant HIV-2 subtypes that are important in human disease.
authors.affiliation: Department of Virology, Windeyer Institute of Medical Sciences, Royal Free and University College, London, United Kingdom. nberry@nibsc.ac.uk
authors.forename: N
authors.initials: N
authors.lastname: Berry
authors.forename: K
authors.initials: K
authors.lastname: Ariyoshi
authors.forename: P
authors.initials: P
authors.lastname: Balfe
authors.forename: R
authors.initials: R
authors.lastname: Tedder
authors.forename: H
authors.initials: H
authors.lastname: Whittle
mesh_terms: D001483:Base Sequence; D005714:Gambia / Q000453:epidemiology; D015693:Gene Products, nef / Q000235:genetics; D015658:HIV Infections / Q000821:virology*; D015498:HIV-2 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics*; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D015693:Gene Products, nef; D054311:nef Gene Products, Human Immunodeficiency Virus