title: Sequence analysis of selected regions of the env (V3 loop and gp41) and gag (p7) reading frames of Ethiopian human immunodeficiency virus type 1 strains.
abstract: Amplified polymerase chain reaction (PCR) products, corresponding to the V3 loop and gp41 of the env, and p7 of the gag region, from proviral DNA of several Ethiopian and Swedish HIV-1 strains were sequenced. Of the six amino acids (GPGRAF) that constitute the principal neutralizing determinant (PND) within the V3 loop, the Ethiopian isolates all showed two amino acid changes (GPGQTF). Four to five other substitutions were found in the amino acids flanking the PND. Substitution of alanine (A) for threonine (T) should result in a change in the predicted secondary structure, i.e., disappearance of a coil structure. Percentage similarity data on a stretch of 22 amino acids within the V3 loop showed a concordance of the Ethiopian HIV-1 isolates with the sequences of published macrophage-T-cell tropic HIV isolates. Additionally derived protein sequences in two other regions showed two common substitutions in p7 and one to two substitutions in gp41 compared to a recent consensus sequence. These changes are hitherto unique for the Ethiopian strains, and suggest the presence of a clustering of a divergent HIV-1 strain in Addis Ababa, Ethiopia.
authors.affiliation: Department of Biology, Addis Ababa University, Ethiopia.
authors.forename: S
authors.initials: S
authors.lastname: Ayehunie
authors.forename: B
authors.initials: B
authors.lastname: Johansson
authors.forename: A
authors.initials: A
authors.lastname: Sönnerborg
authors.forename: D W
authors.initials: DW
authors.lastname: Zewdie
authors.forename: S
authors.initials: S
authors.lastname: Britton
authors.forename: O
authors.initials: O
authors.lastname: Strannegård
mesh_terms: D000595:Amino Acid Sequence; D036022:Capsid Proteins; D004279:DNA, Viral / Q000737:chemistry; D005002:Ethiopia; D015683:Gene Products, gag / Q000737:chemistry* / Q000235:genetics; D015752:Genes, env / Q000235:genetics; D015750:Genes, gag / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000737:chemistry* / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D011533:Proviruses / Q000235:genetics*; D016364:Reading Frames; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013548:Sweden; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
chemical_list: D036022:Capsid Proteins; D004279:DNA, Viral; D015683:Gene Products, gag; D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; C059762:HIV envelope protein gp120 (305-321); C071884:NCP7 protein, Human immunodeficiency virus 1; D010446:Peptide Fragments; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus