title: V3 sequences in primary HIV-1 infection.
abstract: OBJECTIVE
  To determine HIV-1 genomic RNA and proviral DNA sequences of the third hypervariable region (V3 loop) of the envelope protein in patients with primary HIV-1 infection (PHI), and to compare these sequences with sequences from patients with more advanced HIV-1 infection.
  
  
  METHODS
  Sera and peripheral blood mononuclear cells were collected from 24 patients with PHI living in Geneva. V3 sequences were determined using direct solid-phase sequencing on polymerase chain reaction (PCR) products.
  
  
  RESULTS
  A 100% homology rate was observed between HIV-1 genomic RNA and proviral DNA paired nucleotide sequences from the V3 region in the 24 patients. Using a limiting dilution approach for three patients, a unique V3 sequence was observed for the genomic RNA. Three out of 24 amino-acid sequences presented the characteristic signature sequence QRGPGR, first described for the HIV-1LAI isolate, which is associated with lymphocytotropism. These three isolates also presented, for the V3 loop, a characteristic elevated charge (8) at physiological pH in comparison with the other isolates (3-5). There was no significant difference in the distribution of amino acids between the 24 V3 loop sequences from patients with PHI and 245 V3 loop sequences of the B subtype determined in patients with more advanced HIV-1 infection.
  
  
  CONCLUSIONS
  The paired sequences recovered from HIV-1 genomic RNA and proviral DNA are identical for each of the 24 patients with PHI. Three isolates had the V3 loop characteristic signature sequence QRGPGR first described for the HIV-1LAI isolate. There is no characteristic V3 loop pattern associated with PHI isolates.
authors.affiliation: Department of Medicine, Geneva University Hospital, Switzerland.
authors.forename: I M
authors.initials: IM
authors.lastname: Antonioli
authors.forename: C
authors.initials: C
authors.lastname: Baumberger
authors.forename: S
authors.initials: S
authors.lastname: Yerly
authors.forename: L
authors.initials: L
authors.lastname: Perrin
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral / Q000032:analysis; D018450:Disease Progression; D005260:Female; D015752:Genes, env; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics*; D011533:Proviruses / Q000235:genetics*; D012367:RNA, Viral / Q000032:analysis*; D017386:Sequence Homology, Amino Acid
chemical_list: D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D012367:RNA, Viral