Objective: To determine HIV-1 genomic RNA and proviral DNA sequences of thethird hypervariable region (V3 loop) of the envelope protein in patients with primaryHIV-1 infection (PHI), and to compare these sequences with sequences from patientswith more advanced HIV-1 infection.Methods: Sera and peripheral blood mononuclear cells were collected from 24patients with PHI living in Geneva. V3 sequences were determined using directsolid-phase sequencing on polymerase chain reaction (PCR) products.Results: A 100% homology rate was observed between HIV-1 genomic RNA andproviral DNA paired nucleotide sequences from the V3 region in the 24 patients.Using a limiting dilution approach for three patients, a unique V3 sequence wasobserved for the genomic RNA. Three out of 24 amino-acid sequences presented thecharacteristic signature sequence QRGPGR, first described for the HIV-1 LAI isolate,which is associated with lymphocytotropism. These three isolates also presented, forthe V3 loop, a characteristic elevated charge (8) at physiological pH in comparisonwith the other isolates (3–5). There was no significant difference in the distribution ofamino acids between the 24 V3 loop sequences from patients with PHI and 245 V3loop sequences of the 6 subtype determined in patients with more advanced HIV-1infection.Conclusion: The paired sequences recovered from HIV-1 genomic RNA and proviralDNA are identical for each of the 24 patients with PHI. Three isolates had the V3 loopcharacteristic signature sequence QRGPGR first described for the HIV-1 LAI isolate.There is no characteristic V3 loop pattern associated with PHI isolates.