Abstract: A method of analyzing a sample possibly containing an HIV virus, including a) extracting viral RNA in a biological sample that possibly contains an HIV virus; b) reverse transcription of the RNA obtained of (a) and amplification with a first pair of primers to obtain an amplified product of reverse transcription including all or part of at least two successive genes of a genome of an HIV virus; and one or both of c) and d): c) sequencing the amplified product of (b) to establish a genotype of HIV virus present in the sample and identify mutations that may be present in the amplified product; d1) amplifying the product of (b) with a second pair of primers complementary to the first pair of (b) and capable of generating an amplification product that can be inserted by homologous recombination into a retroviral vector that is defective in a region corresponding to the amplified product; d2) homologously recombining the product of (d1) with the defective vector; d3) functionally analyzing the viral proteins coded