Fig. 1

Phylogenetic analysis of HIV-1 env evolution during clinical follow-up. a Clinical follow-up. Viral load (circles), percentage of CD4 + (squares) and CD8 + T cells (triangles) during the patient follow-up are represented. The x axis refers to years after HIV-1 diagnosis. Colored circles indicate samples taken during the patient follow-up and that are included in the phylogenetic analysis. The dotted grey line separates samples before and after LVC. b Phylogenetic analysis revealed the presence of three HIV-1 variants. Two different viruses (A and B) and two different subpopulations (B1 and B2) are represented. A Maximum likelihood (ML) phylogenetic tree based on the C2-V5 env region was constructed with 201 unique sequences obtained from proviral DNA (circles), plasma viral RNA (triangles) and virions co-cultured RNA (squares). The sequences obtained at different times points during the patient follow-up are color coded. The identical sequences are included in boxes. Branch lengths are presented as the number of substitutions per site. Bootstrap values above 85% are shown with asterisks. ES61 and HXB2 sequences were included as outgroup viruses to root the phylogenetic tree. c. Replacement of viral populations in proviral sequences during follow-up. A, B1 and B frequency (%) obtained at different times points are represented color coded. The grey line indicates samples collected after LVC