Efforts to eradicate HIV-1 require a comprehensive examination of the quantity and genetic makeup of HIV-1 populations within infected cells located in tissues throughout the body. Therefore, we conducted a longitudinal analysis of the infection frequencies and genetic makeup of HIV-1 in specific CD4+ T cell subsets in different tissue compartments from patients on long-term suppressive therapy.
Methods: Using single-genome and single-proviral sequencing techniques, we isolated intracellular HIV-1 genomes derived from defined subsets of T cells (naïve, central-, transitional-, and effector-memory) from peripheral blood, GALT, and lymph node tissue. Samples were collected at 2 time points (separated by 6 months) from 8 subjects on suppressive therapy (4-12 years): 5 who initiated therapy during acute infection and 3 who initiated therapy during chronic infection. Maximum likelihood phylogenetic trees were constructed using the general time reversible model.
Results: Comparison of the infection frequencies between the 2 time points showed similar (<6-fold difference) infection rates of memory T cell subsets from different tissue compartments for most subjects. In agreement with findings for time point 1, infection frequencies of all T cell subsets were higher in subjects treated during chronic infection than acute infection; time point 2 included transitional-memory T cells which were not examined at time point 1 (6-fold higher infection rate in chronic vs acute; p=0.036). Appoximately 30% of the intracellular HIV sequences appeared to encode replication-incompetent virus. Longitudinal phylogenetic analysis revealed the expansion of some HIV genetic populations and the contraction of others with little evidence of viral evolution. In one subject, a clonal species containing a 380bp deletion was dominant, and increased from 71% to 92% over 6 months in peripheral blood effector memory T cells.
Conclusions: Our findings suggest the pool of HIV-infected resting memory CD4+ T cells typically does not change dramatically over 6 months in different tissue compartments, reflecting a relatively stable HIV-infection frequency during suppressive therapy with the early initiation of effective therapy resulting in a lower reservoir size. The increase of clonal HIV-1 sequences, especially a large deletion mutant, indicates an expansion of cells with integrated proviral DNA rather than active viral replication.
