Stereotypic escape from CD8+ T-cell responses represents a major driving force of HIV-1 sequence diversity and reveals constraints on HIV-1 evolution

Background: Understanding the factors driving global HIV-1 sequence diversity is critical for vaccine development. While viral escape from CD8+ T-cell responses is well documented, it remains unclear the extent to which intra-host and global HIV-1 evolution is specifically driven by these selective pressures. Similarly, little is known regarding the extent to which sequence constraints upon protein structure affect the accumulation of mutations arising from immune selection pressures. Methods: We assessed the relationship between genome-wide viral evolution (excluding Env) and HIV-1-specific cellular immune responses in 4 patients followed longitudinally for as long as 5 years after acute infection. Ten additional chronically infected subjects expressing HLA-B57 were examined to assess reproducibility of escape mutations. Full genome population sequencing of HIV-1 was employed, and measurement of HIV-1-specific CD8+ T-cell responses using consensus, and in some cases autologous peptides, was conducted using an IFN-γ ELISpot assay. Results: A total of 98 mutations evolved in the 4 study subjects, 52 of which were associated with detectable virus-specific CD8+ T-cell responses, accounting for 48 to 60% of the mutations in each subject. In addition, 18 mutations reverted to common consensus residues, 9 of which were associated with HLA class I alleles not expressed by the respective subject, consistent with adaptations due to previous CD8+ T-cell selective pressures. Therefore, nearly two-thirds of all mutations were attributable to CD8+ T-cell selective pressures. Although the majority of CD8+ T-cell responses did not result in detectable viral evolution, targeted residues in epitopes that did mutate correlated with the most polymorphic sites in both clade B and C viruses, and selection pressure frequently resulted in identical amino acid substitutions arising in a given CD8 epitope across multiple subjects. Conclusions: These data indicate a dominant role of cellular immune responses in driving both individual and global HIV-1 evolution, and the stereotypic nature of acquired mutations provides evidence for constraints on evolution of highly variable RNA viruses.