Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection

Abstract

To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24 gag were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-␥/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (r ‫؍‬ 0.43; P ‫؍‬ 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack. IMPORTANCERapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens. Exploring the dynamic interplay between human immune responses and the mechanisms by which HIV-1 evades these responses can help inform which types and specificity of immunity a vaccine should elicit. At peak viral load, the viral population is usually homogenous (1-3). In approximately 75% of HIV transmissions, a single variant (the "founder" virus) es...

Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

“…It is important to note that viral escape was detected in some but not all of the initially targeted epitopes. This phenomenon has been previously described and studied by several groups (e.g., [ 29 , 58 , 60 ]), and is likely influenced by host (e.g., genetic background, magnitude/quality of CTL response) and viral factors (e.g., genetic barrier to escape, viral fitness, capacity of targeted protein accommodate sequence change).…”

“…Interestingly, while in some participants CTL escape proceeded as the pVL remained virtually unchanged (e.g., 40100), in other cases we noticed a transient and modest increase of pVL, coinciding with a change in dominance of escape variants (e.g., 20225). Among the possible causes for this are: a) differences in fitness between WT and escape variants, and among escape variants [ 58 ], and b) the emergence of new CTL clonotypes with broader variant recognition [ 59 ]. The underlying mechanism linking pVL dynamics with CTL escape and the change in escape dominance warrant further study.…”

Antibody-Dependent Cellular Cytotoxicity (ADCC)-Mediating Antibodies Constrain Neutralizing Antibody Escape Pathway

“…Deep sequencing revealed that this mutation was strongly selected against and was found at very low frequency by 29 wpi. Sunshine et al showed that dynamic escape processes only resolve with the selection of mutations that confer escape with little/no fitness cost to the virus (30). We showed there was no replicative fitness cost incurred by incorporation of the 392 6(392NXT-) deletion, suggesting other pressures such as ADCC-mediating antibodies played a role in controlling viral populations through constraining nAb escape pathways.…”

Patterns and rates of viral evolution in HIV-1 subtype B infected females and males

“…This was also observed for 5/8 participants (all except F4, F5, and F8) in the gag phylogram ( S2 Fig ) and was also previously observed for individuals within the MACS cohort [ 60 ]. While the branch lengths separating sequences from different individuals are long, and may result in rooting artefacts, such topologies are consistent with the acquisition of reversion of immune escape mutations acquired from the transmitting partner in the early years of infection [ 61 – 66 ]. Further departure from the MRCA then appears to dominate, due to host-specific escape mutations.…”