Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

Abstract

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3–6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses – using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2–7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.

Biology as Population Dynamics: Heuristics for Transmission Risk

“…Starting from this view, a population dynamicstype model 11,12 was previously developed by Welte and Walwyn 13 to capture the initial exposure of susceptible immune system cells to HIV virions. Whether or not an exposure develops into systemic infection is determined by random events within a life cycle model, which includes background and immune system-mediated hazards for invading free virions, cell invasion leading to a first-generation of infected cells, and cell-to-cell transmission of virions.…”

HIV‐1: From escapism to conservatism

“…This means that the induced T-cell responses, although increased in depth, are just as likely to focus on variable regions and this opens the possibility of selecting novel escape variants not yet included in the LANL database. Recent deep sequencing of natural T-cell escape mutations showed that a very large number of alternative amino acids were generated by mutation during infection and 'tested' in these variable epitope positions [20]. In essence, perhaps the best solution to a T-cell vaccine immunogen is one that consists of conserved regions made of mosaic sequences.…”

Impaired immune evasion in HIV through intracellular delays and multiple infection of cells

“…Owing to the high mutation rate of HIV, the virus can acquire immune escape mutations and frequently evades recognition from CTLs during the first months of the infection [4][5][6]. Analysing longitudinal data on the evolution of immune escape variants can give insights into the selective pressure that is induced by the CTLs.…”

“…However, interpreting the data of immune escape is challenging and critically depends on the underlying assumptions of how immune escape variants replace the wild-type virus [8,9]. CTLs definitely impose a very strong selection pressure on HIV during acute infection as several escape variants replace each other very rapidly during the first months of infection [4,5]. During chronic HIV infection, the relation between CTL-mediated killing, immune escape and viral control is less clear [10].…”