Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection

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Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection

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Title: Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection
Author: Ita, Sergio
Citation: Ita, Sergio. 2016. Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
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Abstract: Primate lentiviruses (PLVs), including human immunodeficiency virus type 1 (HIV-1), HIV type 2 (HIV-2), and the simian immunodeficiency viruses (SIVs), cause persistent lifelong infections despite the presence of virus-specific adaptive immune responses. The target of antibodies is the viral envelope glycoprotein (Env), which is expressed on the surface of virions and infected cells as a trimer of gp120:gp41 heterodimers. SIV env sequence variation arising from evasion of antibodies is well established and closely mimics the pattern observed in HIV-infected human patients, yet despite the experimental advantages of the macaque model, the viral dynamics during acute and early infection leading to escape within env have not been well defined. To examine the evolutionary dynamics of SIV env during early infection (< 6 months post-infection), we obtained longitudinal plasma samples from a small cohort of SIVmac251-infected rhesus macaques. We deep-sequenced the env gene from longitudinal samples spanning acute and early infection (2-29 weeks post-infection) from four SIV-infected rhesus macaques and the inoculum (a swarm stock of uncloned SIVmac251) that was used to infect the cohort (by repeated low-dose challenge). Using high-resolution next generation sequencing (NGS), we captured a population bottleneck at the point of transmission from the stock into each animal, tracked the subsequent emergence of Env diversity from the initially homogeneous population, and correlated changes with the onset of Env-specific antibodies. We identified a pattern of common substitutions, insertions, and deletions in env of animals with antibody responses, which repeatedly emerge in SIV-infected primate hosts, and found that adaptive changes clustered within short regions of the V1 and V4 loops of gp120. Surprisingly, we found multiple large in-frame deletions in V4 emerge to become dominant in the viral population in two animals with detectable antibody responses to Env. Furthermore, we developed a novel deep sequencing based viral fitness assay (Fit-Seq) and measured the relative fitness of several key in vivo antibody escape adaptations. Using Fit-Seq, we found that Env adaptations in V1 and V4 that confer antibody escape had no associated fitness costs in the absence of antibody, but rather, replicated to the same level as SIVmac239 WT. Surprisingly, we also found that Fit-Seq was able to detect antibody-mediated neutralization of SIVmac239 even in cases where activity was undetectable by standard neutralization assays. Our observation of reproducible patterns of Env variation clustered in V1 and V4, together with measurements of relative fitness, suggest that antibody responses can select for mutations that confer viral escape yet have little or no associated replicative fitness cost in the absence of antibody, even while providing a clear fitness advantage in the environment of constant antibody selection encountered in vivo. Thus, sites that can change with little or no impact on relative fitness may have evolved as an immune evasion mechanism to facilitate rapid and early escape from Env-specific antibody.
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