HIV-1 Genetic Variation Resulting in the Development of New Quasispecies Continues to Be Encountered in the Peripheral Blood of Well-Suppressed Patients.

Will Dampier,Benjamas Aiamkitsumrit,Garth D Ehrlich,Jean W Williams,Jeffrey M Jacobson,Joshua Earl,Joshua Mell,Brian Wigdahl,Shendra Passic,Vanessa Pirrone,Michael R Nonnemacher,Wen Zhong,Katherine Kercher,Fatah Kashanchi

doi:10.1371/journal.pone.0155382

Abstract

As a result of antiretroviral therapeutic strategies, human immunodeficiency virus type 1 (HIV-1) infection has become a long-term clinically manageable chronic disease for many infected individuals. However, despite this progress in therapeutic control, including undetectable viral loads and CD4+ T-cell counts in the normal range, viral mutations continue to accumulate in the peripheral blood compartment over time, indicating either low level reactivation and/or replication. Using patients from the Drexel Medicine CNS AIDS Research and Eradication Study (CARES) Cohort, whom have been sampled longitudinally for more than 7 years, genetic change was modeled against to the dominant integrated proviral quasispecies with respect to selection pressures such as therapeutic interventions, AIDS defining illnesses, and other factors. Phylogenetic methods based on the sequences of the LTR and tat exon 1 of the HIV-1 proviral DNA quasispecies were used to obtain an estimate of an average mutation rate of 5.3 nucleotides (nt)/kilobasepair (kb)/year (yr) prior to initiation of antiretroviral therapy (ART). Following ART the baseline mutation rate was reduced to an average of 1.02 nt/kb/yr. The post-ART baseline rate of genetic change, however, appears to be unique for each patient. These studies represent our initial steps in quantifying rates of genetic change among HIV-1 quasispecies using longitudinally sampled sequences from patients at different stages of disease both before and after initiation of combination ART. Notably, while long-term ART reduced the estimated mutation rates in the vast majority of patients studied, there was still measurable HIV-1 mutation even in patients with no detectable virus by standard quantitative assays. Determining the factors that affect HIV-1 mutation rates in the peripheral blood may lead to elucidation of the mechanisms associated with changes in HIV-1 disease severity.

Highlights

The introduction of combination therapeutics have extended the life expectancy of those infected with the human immunodeficiency virus type 1 (HIV-1) for many years past what would have been observed even a decade ago
In an effort to simplify the process of longitudinal sampling of HIV-1 quasispecies in the Drexel Medicine CNS AIDS Research and Eradication Study (CARES) Cohort, PCR amplification of specific regions of the HIV-1 genome was performed on genomic DNA and the resulting PCR products were directly sequenced without the traditional step of sub-cloning to isolate individual sequence fragments prior to sequencing the cloned product
We have hypothesized that the genetic variation over time within the integrated HIV-1 proviral genome in the infected cells derived from the peripheral blood represents (1) a combination of sequential mutations within quasispecies, (2) changes in the relative frequencies of distinct quasispecies, and (3) the reemergence of compartmentalized genomes leaking from viral reservoirs including the brain, gastrointestinal tract, and perhaps other tissues that may include the bone marrow

Summary

Introduction

The introduction of combination therapeutics have extended the life expectancy of those infected with the human immunodeficiency virus type 1 (HIV-1) for many years past what would have been observed even a decade ago. Due to the mutable nature of the HIV-1 genome, longer life expectancy and associated selective pressures has led to increased opportunities for the emergence of viral genetic variants that escape therapy [1, 2], contribute to neurocognitive decline [3,4,5], or result in more or less frequent activation/reactivation of persistent/latent infection [6], among many other potential complications resulting from a large number of well-known comorbidities [7]. Intra-host genetic bottlenecks have been identified by a number of mechanisms and at different anatomic sites following the initial encounter, these results are consistent with a small founder population and host tropisms that have previously been observed in the simian immunodeficiency virus (SIV) rhesus macaque model [12, 13]

Methods

Results

Conclusion