Genetic characterization of the HIV-1 reservoir after Vacc-4x and romidepsin therapy in HIV-1-infected individuals.

Anni Winckelmann,Jesper F Hojen,Vincent Morcilla,Martin Tolstrup,Paul W Benton,Mariane H Schleimann,Sarah Palmer,Wei Shao,Timothy E Schlub,Lars Østergaard,Ole S Søgaard

doi:10.1097/qad.0000000000001861

Abstract

Objective:Therapeutic HIV-1 immunization followed by latency reversal has been suggested as a strategy to eradicate HIV-1. Here we investigate the phylogenetic composition of the HIV-1 regions targeted by the therapeutic HIV-1 peptide vaccine Vacc-4x in participants in a clinical trial.Design:Seventeen participants on suppressive antiretroviral therapy were vaccinated with six doses of Vacc-4x followed by three doses of romidepsin. Seven study participants were selected for sequencing analysis. All participants underwent an analytical treatment interruption.Methods:Single-genome/proviral sequencing of the p24-RT region was performed to genetically characterize proviral DNA, cell-associated RNA and outgrowth viruses during therapy as well as plasma HIV-1 RNA during an analytical treatment interruption.Results:There were no changes in cell-associated HIV-1 RNA (P = 0.83) and DNA (P = 0.09) diversity over the course of the study and no difference between cell-associated HIV-1 RNA and DNA diversity (P = 0.32). Only one participant showed signs of potential vaccine-related selection in the rebounding plasma virus. In five of seven participants, we identified human leukocyte antigen-specific cytotoxic T lymphocytes (CTL) epitopes containing nonsilent mutations in 100% of the sequences.Conclusion:We detected no evidence of selective immune pressure reflected in proviral diversity or by occurrence of specific mutation in the vaccine-targeted epitopes. Preexisting CTL epitope mutations may affect the potency of this therapeutic vaccine. This highlights the challenges of developing effective HIV-1 therapeutic vaccines.

Highlights

Primers and PCR conditions cDNA synthesis: Gene specific primers were used to generate cDNA from cell-associated and plasma HIV-1 RNA.
For p24-RT we used the PCR 1 reverse primer, listed in the table below.
For round 1 of the PCR, the following thermocycler parameters were used: 94 °C for 2 minutes, 94 °C for 30 seconds, 53 °C for 30 seconds, 72 °C for 2 minutes and 30 seconds, 44 cycles of steps 2–4 and 72 °C for 3 minutes.

Summary

Introduction

Primers and PCR conditions cDNA synthesis: Gene specific primers were used to generate cDNA from cell-associated and plasma HIV-1 RNA. For p24-RT we used the PCR 1 reverse primer, listed in the table below.

Results

Conclusion