Detection of treatment-resistant infectious HIV after genome-directed antiviral endonuclease therapy

Antiviral Res. 2016 Feb;126:90-8. doi: 10.1016/j.antiviral.2015.12.007. Epub 2015 Dec 22.


Incurable chronic viral infections are a major cause of morbidity and mortality worldwide. One potential approach to cure persistent viral infections is via the use of targeted endonucleases. Nevertheless, a potential concern for endonuclease-based antiviral therapies is the emergence of treatment resistance. Here we detect for the first time an endonuclease-resistant infectious virus that is found with high frequency after antiviral endonuclease therapy. While testing the activity of HIV pol-specific zinc finger nucleases (ZFNs) alone or in combination with three prime repair exonuclease 2 (Trex2), we identified a treatment-resistant and infectious mutant virus that was derived from a ZFN-mediated disruption of reverse transcriptase (RT). Although gene disruption of HIV protease, RT and integrase could inhibit viral replication, a chance single amino acid insertion within the thumb domain of RT produced a virus that could actively replicate. The endonuclease-resistant virus could replicate in primary CD4(+) T cells, but remained susceptible to treatment with antiretroviral RT inhibitors. When secondary ZFN-derived mutations were introduced into the mutant virus's RT or integrase domains, replication could be abolished. Our observations suggest that caution should be exercised during endonuclease-based antiviral therapies; however, combination endonuclease therapies may prevent the emergence of resistance.

Keywords: Endonuclease; Resistance; Reverse transcriptase; Zinc finger nuclease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-HIV Agents / pharmacology*
  • Base Sequence
  • Cell Line
  • DNA, Viral / genetics
  • Drug Resistance, Viral
  • Endonucleases / metabolism
  • Exodeoxyribonucleases / metabolism
  • Exodeoxyribonucleases / pharmacology
  • Gene Products, pol / genetics
  • Gene Products, pol / metabolism
  • HEK293 Cells
  • HIV Infections / drug therapy
  • HIV Infections / genetics
  • HIV Infections / therapy
  • HIV Infections / virology*
  • HIV Protease / genetics
  • HIV Protease / metabolism
  • HIV Reverse Transcriptase / genetics
  • HIV Reverse Transcriptase / metabolism
  • HIV-1 / drug effects*
  • HIV-1 / genetics*
  • Humans
  • Molecular Sequence Data
  • Mutation
  • Phosphoproteins / metabolism
  • Phosphoproteins / pharmacology
  • Reverse Transcriptase Inhibitors / pharmacology*
  • Transduction, Genetic
  • Virus Replication / drug effects
  • Zinc Fingers*


  • Anti-HIV Agents
  • DNA, Viral
  • Gene Products, pol
  • Phosphoproteins
  • Reverse Transcriptase Inhibitors
  • HIV Reverse Transcriptase
  • Endonucleases
  • Exodeoxyribonucleases
  • TREX2 protein, human
  • HIV Protease