Phylogenetic evidence of HIV-1 sequence evolution in subjects with persistent low-level viraemia

Antivir Ther. 2015;20(1):73-6. doi: 10.3851/IMP2772. Epub 2014 Apr 4.


Background: Persistent low-level viraemia (LLV) during the treatment of antiretroviral therapy (ART) is associated with emergent drug resistance mutation (DRM); however, insight into its driver is limited. The objectives were to study HIV-1 pol sequence evolution in subjects with persistent LLV and evaluate factors associated with sequence changes.

Methods: HIV-1 pol sequences from 54 treatment-naive subjects undergoing first-line lopinavir/ritonavir- or efavirenz-containing ART were obtained at pre-ART and end of LLV. HIV-1 sequence evolution was evaluated using phylogenetic analysis and Hamming distance calculation. DRMs were interpreted based on the International AIDS Society-USA 2011 update.

Results: Subjects with new DRM during LLV had greater HIV-1 evolution across pol from the pre-ART to end of LLV compared with subjects without DRM. Evolution over non-DRM sites was similar between groups. Higher degree of genetic evolution was positively associated with higher HIV-1 RNA levels during LLV, both at DRM and non-DRM sites.

Conclusions: The magnitude of LLV was the primary driver of evolution rate at DRM as well as non-DRM sites. Higher viral load was associated with DRM emergence in these subjects. These findings provide insights that may be applicable to the management of patients with persistent LLV during ART.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Alkynes
  • Anti-HIV Agents / therapeutic use*
  • Antiretroviral Therapy, Highly Active
  • Benzoxazines / therapeutic use
  • Cyclopropanes
  • Drug Resistance, Viral / drug effects
  • Drug Resistance, Viral / genetics*
  • Evolution, Molecular
  • Female
  • HIV Infections / drug therapy
  • HIV Infections / virology*
  • HIV-1 / classification
  • HIV-1 / drug effects
  • HIV-1 / genetics*
  • Humans
  • Lopinavir / therapeutic use
  • Male
  • Middle Aged
  • Mutation*
  • Phylogeny
  • RNA, Viral / antagonists & inhibitors
  • RNA, Viral / genetics
  • Retrospective Studies
  • Ritonavir / therapeutic use
  • Viral Load / drug effects
  • Viral Load / genetics
  • Viremia / drug therapy
  • Viremia / virology*
  • pol Gene Products, Human Immunodeficiency Virus / genetics*


  • Alkynes
  • Anti-HIV Agents
  • Benzoxazines
  • Cyclopropanes
  • RNA, Viral
  • pol Gene Products, Human Immunodeficiency Virus
  • Lopinavir
  • efavirenz
  • Ritonavir