HIVepsilon-seq-scalable characterization of intact persistent proviral HIV reservoirs in women

J Virol. 2023 Nov 30;97(11):e0070523. doi: 10.1128/jvi.00705-23. Epub 2023 Oct 16.


The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics to scrutinize the HIV genome at the nucleotide level, distinguishing between defective and intact HIV. This study included 30 participants on antiretroviral therapy, including 17 women, and was able to discriminate between defective and genetically intact viruses at the single DNA strand level. The HIVε-seq assay is an improvement over previous methods, as it requires minimal sample, less specialized lab equipment, and offers a shorter turnaround time. The HIVε-seq assay offers a promising new tool for researchers to measure the intact HIV reservoir, advancing efforts towards finding a cure for this devastating disease.

Keywords: HIV; HIV persistence; third-generation sequencing.

MeSH terms

  • CD4-Positive T-Lymphocytes
  • DNA, Viral / genetics
  • Female
  • HIV Infections* / drug therapy
  • HIV Infections* / epidemiology
  • HIV Infections* / virology
  • HIV* / genetics
  • Humans
  • Male
  • Nucleotides
  • Proviruses* / genetics
  • Sequence Analysis, DNA
  • Sex Factors
  • Viral Load


  • DNA, Viral
  • Nucleotides