Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene

J Med Virol. 2018 Sep;90(9):1486-1492. doi: 10.1002/jmv.25224. Epub 2018 May 25.


The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson's analysis showed good concordance between the percentage of drug-resistant variants determined by MiSeq and 454 GS-FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS-FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.

Keywords: MiSeq; deep sequencing; polymerase drug resistance.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Resistance, Viral
  • Genetic Variation*
  • HIV Infections / virology*
  • HIV Protease / genetics
  • HIV Reverse Transcriptase / genetics
  • HIV-1 / classification*
  • HIV-1 / genetics*
  • HIV-1 / isolation & purification
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mutation*
  • pol Gene Products, Human Immunodeficiency Virus / genetics*


  • pol Gene Products, Human Immunodeficiency Virus
  • HIV Reverse Transcriptase
  • HIV Protease