Using Primer-ID Deep Sequencing to Detect Recent Human Immunodeficiency Virus Type 1 Infection

J Infect Dis. 2018 Oct 20;218(11):1777-1782. doi: 10.1093/infdis/jiy426.


Intrahost viral sequence diversity can be evaluated over multiple genomic regions using next-generation sequencing (NGS) and scaled to population-level diversity to identify recent human immunodeficiency virus type 1 infection. Using Primer-ID NGS, we sequenced the reverse transcriptase (RT) and env V1-V3 regions from persons with known infection dates, and assessed the mean (π) and first quintile of pairwise diversity distributions over time. The receiver operating characteristic area under the curve (AUC) of RT and V1-V3 combined showed excellent discrimination of recent infection <9 months: using π (only single transmitted variants: AUC, 0.98; threshold <1.03%; sensitivity, 97%; specificity, 89%) and the first quintile (including all variants: AUC, 0.90; threshold <0.60%; sensitivity, 91%; specificity, 92%).

Publication types

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

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Cohort Studies
  • Early Diagnosis
  • Female
  • HIV Infections / diagnosis*
  • HIV Infections / virology
  • HIV-1 / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Male
  • Middle Aged
  • RNA, Viral / genetics*
  • Sequence Analysis, DNA / methods*
  • Young Adult


  • RNA, Viral