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Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase.

Publication ,  Journal Article
Moore, HP; Palumbo, PJ; Notarte, KI; Fogel, JM; Cummings, V; Gamble, T; Del Rio, C; Batey, DS; Mayer, KH; Farley, JE; Remien, RH; Beyrer, C ...
Published in: J Clin Microbiol
June 12, 2024

HIV genotyping is used to assess HIV susceptibility to antiretroviral drugs. The Applied Biosystems HIV-1 Genotyping Kit with Integrase (AB kit, Thermo Fisher Scientific) detects resistance-associated mutations (RAMs) in HIV protease (PR), reverse transcriptase (RT), and integrase (IN). We compared results from the AB kit with results obtained previously with the ViroSeq HIV-1 Genotyping System. DNA amplicons from the AB kit were also analyzed using next-generation sequencing (NGS). HIV RNA was extracted using the MagNA Pure 24 instrument (Roche Diagnostics; 96 plasma samples, HIV subtype B, viral load range: 530-737,741 copies/mL). FASTA files were generated from AB kit data using Exatype (Hyrax Biosciences). DNA amplicons from the AB kit were also analyzed by NGS using the Nextera XT kit (Illumina). Drug resistance was predicted using the Stanford HIV Drug Resistance Database. The mean genetic distance for sequences from ViroSeq and the AB kit was 0.02% for PR/RT and 0.04% for IN; 103 major RAMs were detected by both methods. Four additional major RAMs were detected by the AB kit only. These four major RAMs were also detected by NGS (detected in 18.1%-38.2% of NGS reads). NGS detected 27 major RAMs that were not detected with either of the Sanger sequencing-based kits. All major RAMs detected with ViroSeq were detected with the AB kit; additional RAMs were detected with the AB kit only. DNA amplicons from the AB kit can be used for NGS for more sensitive detection of RAMs.

Duke Scholars

Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

June 12, 2024

Volume

62

Issue

6

Start / End Page

e0013624

Location

United States

Related Subject Headings

  • Reagent Kits, Diagnostic
  • RNA, Viral
  • Mutation
  • Microbiology
  • Humans
  • High-Throughput Nucleotide Sequencing
  • HIV-1
  • HIV Reverse Transcriptase
  • HIV Protease
  • HIV Integrase
 

Citation

APA
Chicago
ICMJE
MLA
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Moore, H. P., Palumbo, P. J., Notarte, K. I., Fogel, J. M., Cummings, V., Gamble, T., … HPTN 078 study, . (2024). Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase. J Clin Microbiol, 62(6), e0013624. https://doi.org/10.1128/jcm.00136-24
Moore, Hannah P., Philip J. Palumbo, Kin Israel Notarte, Jessica M. Fogel, Vanessa Cummings, Theresa Gamble, Carlos Del Rio, et al. “Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase.J Clin Microbiol 62, no. 6 (June 12, 2024): e0013624. https://doi.org/10.1128/jcm.00136-24.
Moore HP, Palumbo PJ, Notarte KI, Fogel JM, Cummings V, Gamble T, et al. Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase. J Clin Microbiol. 2024 Jun 12;62(6):e0013624.
Moore, Hannah P., et al. “Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase.J Clin Microbiol, vol. 62, no. 6, June 2024, p. e0013624. Pubmed, doi:10.1128/jcm.00136-24.
Moore HP, Palumbo PJ, Notarte KI, Fogel JM, Cummings V, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Remien RH, Beyrer C, Hudelson SE, Eshleman SH, HPTN 078 study. Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase. J Clin Microbiol. 2024 Jun 12;62(6):e0013624.

Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

June 12, 2024

Volume

62

Issue

6

Start / End Page

e0013624

Location

United States

Related Subject Headings

  • Reagent Kits, Diagnostic
  • RNA, Viral
  • Mutation
  • Microbiology
  • Humans
  • High-Throughput Nucleotide Sequencing
  • HIV-1
  • HIV Reverse Transcriptase
  • HIV Protease
  • HIV Integrase