Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy

Viruses. 2024 Sep 6;16(9):1422. doi: 10.3390/v16091422.

Abstract

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting.

Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories with the AD4SEQ HIV-1 Solution v2 commercial kit. NGS results were interpreted by the SmartVir system provided by the kit and by two online tools (HyDRA Web and Stanford HIVdb). NGS-GRT was considered valid when the coverage was >100 reads (100×) at each PR/RT/IN resistance-associated position listed in the HIVdb 9.5.1 algorithm.

Results: Among 629 NGS-GRT, 75.2%, 74.2%, and 70.9% were valid according to SmartVir, HyDRA Web, and HIVdb. Considering at least two interpretation tools, 463 (73.6%) NGS-GRT had a valid coverage for resistance analyses. The proportion of valid samples was affected by viremia <10,000-1000 copies/mL and non-B subtypes. Mutations at an NGS frequency >10% showed fair concordance among different interpretation tools.

Conclusion: This Italian survey on NGS resistance testing suggests that viremia levels and HIV subtype affect NGS-GRT coverage. Within the current routine method for NGS-GRT, only mutations with frequency >10% seem reliably detected across different interpretation tools.

Keywords: HIV drug resistance; HIV-1 subtype; bioinformatic interpretation tools; minority variants; next-generation sequencing; viremia.

Publication types

  • Comparative Study

MeSH terms

  • Anti-HIV Agents / pharmacology
  • Anti-HIV Agents / therapeutic use
  • Drug Resistance, Viral* / genetics
  • Genotype
  • HIV Infections* / virology
  • HIV-1* / drug effects
  • HIV-1* / genetics
  • High-Throughput Nucleotide Sequencing* / methods
  • Humans
  • Italy
  • Mutation
  • RNA, Viral / genetics

Substances

  • RNA, Viral
  • Anti-HIV Agents

Grants and funding

No specific funding was provided for this study. The current work was a joint activity of the Italian HIV NGS Network and the ARCA database cohort. The ARCA Database and initiatives are supported by unconditional and educational grants from Arrow Diagnostics, MSD, Gilead Sciences, Janssen Infectious Diseases & Vaccines, and ViiV Healthcare.