Scientific article

Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1

Published inJournal of antimicrobial chemotherapy, vol. 78, no. 3, p. 656-664
Publication date2023-03
First online date2023-02-04

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds.

Methods: To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds.

Results: We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%.

Conclusions: We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.

  • Male
  • Humans
  • HIV-1
  • HIV Infections / drug therapy
  • Cohort Studies
  • Drug Resistance, Viral / genetics
  • Viral Load
  • HIV Seropositivity / drug therapy
  • Mutation
  • High-Throughput Nucleotide Sequencing / methods
  • Genotype
  • Anti-HIV Agents / therapeutic use
Citation (ISO format)
BALAKRISHNA, Suraj et al. Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. In: Journal of antimicrobial chemotherapy, 2023, vol. 78, n° 3, p. 656–664. doi: 10.1093/jac/dkac430
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Article (Published version)
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ISSN of the journal0305-7453

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