ArticleViruses2024
Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy.
Article in Viruses, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- HIV-1 APOBEC-context Mutations Detected by Next-Generation Sequencing in Plasma: Implications for Drug Resistance Interpretation.The Journal of infectious diseases · 2026Article
- HIV drug resistance and treatment success in the Republic of Congo: Implications for optimized treatment.HIV medicine · 2026Article
- Ion Torrent Genexus as a Fast and Reliable Solution for HIV-1 Drug Resistance Testing: Comparison with the GeneStudio S5 Workflow.International journal of molecular sciences · 2026Article
- Development of a Next-Generation Sequencing Protocol for Assessing Lenacapavir Resistance in HIV-1 Capsid.Journal of medical virology · 2026Article
- VANTAGE: van-based real-time HIV sequencing for transmission mapping and drug resistance profiling in war-affected Ukraine.AIDS (London, England) · 2026Article
- Next-Generation Sequencing Analysis for HIV-1 Genotyping and Drug Resistance Mutations Mapping in Sicily, Italy.Viruses · 2025Article
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Authors and funding
26 authors.
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Abstract
backgroundNext-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.
methodsRoutine 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.
resultsAmong 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.
conclusionThis 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.
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