ArticleViruses2020
Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping.
Article in Viruses, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Pooled it
- 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
- HIV-1 variants in population-based national surveys in sub-Saharan Africa, 2015-2022.AIDS (London, England) · 2026Article
- Evaluation of a HIV-1 drug resistance genotyping method based on high-throughput sequencing (HTS).BMC infectious diseases · 2026Article
- National representative survey of pretreatment HIV drug resistance in Colombia: analysis of antiretroviral resistance-associated mutations using next-generation sequencing.The Journal of antimicrobial chemotherapy · 2026Article
- Article
- Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management.Diagnostics (Basel, Switzerland) · 2025Review
- Unique molecular signatures in rebound viruses from antiretroviral drug and CRISPR-treated HIV-1-infected humanized mice.Communications biology · 2025Article
- HIV molecular network in Mexico City (2021-2022): Understanding transmission dynamics through the role of newly diagnosed cases.HIV medicine · 2025Article
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- Patterns of inflammation and immune activation by coreceptor use in people living with HIV-1.Frontiers in immunology · 2025Article
- Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy.Viruses · 2024Article
- MARVEL-minimising the emergence and dissemination of HIV-1 drug resistance in Portuguese-speaking African Countries (PALOP): low-cost portable NGS platform for HIV-1 surveillance in Africa.BMC infectious diseases · 2024Article
- Impact of Low-Frequency Human Immunodeficiency Virus Type 1 Drug Resistance Mutations on Antiretroviral Therapy Outcomes.The Journal of infectious diseases · 2024Article
- Article
- Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal.Viruses · 2024Article
- Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.Frontiers in molecular biosciences · 2024Article
- Sensitive HIV-1 DNA Pol Next-Generation Sequencing for the Characterisation of Archived Antiretroviral Drug Resistance.Viruses · 2023Article
- Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage.Viruses · 2022Article
- Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
22 authors at 14 institutions in 6 countries.
Funding
Abstract
Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4-99; reverse transcriptase 38-247). The concordance among laboratories' sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1-100%), compared to 15% (99.4%, 88.5-100%), 10% (99.2%, 87.4-100%), or 5% (98.5%, 86.4-100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.
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Registered trials
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