The Role of HIV-1 Drug-Resistant Minority Variants in Treatment Failure

Stella-Ascariz, Natalia; Arribas, José Ramón; Paredes, Roger; Li, Jonathan Z.

doi:10.1093/infdis/jix430

Cited by 50 publications

(40 citation statements)

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“…First, the cost of NGS can be considerably lower than that of dideoxynucleotide Sanger sequencing should a sufficient number of samples be tested in the same sequencing run (1,2). Second, the ability of NGS to detect low-frequency drug resistance mutations (DRMs) not detected by Sanger sequencing has potential advantages for improved patient outcomes (3).…”

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confidence: 99%

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

et al. 2018

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The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.

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confidence: 99%

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

et al. 2018

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“…The additional variant QC strategies significantly improve the reliability of calling variants of low abundance, undetectable by Sanger sequencing. It is acknowledged that the threshold of minority variant frequency considered to be clinically relevant remains debatable . “ NGS HIVDR interpretation and reporting ” is the only component designed specifically for HIVDR application, while all other blocks and associated strategies may find broader application, especially for genomic sequence analysis of microbes harbouring high genomic diversity, similar to HIV. This specific element of the pipeline streamlines the strategies to convert valid NGS‐derived amino acid variant data into end‐user‐interpretable HIVDR results.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg Consensus

Enns

Brumme

et al. 2018

J Intern AIDS Soc

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IntroductionNext‐generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low‐abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS‐based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting.DiscussionEssential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use.ConclusionsWhile NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this “Winnipeg Consensus” may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.

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“…Of course, the lack of linkage between isolate and antimicrobial susceptibility loci in complex, mixed sample could be seen as a liability, but it could serve as an advantage if one assumes that antimicrobial mobile elements associated with antimicrobial resistance will be rapidly shared. Finally, mNGS can potentially recover resistance loci prior to allele fixation and clinical resistance, though more clinical follow-up data is required to understand how best to interpret these different low frequency variants [11,12].…”

Section: Lacking Culture: Putting Antimicrobial Susceptibility In Rangementioning

confidence: 99%

One future of clinical metagenomic sequencing for infectious diseases

Shean

Greninger

2019

Expert Review of Molecular Diagnostics

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The Role of HIV-1 Drug-Resistant Minority Variants in Treatment Failure

Cited by 50 publications

References 50 publications

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg Consensus

One future of clinical metagenomic sequencing for infectious diseases

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