ArticleScientific reports2020
Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
41 citing papers in PubMed, 66 citations in OpenAlex.
- Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial.Nature microbiology · 2022Trial
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- G-HIV: An Integrated Long-Read Sequencing and Automated Bioinformatics Platform for Rapid and Precise HIV-1 Surveillance.Microorganisms · 2026Article
- HIV-1 variants in population-based national surveys in sub-Saharan Africa, 2015-2022.AIDS (London, England) · 2026Article
- Longitudinal Analysis of HIV-2 Proviral DNA Reveals Archived Protease Inhibitor Resistance and Reservoir Evolution over Eight Years.International journal of molecular sciences · 2026Article
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- Unique molecular signatures in rebound viruses from antiretroviral drug and CRISPR-treated HIV-1-infected humanized mice.Communications biology · 2025Article
- A bibliometric analysis of HIV-1 drug-resistant minority variants from 1999 to 2024.AIDS research and therapy · 2025Article
- The utility of integrating nanopore sequencing into routine HIV-1 drug resistance surveillance.Microbial genomics · 2025Review
- Prevalence of Naturally Occurring HIV-1 Capsid Inhibitor Resistance-Related Mutations in Antiretroviral Therapy-Naïve and -Experienced Individuals in Taiwan.Open forum infectious diseases · 2025Article
- HIV phylogenetic clusters point to unmet hiv prevention, testing and treatment needs among men who have sex with men in kenya.BMC infectious diseases · 2024Article
- Review
- Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy.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
- A cross-sectional survey exploring HIV and HCV prevalence among men who purchase sex in Dnipro, Ukraine.BMC public health · 2023Article
- Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2023Article
- Article
- Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries.PLOS global public health · 2023Review
- The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles.Viruses · 2022Review
Corrections and comments
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Authors and funding
21 authors at 8 institutions in 4 countries.
Funding
Abstract
Next generation sequencing (NGS) is a trending new standard for genotypic HIV-1 drug resistance (HIVDR) testing. Many NGS HIVDR data analysis pipelines have been independently developed, each with variable outputs and data management protocols. Standardization of such analytical methods and comparison of available pipelines are lacking, yet may impact subsequent HIVDR interpretation and other downstream applications. Here we compared the performance of five NGS HIVDR pipelines using proficiency panel samples from NIAID Virology Quality Assurance (VQA) program. Ten VQA panel specimens were genotyped by each of six international laboratories using their own in-house NGS assays. Raw NGS data were then processed using each of the five different pipelines including HyDRA, MiCall, PASeq, Hivmmer and DEEPGEN. All pipelines detected amino acid variants (AAVs) at full range of frequencies (1~100%) and demonstrated good linearity as compared to the reference frequency values. While the sensitivity in detecting low abundance AAVs, with frequencies between 1~20%, is less a concern for all pipelines, their specificity dramatically decreased at AAV frequencies <2%, suggesting that 2% threshold may be a more reliable reporting threshold for ensured specificity in AAV calling and reporting. More variations were observed among the pipelines when low abundance AAVs are concerned, likely due to differences in their NGS read quality control strategies. Findings from this study highlight the need for standardized strategies for NGS HIVDR data analysis, especially for the detection of minority HIVDR variants.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.