ArticleNucleic acids research2021
Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Analysis of temporal virus evolution and intra-host diversity in long-term non-progressors by bulk next-generation sequencing.Microbiology spectrum · 2026Article
- HIV persistence in tissues on dolutegravir-based therapy is not associated with resistance mutations to dolutegravir.Communications medicine · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Article
- Intra-host diversity of proviral FeLV and clinical outcomes.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
- Tissue tropism and functional adaptation of the SARS-CoV-2 spike protein in a fatal case of COVID-19.Journal of virology · 2025Article
- Viral and Immune Risk Factors of HIV Rebound After Interruption of Antiretroviral Therapy.The Journal of infectious diseases · 2025Observational
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
- A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components.Nucleic acids research · 2025Article
- Differential mosaicism of recombinant foot-and-mouth disease viruses resulting from heterologous superinfection of cattle.Journal of virology · 2025Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2025Review
- VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.NAR genomics and bioinformatics · 2024Article
- Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks.Nature communications · 2024Article
- Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.Microbial genomics · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- ClusterV-Web: a user-friendly tool for profiling HIV quasispecies and generating drug resistance reports from nanopore long-read data.Bioinformatics advances · 2024Article
- Brain tropism acquisition: The spatial dynamics and evolution of a measles virus collective infectious unit that drove lethal subacute sclerosing panencephalitis.PLoS pathogens · 2023Article
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Authors and funding
12 authors.
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Abstract
Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.
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