ArticleJournal of computational biology : a journal of computational molecular cell biology2017
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- 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
- QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.Bioinformatics (Oxford, England) · 2022Article
- Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.Nucleic acids research · 2021Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.Molecular biology and evolution · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Systematic benchmarking of omics computational tools.Nature communications · 2019Review
- Long-read sequence and assembly of segmental duplications.Nature methods · 2019Article
- Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.Nature communications · 2018Article
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Authors and funding
6 authors.
Funding
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Abstract
As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous "swarm" of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this article, we present two single-nucleotide variants (2SNV), a method able to tolerate the high error rate of the single-molecule protocol and reconstruct mutant variants. 2SNV uses linkage between single-nucleotide variations to efficiently distinguish them from read errors. To benchmark the sensitivity of 2SNV, we performed a single-molecule sequencing experiment on a sample containing a titrated level of known viral mutant variants. Our method is able to accurately reconstruct clone with frequency of 0.2% and distinguish clones that differed in only two nucleotides distantly located on the genome. 2SNV outperforms existing methods for full-length viral mutant reconstruction.
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