ArticleGenome research2019
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers, 1 of them a synthesis that pooled it.
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Who cites it
150 citing papers in PubMed, 1 synthesis or guideline pooled it, 245 citations in OpenAlex.
- A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.Briefings in bioinformatics · 2020Guideline
- Transcriptional architecture of African swine fever virus.PLoS pathogens · 2026Article
- VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.Nucleic acids research · 2026Article
- Whole transcriptome sequencing and ceRNA regulatory network in diabetic peripheral neuropathy.Scientific reports · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7.Microbial genomics · 2026Article
- Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E. coli throughout its life cycles reveals a complex transcriptional activity to control and maintain its growth.Virology journal · 2026Article
- Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications.Veterinary sciences · 2026Review
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- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Long-read sequencing-based analyses of the adult Drosophila brain transcriptome in physiological and pathological settings.BMC genomics · 2025Article
- Targeted decontamination of sequencing data with CLEAN.NAR genomics and bioinformatics · 2025Article
- Validation of diverse and previously untraceable Sendai virus copyback viral genomes by direct RNA sequencing.Journal of virology · 2025Article
- Trehalose catalytic shift inherently enhances phenotypic heterogeneity and multidrug resistance in Mycobacterium tuberculosis.Nature communications · 2025Article
- Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers.BMC infectious diseases · 2025Article
- Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger.Genome research · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.Cell genomics · 2025Article
- Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.The Journal of molecular diagnostics : JMD · 2025Review
90 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses. Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called "quasispecies." Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous genome regions. Here, we used a full-length, direct RNA sequencing (DRS) approach based on nanopores to characterize viral RNAs produced in cells infected with a human coronavirus. By using DRS, we were able to map the longest (∼26-kb) contiguous read to the viral reference genome. By combining Illumina and Oxford Nanopore sequencing, we reconstructed a highly accurate consensus sequence of the human coronavirus (HCoV)-229E genome (27.3 kb). Furthermore, by using long reads that did not require an assembly step, we were able to identify, in infected cells, diverse and novel HCoV-229E sg RNAs that remain to be characterized. Also, the DRS approach, which circumvents reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. Our work paves the way for haplotype-based analyses of viral quasispecies by showing the feasibility of intra-sample haplotype separation. Even though several technical challenges remain to be addressed to exploit the potential of the nanopore technology fully, our work illustrates that DRS may significantly advance genomic studies of complex virus populations, including predictions on long-range interactions in individual full-length viral RNA haplotypes.
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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.