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Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

https://doi.org/10.1101/483693
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Reverse Genetics of Coronaviruses Using Vaccinia Virus Vectors
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Coronaviruses use Discontinuous Extension for Synthesis of Subgenome-Length Negative Strands
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A New Model for Coronavirus Transcription
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Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E
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What is a quasispecies?
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Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
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Dynamic RNA Modifications in Gene Expression Regulation
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Middle East respiratory syndrome and severe acute respiratory syndrome
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Jumping species—a mechanism for coronavirus persistence and survival
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Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions
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Multi-platform analysis reveals a complex transcriptome architecture of a circovirus
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Basic Local Alignment Search Tool
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The Molecular Biology of Coronaviruses
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Is CD46 the cellular receptor for measles virus?
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Real-time, portable genome sequencing for Ebola surveillance
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Establishment and cryptic transmission of Zika virus in Brazil and the Americas
inferredcites →https://doi.org/10.1038/nature24156openalex-snapshot
Shrinking maps of RNA modifications
inferredcites →https://doi.org/10.1038/nbt.4045openalex-snapshot
Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
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Highly parallel direct RNA sequencing on an array of nanopores
inferredcites →https://doi.org/10.1038/s41467-019-08289-9openalex-snapshot
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
inferredcites →https://doi.org/10.1038/s41467-019-08734-9openalex-snapshot
Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen
inferredcites →https://doi.org/10.1038/s41592-019-0617-2openalex-snapshot
Nanopore native RNA sequencing of a human poly(A) transcriptome
inferredcites →https://doi.org/10.1038/s41598-018-26955-8openalex-snapshot
Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus
inferredcites →https://doi.org/10.1038/s41598-018-32615-8openalex-snapshot
Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome
inferredcites →https://doi.org/10.1073/pnas.1000378107openalex-snapshot
Subgenomic messenger RNA amplification in coronaviruses
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty521openalex-snapshot
Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph
inferredcites →https://doi.org/10.1093/nar/gks1007openalex-snapshot
MODOMICS: a database of RNA modification pathways—2013 update
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The Evolution and Emergence of RNA Viruses
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Nucleotide Sequence of the Gene Encoding the Spike Glycoprotein of Human Coronavirus HCV 229E
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Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus
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Mechanisms and enzymes involved in SARS coronavirus genome expression
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Rapid identification of coronavirus replicase inhibitors using a selectable replicon RNA
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Nidovirus transcription: how to make sense…?
inferredcites →https://doi.org/10.1101/094672openalex-snapshot
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
inferredcites →https://doi.org/10.1101/132274openalex-snapshot
Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
inferredcites →https://doi.org/10.1101/gr.215038.116openalex-snapshot
De novo assembly of viral quasispecies using overlap graphs
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1111/1755-0998.12324openalex-snapshot
A first look at the Oxford Nanopore MinION sequencer
inferredcites →https://doi.org/10.1128/jvi.00160-09openalex-snapshot
Bovine Coronavirus Nonstructural Protein 1 (p28) Is an RNA Binding Protein That Binds Terminal Genomic cis -Replication Elements
inferredcites →https://doi.org/10.1128/jvi.00549-07openalex-snapshot
An RNA Stem-Loop within the Bovine Coronavirus nsp1 Coding Region Is a cis -Acting Element in Defective Interfering RNA Replication
inferredcites →https://doi.org/10.1128/jvi.01358-06openalex-snapshot
A Contemporary View of Coronavirus Transcription
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RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments
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Mutagenic analysis of the coronavirus intergenic consensus sequence
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A cis-acting function for the coronavirus leader in defective interfering RNA replication
inferredcites →https://doi.org/10.1128/jvi.70.12.8660-8668.1996openalex-snapshot
Replication and packaging of coronavirus infectious bronchitis virus defective RNAs lacking a long open reading frame
inferredcites →https://doi.org/10.1128/jvi.70.5.2720-2729.1996openalex-snapshot
The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA
inferredcites →https://doi.org/10.1128/jvi.73.2.1535-1545.1999openalex-snapshot
Replication and Packaging of Transmissible Gastroenteritis Coronavirus-Derived Synthetic Minigenomes
inferredcites →https://doi.org/10.1128/jvi.75.16.7362-7374.2001openalex-snapshot
Downstream Sequences Influence the Choice between a Naturally Occurring Noncanonical and Closely Positioned Upstream Canonical Heptameric Fusion Motif during Bovine Coronavirus Subgenomic mRNA Synthesis
inferredcites →https://doi.org/10.1128/jvi.76.3.1293-1308.2002openalex-snapshot
Transcription Regulatory Sequences and mRNA Expression Levels in the Coronavirus Transmissible Gastroenteritis Virus
inferredcites →https://doi.org/10.1128/jvi.78.12.6271-6281.2004openalex-snapshot
RNA Recombination In Vivo in the Absence of Viral Replication
inferredcites →https://doi.org/10.1128/jvi.78.2.980-994.2004openalex-snapshot
Sequence Motifs Involved in the Regulation of Discontinuous Coronavirus Subgenomic RNA Synthesis
inferredcites →https://doi.org/10.1128/mmbr.56.1.61-79.1992openalex-snapshot
RNA recombination in animal and plant viruses
inferredcites →https://doi.org/10.1146/annurev-virology-100114-055218openalex-snapshot
Continuous and Discontinuous RNA Synthesis in Coronaviruses
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.1186/s13072-015-0016-6openalex-snapshot
Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond
inferredcites →https://doi.org/10.1534/g3.113.008995openalex-snapshot
The Reference Genome Sequence ofSaccharomyces cerevisiae: Then and Now
inferredcites →https://doi.org/10.3389/fmicb.2017.01079openalex-snapshot
Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
inferredcites →https://doi.org/10.3389/fmicb.2017.02708openalex-snapshot
Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus
inferredcites →https://doi.org/10.3389/fphar.2016.00156openalex-snapshot
MinION: A Novel Tool for Predicting Drug Hypersensitivity?
inferredcites →https://doi.org/10.3390/v1030895openalex-snapshot
Defective Interfering RNAs: Foes of Viruses and Friends of Virologists
inferredcites →https://doi.org/10.4161/rna.8.2.14991openalex-snapshot
RNA-RNA and RNA-protein interactions in coronavirus replication and transcription

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides
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Nanopore sequencing: a rapid solution for infectious disease epidemics
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Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community
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Recent advances in the detection of base modifications using the Nanopore sequencer
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On the origin and evolution of SARS-CoV-2
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Genomic analysis of human noroviruses using combined Illumina–Nanopore data
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Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing
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Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing
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nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification
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Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing
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Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools
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Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing
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Peer Review #2 of "Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands (v0.1)"
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Peer Review #3 of "Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands (v0.1)"
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Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
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