High Throughput Sequencing for the Detection and Characterization of RNA Viruses

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

(2020) Jing Lu et al.   CELL

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver et al.   CELL

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

(2020) Hong Zhou et al.   CURRENT BIOLOGY

A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies

(2020) Peter H. Culviner et al.   mBio

Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment

(2020) Sofia Strubbia et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

(2020) Yuri I. Wolf et al.   Nature Microbiology

Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness

(2020) Ellen C. Carbo et al.   JOURNAL OF CLINICAL VIROLOGY

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses

(2020) Md. Nafis Ul Alam et al.   PLoS One

Unique dual indexing PCR reduces chimeric contamination and improves mutation detection in cell-free DNA of pregnant women

(2020) Meijie Du et al.   TALANTA

A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

(2020) Jalees A. Nasir et al.   Viruses-Basel

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Rapid Sequencing of Multiple RNA Viruses in Their Native Form

(2019) Thidathip Wongsurawat et al.   Frontiers in Microbiology

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

(2019) Daniel P. Depledge et al.   Nature Communications

Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses

(2019) Amit C. Sukal et al.   VIROLOGY

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

(2019) Hayden C. Metsky et al.   NATURE BIOTECHNOLOGY

Modified protocol for RNA isolation from different parts of field-grown jute plant suitable for NGS data generation and quantitative real-time RT-PCR

(2019) Ahmed Rasel et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples

(2019) Marie-Ange Palomares et al.   Scientific Reports

In-silico Design of DNA Oligonucleotides: Challenges and Approaches

(2019) Michaela Hendling et al.   Computational and Structural Biotechnology Journal

A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

(2019) Ryan K.Y. Wong et al.   BMC GENOMICS

Comparison of nucleic acid extraction methods for next-generation sequencing of avian influenza A virus from ferret respiratory samples

(2019) Han Di et al.   JOURNAL OF VIROLOGICAL METHODS

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

(2019) Sofia Strubbia et al.   Food and Environmental Virology

Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells

(2019) Carole Grädel et al.   Genes

Efficient depletion of ribosomal RNA for RNA sequencing in planarians

(2019) Iana V. Kim et al.   BMC GENOMICS

Performance Comparison of Reverse Transcriptases for Single-Cell Studies

(2019) Daniel Zucha et al.   CLINICAL CHEMISTRY

Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples

(2019) Nagendrakumar B. Singanallur et al.   JOURNAL OF VIROLOGICAL METHODS

Impact of nucleic acid extraction platforms on hepatitis virus genome detection

(2019) Matthew D. Pauly et al.   JOURNAL OF VIROLOGICAL METHODS

Molecular Detection of Human Salivirus in Italy Through Monitoring of Urban Sewages

(2019) Pamela Mancini et al.   Food and Environmental Virology

Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters

(2019) Sofia Strubbia et al.   Frontiers in Microbiology

Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics

(2019) Yiming Huang et al.   NUCLEIC ACIDS RESEARCH

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

(2018) Zachary T. Herbert et al.   BMC GENOMICS

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico

(2018) Julien Thézé et al.   Cell Host & Microbe

Metagenomic Analysis of the Jinding Duck Fecal Virome

(2018) Lili Zhao et al.   CURRENT MICROBIOLOGY

Accurate fidelity analysis of the reverse transcriptase by a modified next-generation sequencing

(2018) Hiroyuki Okano et al.   ENZYME AND MICROBIAL TECHNOLOGY

Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR

(2018) Christina Bartsch et al.   FOOD MICROBIOLOGY

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing

(2018) Brigid M. O'Flaherty et al.   GENOME RESEARCH

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

(2018) Hao Wang et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

Comparison of different nucleic acid preparation methods to improve specific HIV-1 RNA isolation for viral load testing on dried blood spots

(2018) Emilande Guichet et al.   JOURNAL OF VIROLOGICAL METHODS

Complexities of Viral Mutation Rates

(2018) Kayla M. Peck et al.   JOURNAL OF VIROLOGY

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates

(2018) Stephanie Goya et al.   PLoS One

Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique

(2018) Harindranath Cholleti et al.   Virology Journal

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

(2018) Shanrong Zhao et al.   Scientific Reports

Emerging recombinant noroviruses identified by clinical and waste water screening

(2018) Jennifer H. Lun et al.   Emerging Microbes & Infections

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom

(2018) Lydia J. Leon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a method for direct extraction of viral RNA from bivalve mollusks

(2018) Hoa Quang Le et al.   LETTERS IN APPLIED MICROBIOLOGY

Next-generation amplicon sequencing identifies genetically diverse human astroviruses, including recombinant strains, in environmental waters

(2018) Akihiko Hata et al.   Scientific Reports

Why are RNA virus mutation rates so damn high?

(2018) Siobain Duffy   PLOS BIOLOGY

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow

(2018) A. Bal et al.   BMC INFECTIOUS DISEASES

Virus genotyping by massive parallel amplicon sequencing: adenovirus and enterovirus in the Norwegian MIDIA study

(2018) Ondrej Cinek et al.   JOURNAL OF MEDICAL VIROLOGY

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

1647. Real-Time Metagenomic Sequencing Reveals Discrete Transmission Clusters Within a Hospital-Associated Norovirus Outbreak

(2018) Amanda Casto et al.   Open Forum Infectious Diseases

A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery

(2018) Joseph R. Fauver et al.   VIROLOGY

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing

(2018) Tulio M. Fumian et al.   ENVIRONMENT INTERNATIONAL

A large outbreak of acute gastroenteritis in Shippensburg, Pennsylvania, 1972 revisited: evidence for common source exposure to a recombinant GII.Pg/GII.3 norovirus

(2017) J. A. JOHNSON et al.   EPIDEMIOLOGY AND INFECTION

Next-Generation Sequencing Analysis of the Diversity of Human Noroviruses in Japanese Oysters

(2017) Saiki Imamura et al.   Foodborne Pathogens and Disease

Whole-Genome Next-Generation Sequencing to Study Within-Host Evolution of Norovirus (NoV) Among Immunocompromised Patients With Chronic NoV Infection

(2017) Janko van Beek et al.   JOURNAL OF INFECTIOUS DISEASES

Variables influencing the efficiency and interpretation of reverse transcription quantitative PCR (RT-qPCR): An empirical study using Bacteriophage MS2

(2017) Jaclyn A. Miranda et al.   JOURNAL OF VIROLOGICAL METHODS

Distribution of norovirus genotypes and subtypes in river water by ultra-deep sequencing-based analysis

(2017) M. Boonchan et al.   LETTERS IN APPLIED MICROBIOLOGY

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)

(2017) Mette Myrmel et al.   PLoS One

Error baseline rates of five sample preparation methods used to characterize RNA virus populations

(2017) Jeffrey R. Kugelman et al.   PLoS One

Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

(2017) Klaudia Chrzastek et al.   VIROLOGY

Genetic Diversity Among Genogroup II Noroviruses and Progressive Emergence of GII.17 in Wastewaters in Italy (2011–2016) Revealed by Next-Generation and Sanger Sequencing

(2017) E. Suffredini et al.   Food and Environmental Virology

Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus

(2017) Elizabeth Jaworski et al.   PLoS Pathogens

Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

(2017) Gabriel I. Parra et al.   PLoS Pathogens

Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach

(2017) Neda Nasheri et al.   Frontiers in Microbiology

Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches

(2017) Anja Pecman et al.   Frontiers in Microbiology

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

(2017) Adriana Alberti et al.   Scientific Data

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

(2017) Mathis Hjort Hjelmsø et al.   PLoS One

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

(2017) Olga E. Petrova et al.   Scientific Reports

A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants

(2017) Jannik Fonager et al.   Scientific Reports

A next generation sequencing-based method to study the intra-host genetic diversity of norovirus in patients with acute and chronic infection

(2016) Maria E. Hasing et al.   BMC GENOMICS

Application of Next-Generation Sequencing to Evaluate the Profile of Noroviruses in Pre- and Post-Depurated Oysters

(2016) Saiki Imamura et al.   Foodborne Pathogens and Disease

Human norovirus hyper-mutation revealed by ultra-deep sequencing

(2016) José M. Cuevas et al.   INFECTION GENETICS AND EVOLUTION

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

(2016) Julianne R. Brown et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Targeted full-genome amplification and sequencing of dengue virus types 1–4 from South America

(2016) Cristopher D. Cruz et al.   JOURNAL OF VIROLOGICAL METHODS

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects

(2016) Ruth R. Miller et al.   PLoS One

Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

(2016) Bram Vrancken et al.   Viruses-Basel

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland

(2016) Dennis Hanke et al.   PLoS Neglected Tropical Diseases

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

(2016) Lindsey A. Moser et al.   mSystems

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome

(2016) Paola Miyazato et al.   Scientific Reports

Comparison of Three Magnetic Bead Surface Functionalities for RNA Extraction and Detection

(2015) Nicholas M. Adams et al.   ACS Applied Materials & Interfaces

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing

(2015) Eric Samorodnitsky et al.   HUMAN MUTATION

Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus

(2015) Herjan H.J. Bavelaar et al.   JOURNAL OF CLINICAL VIROLOGY

ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs

(2015) Andrew Routh et al.   JOURNAL OF MOLECULAR BIOLOGY

Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples

(2015) Toon Rosseel et al.   JOURNAL OF VIROLOGICAL METHODS

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent

(2015) Linlin Li et al.   JOURNAL OF VIROLOGICAL METHODS

High-quality RNA extraction from copepods for Next Generation Sequencing: A comparative study

(2015) Sneha Asai et al.   Marine Genomics

Molecular Evidence of Sexual Transmission of Ebola Virus

(2015) Suzanne E. Mate et al.   NEW ENGLAND JOURNAL OF MEDICINE

Duplex-specific nuclease-mediated bioanalysis

(2015) Xiaopei Qiu et al.   TRENDS IN BIOTECHNOLOGY

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library

(2015) Caryll Waugh et al.   Virology Journal

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results

(2015) Claudia Brandariz-Fontes et al.   Scientific Reports

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

(2014) Adriana Alberti et al.   BMC GENOMICS

Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage

(2014) Stuart K Archer et al.   BMC GENOMICS

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Variability of the Reverse Transcription Step: Practical Implications

(2014) S. Bustin et al.   CLINICAL CHEMISTRY

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

(2014) M. Cotten et al.   JOURNAL OF VIROLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

(2014) Matthew Cotten et al.   PLoS One

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

(2014) Jakob Hedegaard et al.   PLoS One

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

(2014) Sarah A. Munro et al.   Nature Communications

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer

(2014) Haiying Jia et al.   Scientific Reports

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

(2014) Derong Xu et al.   Protein & Cell

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

Next generation sequencing of viral RNA genomes

(2013) Denise A Marston et al.   BMC GENOMICS

Next-Generation Whole Genome Sequencing Identifies the Direction of Norovirus Transmission in Linked Patients

(2013) Samit Kundu et al.   CLINICAL INFECTIOUS DISEASES

Role of norovirus in acute gastroenteritis in the Northwest of Spain during 2010-2011

(2013) Carmen F. Manso et al.   JOURNAL OF MEDICAL VIROLOGY

Improved rolling circle amplification (RCA) of hepatitis B virus (HBV) relaxed-circular serum DNA (RC-DNA)

(2013) Nora Martel et al.   JOURNAL OF VIROLOGICAL METHODS

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

(2013) Zhifu Sun et al.   PLoS One

Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

(2013) Guoyan Zhao et al.   PLoS One

mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies

(2013) Tao Qing et al.   Science China-Life Sciences

Coronaviruses as DNA Wannabes: A New Model for the Regulation of RNA Virus Replication Fidelity

(2013) Everett Clinton Smith et al.   PLoS Pathogens

Bayesian modeling of reproducibility and robustness of RNA reverse transcription and quantitative real-time polymerase chain reaction

(2012) Jere Lindén et al.   ANALYTICAL BIOCHEMISTRY

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species

(2012) Doreen Schwochow et al.   BMC BIOTECHNOLOGY

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic

(2012) Yong-Li Xiao et al.   JOURNAL OF PATHOLOGY

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

(2012) Kelvin Li et al.   Virology Journal

Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue

(2011) Eric J. Duncavage et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

(2011) Michel de Vries et al.   PLoS One

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

(2010) Stephen A Bustin et al.   BMC MOLECULAR BIOLOGY

Comparison of commercially-available RNA extraction methods for effective bacterial RNA isolation from milk spiked samples

(2010) Paula García-Nogales et al.   ELECTRONIC JOURNAL OF BIOTECHNOLOGY

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS