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

A decade of RNA virus metagenomics is (not) enough

(2018) Alexander L. Greninger   VIRUS RESEARCH

Application of next generation sequencing for the detection of human viral pathogens in clinical specimens

(2017) Jayme Parker et al.   JOURNAL OF CLINICAL VIROLOGY

Comprehensive detection of viruses in pediatric patients with acute liver failure using next-generation sequencing

(2017) Takako Suzuki et al.   JOURNAL OF CLINICAL VIROLOGY

Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait

(2017) Nada Madi et al.   JOURNAL OF MEDICAL VIROLOGY

Clinical and biological insights from viral genome sequencing

(2017) Charlotte J. Houldcroft et al.   NATURE REVIEWS MICROBIOLOGY

Distinct patterns of innate immune activation by clinical isolates of respiratory syncytial virus

(2017) Ruth Levitz et al.   PLoS One

The interdependencies of viral load, the innate immune response, and clinical outcome in children presenting to the emergency department with respiratory syncytial virus-associated bronchiolitis

(2017) Felipe-Andrés Piedra 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

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

(2017) Kiril M. Dimitrov et al.   Virology Journal

Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention

(2017) Alexander L. Greninger et al.   Journal of the Pediatric Infectious Diseases Society

Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

(2016) Alexander L. Greninger et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing

(2016) Jun-ichi Kawada et al.   Scientific Reports

Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene

(2016) Seth A. Schobel et al.   Scientific Reports

Rapid next-generation sequencing of dengue, EV-A71 and RSV-A viruses

(2015) Cécile Baronti et al.   JOURNAL OF VIROLOGICAL METHODS

Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach

(2015) Waleed Aljabr et al.   JOURNAL OF VIROLOGY

Local Evolutionary Patterns of Human Respiratory Syncytial Virus Derived from Whole-Genome Sequencing

(2015) Charles N. Agoti et al.   JOURNAL OF VIROLOGY

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study

(2015) Alexander L Greninger et al.   LANCET INFECTIOUS DISEASES

A gene deletion that up-regulates viral gene expression yields an attenuated RSV vaccine with improved antibody responses in children

(2015) Ruth A. Karron et al.   Science Translational Medicine

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Within-Host Whole-Genome Deep Sequencing and Diversity Analysis of Human Respiratory Syncytial Virus Infection Reveals Dynamics of Genomic Diversity in the Absence and Presence of Immune Pressure

(2014) Y. H. Grad et al.   JOURNAL OF VIROLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Next generation sequencing of viral RNA genomes

(2013) Denise A Marston et al.   BMC GENOMICS

Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

(2013) Richard J. Hall et al.   JOURNAL OF VIROLOGICAL METHODS

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

(2013) Toon Rosseel et al.   PLoS One

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

(2012) Christine M. Malboeuf et al.   NUCLEIC ACIDS RESEARCH

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Comparison of Nasopharyngeal and Oropharyngeal Swabs for the Diagnosis of Eight Respiratory Viruses by Real-Time Reverse Transcription-PCR Assays

(2011) Curi Kim et al.   PLoS One

Whole Genome Sequencing and Evolutionary Analysis of Human Respiratory Syncytial Virus A and B from Milwaukee, WI 1998-2010

(2011) Cecilia Rebuffo-Scheer et al.   PLoS One

Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies

(2011) Toon Rosseel et al.   Virology Journal

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Viral genome sequencing by random priming methods

(2008) Appolinaire Djikeng et al.   BMC GENOMICS