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

Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

(2015) Silvie Van den Hoecke et al.   BMC GENOMICS

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

Long-term viral shedding and viral genome mutation in norovirus infection

(2015) Tatsuya Miyoshi et al.   JOURNAL OF MEDICAL VIROLOGY

GII.4 Sydney_2012 norovirus infection in immunocompromised patients in Beijing and its rapid evolution in vivo

(2015) Huan Mai et al.   JOURNAL OF MEDICAL VIROLOGY

Genetic characterization of norovirus strains in hospitalized children from Pakistan

(2015) Amna Alam et al.   JOURNAL OF MEDICAL VIROLOGY

Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants

(2015) Kim Thys et al.   JOURNAL OF VIROLOGICAL METHODS

What Is the Reservoir of Emergent Human Norovirus Strains?

(2015) Stephanie M. Karst et al.   JOURNAL OF VIROLOGY

Detection and analysis of recombination in GII.4 norovirus strains causing gastroenteritis outbreaks in Alberta

(2014) Maria E. Hasing et al.   INFECTION GENETICS AND EVOLUTION

Advances in Laboratory Methods for Detection and Typing of Norovirus

(2014) Jan Vinjé   JOURNAL OF CLINICAL MICROBIOLOGY

RNA Populations in Immunocompromised Patients as Reservoirs for Novel Norovirus Variants

(2014) E. Vega et al.   JOURNAL OF VIROLOGY

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

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

Within-Host Evolution Results in Antigenically Distinct GII.4 Noroviruses

(2014) K. Debbink et al.   JOURNAL OF VIROLOGY

Global prevalence of norovirus in cases of gastroenteritis: a systematic review and meta-analysis

(2014) Sharia M Ahmed et al.   LANCET INFECTIOUS DISEASES

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

(2013) Samit Kundu et al.   CLINICAL INFECTIOUS DISEASES

Emergence of a New Norovirus GII.4 Variant and Changes in the Historical Biennial Pattern of Norovirus Outbreak Activity in Alberta, Canada, from 2008 to 2013

(2013) M. E. Hasing et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Norwalk Virus Minor Capsid Protein VP2 Associates within the VP1 Shell Domain

(2013) S. Vongpunsawad et al.   JOURNAL OF VIROLOGY

Recombination within the Pandemic Norovirus GII.4 Lineage

(2013) J.-S. Eden et al.   JOURNAL OF VIROLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

(2013) Elizabeth M. Batty et al.   PLoS One

Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England

(2013) T H Wong et al.   Virology Journal

Identification of Immune and Viral Correlates of Norovirus Protective Immunity through Comparative Study of Intra-Cluster Norovirus Strains

(2013) Shu Zhu et al.   PLoS Pathogens

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Norovirus GII.4 and GII.7 capsid sequences undergo positive selection in chronically infected patients

(2012) Dieter Hoffmann et al.   INFECTION GENETICS AND EVOLUTION

Prevalence and Clinical Impact of Norovirus Fecal Shedding in Children with Inherited Immune Deficiencies

(2012) Pierre Frange et al.   JOURNAL OF INFECTIOUS DISEASES

Emergence of a Norovirus GII.4 Strain Correlates with Changes in Evolving Blockade Epitopes

(2012) L. C. Lindesmith et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Performance of VIDISCA-454 in Feces-Suspensions and Serum

(2012) Michel de Vries et al.   Viruses-Basel

Immunogenetic Mechanisms Driving Norovirus GII.4 Antigenic Variation

(2012) Lisa C. Lindesmith et al.   PLoS Pathogens

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Covariation of Major and Minor Viral Capsid Proteins in Norovirus Genogroup II Genotype 4 Strains

(2011) M. C.-W. Chan et al.   JOURNAL OF VIROLOGY

Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection

(2011) S. Ramachandran et al.   JOURNAL OF VIROLOGY

Contribution of Intra- and Interhost Dynamics to Norovirus Evolution

(2011) R. A. Bull et al.   JOURNAL OF VIROLOGY

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

(2011) Rowena A. Bull et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chronic Norovirus Infection after Kidney Transplantation: Molecular Evidence for Immune‐Driven Viral Evolution

(2010) Robert Schorn et al.   CLINICAL INFECTIOUS DISEASES

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

Chronic Shedders as Reservoir for Nosocomial Transmission of Norovirus

(2010) F. H. A. Sukhrie et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Influence of Novel Norovirus GII.4 Variants on Gastroenteritis Outbreak Dynamics in Alberta and the Northern Territories, Canada between 2000 and 2008

(2010) Xiaoli L. Pang et al.   PLoS One

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection

(2009) B. Carlsson et al.   JOURNAL OF GENERAL VIROLOGY

Norovirus Illness Is a Global Problem: Emergence and Spread of Norovirus GII.4 Variants, 2001–2007

(2009) J. Joukje Siebenga et al.   JOURNAL OF INFECTIOUS DISEASES

Evolutionary Dynamics of GII.4 Noroviruses over a 34-Year Period

(2009) K. Bok et al.   JOURNAL OF VIROLOGY

High Prevalence of Prolonged Norovirus Shedding and Illness among Hospitalized Patients: A Model for In Vivo Molecular Evolution

(2008) J. Joukje Siebenga et al.   JOURNAL OF INFECTIOUS DISEASES

Quantitative detection of norovirus excretion in pediatric patients with cancer and prolonged gastroenteritis and shedding of norovirus

(2008) A. Ludwig et al.   JOURNAL OF MEDICAL VIROLOGY

Mechanisms of GII.4 Norovirus Persistence in Human Populations

(2008) Lisa C Lindesmith et al.   PLOS MEDICINE