Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

(2020) Xianding Deng et al.   Nature Microbiology

Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness

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

Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

(2019) Timothy A. Blauwkamp et al.   Nature Microbiology

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

(2019) Maria Asplund et al.   CLINICAL MICROBIOLOGY AND INFECTION

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

(2019) Steve Miller et al.   GENOME RESEARCH

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

Viral Metagenomics on Cerebrospinal Fluid

(2019) Edridge et al.   Genes

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

(2019) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Metagenomic Next-Generation Sequencing for the Identification and Quantitation of Transplant-Related DNA Viruses

(2019) Meredith L. Carpenter et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial

(2019) Junier et al.   Genes

Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases

(2019) Kufner et al.   Genes

The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

(2019) Anneloes L. van Rijn et al.   PLoS One

Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients

(2019) Sander van Boheemen et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Improving saliva shotgun metagenomics by chemical host DNA depletion

(2018) Clarisse A. Marotz et al.   Microbiome

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

Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

(2018) Matthew W. Keller et al.   Scientific Reports

Identification and removal of contaminating microbial DNA from PCR reagents: impact on low‐biomass microbiome analyses

(2018) L.F. Stinson et al.   LETTERS IN APPLIED MICROBIOLOGY

Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples

(2018) Corinne P. Oechslin et al.   Frontiers in Cellular and Infection Microbiology

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

(2018) Nicole M. Davis et al.   Microbiome

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology

(2017) Robert Schlaberg et al.   JOURNAL OF INFECTIOUS DISEASES

Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

(2017) Lawrence J. Jennings et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

(2017) Michael Huber et al.   JOURNAL OF VIROLOGICAL METHODS

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

(2016) Mohammad R. Hasan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Real-time selective sequencing using nanopore technology

(2016) Matthew Loose et al.   NATURE METHODS

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

(2016) Edward T. Mee et al.   VACCINE

Enhanced virome sequencing using targeted sequence capture

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

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

(2013) S. N. Naccache et al.   JOURNAL OF VIROLOGY

Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination

(2013) Francesca Di Giallonardo et al.   PLoS One

Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

(2012) Samuel O. Oyola et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

(2011) Michel de Vries et al.   PLoS One

Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing

(2011) Filip Van Nieuwerburgh et al.   PLoS One

Non-template functions of viral RNA in picornavirus replication

(2011) Sushma A Ogram et al.   Current Opinion in Virology

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Presence and role of cytosine methylation in DNA viruses of animals

(2008) K. Hoelzer et al.   NUCLEIC ACIDS RESEARCH