Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

Clinical Impact of Rapid Point-of-Care Polymerase Chain Reaction Influenza Testing In An Urgent Care Setting: A Single Center Study

(2019) Robert C. Benirschke et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

(2019) L. E. Kafetzopoulou et al.   SCIENCE

Heterosubtypic cross-protection correlates with cross-reactive interferon-gamma-secreting lymphocytes in the ferret model of influenza

(2019) Karen E. Gooch et al.   Scientific Reports

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

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

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

(2019) Steve Miller et al.   GENOME RESEARCH

Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

(2019) Anna L. McNaughton et al.   Scientific Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Rapid Antigen Tests for Influenza: Rationale and Significance of the FDA Reclassification

(2018) Daniel A. Green et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evolutionary dynamics of avian influenza A H7N9 virus across five waves in mainland China, 2013–2017

(2018) Dan Xiang et al.   JOURNAL OF INFECTION

Estimates of global seasonal influenza-associated respiratory mortality: a modelling study

(2018) A Danielle Iuliano et al.   LANCET

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology

(2018) Dylan H. Morris et al.   TRENDS IN MICROBIOLOGY

Influenza

(2018) Florian Krammer et al.   Nature Reviews Disease Primers

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

(2018) Timokratis Karamitros et al.   BMC GENOMICS

Molecular characterization of a nosocomial outbreak of influenza B virus in an acute care hospital setting

(2018) M. Sansone et al.   JOURNAL OF HOSPITAL INFECTION

The Pandemic Threat of Emerging H5 and H7 Avian Influenza Viruses

(2018) Troy Sutton   Viruses-Basel

A naturally protective epitope of limited variability as an influenza vaccine target

(2018) Craig P. Thompson et al.   Nature Communications

Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

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

Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk

(2018) Yifei Xu et al.   Frontiers in Microbiology

A novel PCR-based point-of-care method facilitates rapid, efficient, and sensitive diagnosis of influenza virus infection

(2018) Ralf L.J. Schmidt et al.   CLINICAL MICROBIOLOGY AND INFECTION

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples

(2018) Liana E. Kafetzopoulou et al.   Eurosurveillance

Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study

(2018) Kazuo Imai et al.   Frontiers in Microbiology

Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods

(2017) Dominik M. Meinel et al.   INFECTION

Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples

(2017) Antonina A. Votintseva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Effect of Nucleic Acid Extraction Platforms and Sample Storage on the Integrity of Viral RNA for Use in Whole Genome Sequencing

(2017) Kuiama Lewandowski et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

What Transmission Precautions Best Control Influenza Spread in a Hospital?

(2016) Natalia Blanco et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

The ecology and adaptive evolution of influenza A interspecies transmission

(2016) Udayan Joseph et al.   Influenza and Other Respiratory Viruses

Dynamic quantification of avian influenza H7N9(A) virus in a human infection during clinical treatment using droplet digital PCR

(2016) Yong Yan et al.   JOURNAL OF VIROLOGICAL METHODS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Enhanced virome sequencing using targeted sequence capture

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

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

MinION nanopore sequencing of an influenza genome

(2015) Jing Wang   Frontiers in Microbiology

Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks

(2015) Ana Raquel Penedos et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Low Dose Influenza Virus Challenge in the Ferret Leads to Increased Virus Shedding and Greater Sensitivity to Oseltamivir

(2014) Anthony C. Marriott et al.   PLoS One

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

(2012) R. Burke Squires et al.   Influenza and Other Respiratory Viruses

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Seasonal Influenza in Adults and Children—Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management: Clinical Practice Guidelines of the Infectious Diseases Society of America

(2009) Scott A. Harper et al.   CLINICAL INFECTIOUS DISEASES

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

The genomic and epidemiological dynamics of human influenza A virus

(2008) Andrew Rambaut et al.   NATURE