Agnostic Sequencing for Detection of Viral Pathogens

Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

(2022) My V. T. Phan et al.   Scientific Reports

Performance of Rapid Antigen Tests for COVID-19 Diagnosis: A Systematic Review and Meta-Analysis

(2022) Muhammad Fazli Khalid et al.   Diagnostics

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies

(2022) Induja Chandrakumar et al.   Communications Biology

A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus

(2022) Klaudia Chrzastek et al.   BMC GENOMICS

Epidemiological, clinical and virological characteristics of four cases of monkeypox support transmission through sexual contact, Italy, May 2022

(2022) Andrea Antinori et al.   Eurosurveillance

Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns

(2022) Alla Mikheenko et al.   GENOME RESEARCH

Publisher Correction: Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater

(2022) Davida S. Smyth et al.   Nature Communications

Evidence of human-to-dog transmission of monkeypox virus

(2022) Sophie Seang et al.   LANCET

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

(2022) Mantas Sereika et al.   NATURE METHODS

Monkeypox Virus Infection in Humans across 16 Countries — April–June 2022

(2022) John P. Thornhill et al.   NEW ENGLAND JOURNAL OF MEDICINE

Laboratory diagnostics for monkeypox: An overview of sensitivities from various published tests

(2022) Zhiwen Jiang et al.   Travel Medicine and Infectious Disease

Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery

(2022) Philippe Pérot et al.   Viruses-Basel

Diagnosis of monkeypox virus – An overview

(2022) Mustafa Altindis et al.   Travel Medicine and Infectious Disease

Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections

(2022) Kazuhiro Horiba et al.   Open Forum Infectious Diseases

LAMP Diagnostics at the Point of Care: Emerging Trends and Perspectives for the Developer Community

(2021) Taylor J. Moehling et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

(2021) Amir Asri Kojabad et al.   JOURNAL OF MEDICAL VIROLOGY

Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection

(2021) Fernando Lázaro-Perona et al.   PLoS One

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

(2021) Ki Wook Kim et al.   Scientific Reports

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses

(2021) Jeremy Fan et al.   BMC BIOINFORMATICS

Challenges in the application of NGS in the clinical laboratory

(2021) Yuxin Yin et al.   HUMAN IMMUNOLOGY

Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies

(2021) Kumeren N. Govender et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

(2021) Jutte J.C. de Vries et al.   JOURNAL OF CLINICAL VIROLOGY

Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis

(2021) Nicole Ngai Yung Tsang et al.   LANCET INFECTIOUS DISEASES

Abbott ID NOW COVID-19 Assay Performance: A Year in Review

(2021) Phyu M. Thwe et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season

(2021) Yifei Xu et al.   Eurosurveillance

Whole Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina-MiSeq ARTIC Protocol

(2021) Jonathan Plitnick et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

(2021) Jutte J.C. de Vries et al.   JOURNAL OF CLINICAL VIROLOGY

Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

(2021) Simon Haile et al.   JOURNAL OF VIROLOGICAL METHODS

Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples

(2021) Nick P. G. Gauthier et al.   PLoS One

Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia

(2020) Daniel K W Chu et al.   CLINICAL CHEMISTRY

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

(2020) Victor M Corman et al.   Eurosurveillance

Nanopore sequencing reveals novel targets for the diagnosis and surveillance of human and avian influenza A virus

(2020) Cyril Chik-Yan Yip et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2020) Xianding Deng et al.   Nature Microbiology

Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit

(2020) Arun K. Nalla et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comparison of SARS‐CoV‐2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed real‐time RT‐PCR test

(2020) Elisabet Pujadas et al.   JOURNAL OF MEDICAL VIROLOGY

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

(2020) Jiayu Shang et al.   METHODS

NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline

(2020) Yifei Xu et al.   NUCLEIC ACIDS RESEARCH

Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

(2020) Becky Fung et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

(2020) Andrew J. Gorzalski et al.   JOURNAL OF CLINICAL VIROLOGY

Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2

(2020) Catherine A. Hogan et al.   JOURNAL OF CLINICAL VIROLOGY

Validation of SARS-CoV-2 detection across multiple specimen types

(2020) Garrett A. Perchetti et al.   JOURNAL OF CLINICAL VIROLOGY

Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics

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

Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays

(2020) Katharine Uhteg et al.   JOURNAL OF CLINICAL VIROLOGY

Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2

(2020) Marie C. Smithgall et al.   JOURNAL OF CLINICAL VIROLOGY

Multi-center evaluation of cepheid xpert® xpress SARS-CoV-2 point-of-care test during the SARS-CoV-2 pandemic

(2020) Femke Wolters et al.   JOURNAL OF CLINICAL VIROLOGY

Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories

(2020) Jason J. LeBlanc et al.   JOURNAL OF CLINICAL VIROLOGY

SARS-CoV-2 and co-infections detection in nasopharyngeal throat swabs of COVID-19 patients by metagenomics

(2020) Le Van Tan et al.   JOURNAL OF INFECTION

Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis

(2020) Cui-Lin Shi et al.   JOURNAL OF INFECTION

Detection profile of SARS‐CoV‐2 using RT‐PCR in different types of clinical specimens: A systematic review and meta‐analysis

(2020) George M. Bwire et al.   JOURNAL OF MEDICAL VIROLOGY

Performance Assessment of SARS-CoV-2 PCR Assays Developed by WHO Referral Laboratories

(2020) Sibyle Etievant et al.   Journal of Clinical Medicine

High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States

(2020) Ryan P. McNamara et al.   Cell Reports

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

(2020) Katrina L Kalantar et al.   GigaScience

A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2

(2020) Daryl M. Gohl et al.   BMC GENOMICS

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

(2020) Matteo Chiara et al.   BRIEFINGS IN BIOINFORMATICS

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

(2020) F. Xavier López-Labrador et al.   JOURNAL OF CLINICAL VIROLOGY

Fully automated detection and differentiation of pandemic and endemic coronaviruses (NL63, 229E, HKU1, OC43 and SARS‐CoV‐2) on the Hologic Panther Fusion

(2020) Anne K. Cordes et al.   JOURNAL OF MEDICAL VIROLOGY

Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses

(2020) Kelsey T. Young et al.   JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION

Clinical metagenomics

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

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

(2019) Steve Miller et al.   GENOME RESEARCH

Viral Metagenomics on Cerebrospinal Fluid

(2019) Edridge et al.   Genes

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

(2019) Jiao Chen et al.   BMC BIOINFORMATICS

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

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

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

(2019) Heike Sichtig et al.   Nature Communications

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

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

(2019) Junier et al.   Genes

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

(2019) Lauren M. Petersen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

(2019) Kuiama Lewandowski et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

(2019) Volkan Sevim et al.   Scientific Data

Performance evaluation of the Panther Fusion® respiratory tract panel

(2019) Jolanda J.C. Voermans et al.   JOURNAL OF CLINICAL VIROLOGY

Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza

(2019) Laura A.E. Van Poelvoorde et al.   TRENDS IN BIOTECHNOLOGY

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

The challenge of diagnostic metagenomics

(2018) Alexander L. Greninger   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebral Spinal Fluid Diagnostics

(2018) Patricia J Simner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

(2018) Stephanie Goya et al.   PLoS One

Machine Learning for detection of viral sequences in human metagenomic datasets

(2018) Zurab Bzhalava et al.   BMC BIOINFORMATICS

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

(2018) Yifei Xu et al.   Frontiers in Microbiology

Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches

(2018) Simon H. Williams et al.   mSphere

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

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

(2018) Charles Langelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses

(2017) Bin Zhou et al.   JOURNAL OF CLINICAL 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

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

(2017) Klaudia Chrzastek et al.   VIROLOGY

Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

(2017) H.-S. Huang et al.   CLINICAL MICROBIOLOGY AND INFECTION

Targeted reduction of highly abundant transcripts using pseudo-random primers

(2016) Ophélie Arnaud et al.   BIOTECHNIQUES

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

(2016) Silvia I. Sardi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next generation sequencing for whole genome analysis and surveillance of influenza A viruses

(2016) Jana McGinnis et al.   JOURNAL OF CLINICAL VIROLOGY

Clinical Performance Evaluation of Molecular Diagnostic Tests

(2016) Bipasa Biswas   JOURNAL OF MOLECULAR DIAGNOSTICS

Translating diagnostic assays from the laboratory to the clinic: analytical and clinical metrics for device development and evaluation

(2016) Mark D. Borysiak et al.   LAB ON A CHIP

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Human Coronavirus OC43 Associated with Fatal Encephalitis

(2016) Sofia Morfopoulou et al.   NEW ENGLAND JOURNAL OF MEDICINE

Probable transfusion-transmitted Zika virus in Brazil

(2016) Maria L. Barjas-Castro et al.   TRANSFUSION

Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens

(2016) Anh To Nguyen et al.   Virology Journal

Current Approaches for Diagnosis of Influenza Virus Infections in Humans

(2016) Sai Vemula et al.   Viruses-Basel

Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics

(2016) Jiangqin Zhao et al.   PLoS One

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing

(2015) Samia N. Naccache et al.   CLINICAL INFECTIOUS DISEASES

Prospective and retrospective evaluation of the Cepheid Xpert® Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus

(2015) Nicolas Salez et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens

(2015) Karol Perlejewski et al.   JOURNAL OF VIROLOGICAL METHODS

Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa

(2015) Miles W. Carroll et al.   NATURE

The role of rapid diagnostics in managing Ebola epidemics

(2015) Pierre Nouvellet et al.   NATURE

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Whole-Genome Sequence Analysis Reveals the Enterovirus D68 Isolates during the United States 2014 Outbreak Mainly Belong to a Novel Clade

(2015) Weihua Huang et al.   Scientific Reports

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

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

Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis

(2015) M.-L. Frémond et al.   Journal of the Pediatric Infectious Diseases Society

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

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

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform

(2013) Wiriya Rutvisuttinunt et al.   JOURNAL OF VIROLOGICAL METHODS

Modern clinical microbiology: new challenges and solutions

(2013) Pierre-Edouard Fournier et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Update on Influenza Diagnostics: Lessons from the Novel H1N1 Influenza A Pandemic

(2012) S. Kumar et al.   CLINICAL MICROBIOLOGY REVIEWS

Molecular Surveillance of Low Pathogenic Avian Influenza Viruses in Wild Birds across the United States: Inferences from the Hemagglutinin Gene

(2012) Antoinette J. Piaggio et al.   PLoS One

Detection of Hemagglutinin Variants of the Pandemic Influenza A (H1N1) 2009 Virus by Pyrosequencing

(2011) M. Levine et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples

(2011) Justine Cheval et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Real-time PCR versus viral culture on urine as a gold standard in the diagnosis of congenital cytomegalovirus infection

(2011) Jutte J.C. de Vries et al.   JOURNAL OF CLINICAL VIROLOGY

A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

(2011) Michel de Vries et al.   PLoS One

Nationwide Molecular Surveillance of Pandemic H1N1 Influenza A Virus Genomes: Canada, 2009

(2011) Morag Graham et al.   PLoS One

A Comprehensive Deep Sequencing Strategy for Full-Length Genomes of Influenza A

(2011) Dirk Höper et al.   PLoS One

The Diagnosis of Viral Respiratory Disease in Older Adults

(2010) H. Keipp Talbot et al.   CLINICAL INFECTIOUS DISEASES

Validation of Laboratory-Developed Molecular Assays for Infectious Diseases

(2010) E. M. Burd   CLINICAL MICROBIOLOGY REVIEWS

Real-time PCR assays for the specific detection of monkeypox virus West African and Congo Basin strain DNA

(2010) Yu Li et al.   JOURNAL OF VIROLOGICAL METHODS

Molecular Detection of a Novel Human Influenza (H1N1) of Pandemic Potential by Conventional and Real-Time Quantitative RT-PCR Assays

(2009) L. L.M. Poon et al.   CLINICAL CHEMISTRY

Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1

(2009) Shawn Vasoo et al.   CLINICAL INFECTIOUS DISEASES

The Role of Community Molecular Diagnostics Laboratories in the H1N1 Pandemic

(2009) Jan A. Nowak et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Incubation periods of acute respiratory viral infections: a systematic review

(2009) Justin Lessler et al.   LANCET INFECTIOUS DISEASES

The development and impact of 454 sequencing

(2008) Jonathan M Rothberg et al.   NATURE BIOTECHNOLOGY