Clinical and biological insights from viral genome sequencing

Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure

(2016) Fred Kyeyune et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A method for near full-length amplification and sequencing for six hepatitis C virus genotypes

(2016) Rowena A. Bull et al.   BMC GENOMICS

Incidental findings of uncertain significance: To know or not to know - that is not the question

(2016) Bjørn Hofmann   BMC Medical Ethics

Human cancers and mammalian retroviruses: should we worry about bovine leukemia virus?

(2016) Andrew C Munro et al.   Future Virology

Hepatitis C Virus Resistance to Direct-Acting Antiviral Drugs in Interferon-Free Regimens

(2016) Jean-Michel Pawlotsky   GASTROENTEROLOGY

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes

(2016) Emma Thomson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

(2016) Julianne R. Brown 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

Novel autologous T-cell therapy for drug-resistant cytomegalovirus disease after lung transplantation

(2016) Paola Pierucci et al.   JOURNAL OF HEART AND LUNG TRANSPLANTATION

Analysis of Mutations in the Gene Encoding Cytomegalovirus DNA Polymerase in a Phase 2 Clinical Trial of Brincidofovir Prophylaxis

(2016) E. Randall Lanier et al.   JOURNAL OF INFECTIOUS DISEASES

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study

(2016) Guilherme Calvet et al.   LANCET INFECTIOUS DISEASES

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Human Coronavirus OC43 Associated with Fatal Encephalitis

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

Zika Virus Associated with Microcephaly

(2016) Jernej Mlakar et al.   NEW ENGLAND JOURNAL OF MEDICINE

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Probable transfusion-transmitted Zika virus in Brazil

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

Viral metagenomics and blood safety

(2016) V. Sauvage et al.   TRANSFUSION CLINIQUE ET BIOLOGIQUE

The genomic sequence of lymphocryptovirus from cynomolgus macaque

(2016) Cris Kamperschroer et al.   VIROLOGY

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

(2016) Timothy A. Johnson et al.   mBio

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

(2016) David M. Aanensen et al.   mBio

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

(2016) Charlotte J. Houldcroft et al.   Frontiers in Microbiology

INC-Seq: accurate single molecule reads using nanopore sequencing

(2016) Chenhao Li et al.   GigaScience

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

(2016) Timokratis Karamitros et al.   PLoS One

Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance

(2016) Robert A. Power et al.   PLoS One

Drug Resistance of Clinical Varicella-Zoster Virus Strains Confirmed by Recombinant Thymidine Kinase Expression and by Targeted Resistance Mutagenesis of a Cloned Wild-Type Isolate

(2015) Anne-Kathrin Brunnemann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Erratum to: Evolutionary trends of European bat lyssavirus type 2 including genetic characterization of Finnish strains of human and bat origin 24 years apart

(2015) Miia Jakava-Viljanen et al.   ARCHIVES OF VIROLOGY

Evidence of Self-Sustaining Drug Resistant HIV-1 Lineages Among Untreated Patients in the United Kingdom

(2015) Jean L. Mbisa et al.   CLINICAL INFECTIOUS DISEASES

Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

(2015) Julianne R. Brown et al.   CLINICAL INFECTIOUS DISEASES

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

Enhanced virome sequencing using targeted sequence capture

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

Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases

(2015) Adam A. Witney et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing

(2015) Jannik Fonager et al.   JOURNAL OF CLINICAL VIROLOGY

A Vision for Investigating the Microbiology of Health and Disease

(2015) W. Ian Lipkin   JOURNAL OF INFECTIOUS DISEASES

Whole-Genome Sequencing of Measles Virus Genotypes H1 and D8 During Outbreaks of Infection Following the 2010 Olympic Winter Games Reveals Viral Transmission Routes

(2015) Jennifer L. Gardy et al.   JOURNAL OF INFECTIOUS DISEASES

Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing

(2015) Hongzhi Guan et al.   JOURNAL OF NEUROVIROLOGY

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

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

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

Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013

(2015) Simon J. Watson et al.   JOURNAL OF VIROLOGY

Genome Diversity of Epstein-Barr Virus from Multiple Tumor Types and Normal Infection

(2015) Anne L. Palser 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

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis

(2015) Bernd Hoffmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits

(2015) Timokratis Karamitros et al.   NUCLEIC ACIDS RESEARCH

The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: A feasibility study

(2015) Upton D. Allen et al.   PEDIATRIC TRANSPLANTATION

Human IFNAR2 deficiency: Lessons for antiviral immunity

(2015) Christopher J. A. Duncan et al.   Science Translational Medicine

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin

(2015) Caroline Denesvre et al.   VIRUS GENES

Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection

(2015) Matthew B. Rogers et al.   mBio

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

Composition and Interactions of Hepatitis B Virus Quasispecies Defined the Virological Response During Telbivudine Therapy

(2015) Bin Zhou et al.   Scientific Reports

Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations

(2015) Haiyan Lei et al.   Scientific Reports

HIV-1 genotypic drug resistance testing: digging deep, reaching wide?

(2015) Kristel Van Laethem et al.   Current Opinion in Virology

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

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

Extremely High Mutation Rate of HIV-1 In Vivo

(2015) José M. Cuevas et al.   PLOS BIOLOGY

Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics

(2015) Charlotte J. Houldcroft et al.   Frontiers in Microbiology

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

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

Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery

(2015) Randi Holm Jensen et al.   PLoS One

Resistance-Associated NS5A Variants of Hepatitis C Virus Are Susceptible to Interferon-Based Therapy

(2015) Jun Itakura et al.   PLoS One

Improved Detection of Emerging Drug-Resistant Mutant Cytomegalovirus Subpopulations by Deep Sequencing

(2014) Sunwen Chou et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing

(2014) Seweryn Bialasiewicz et al.   BMC INFECTIOUS DISEASES

Potential for Zika virus transmission through blood transfusion demonstrated during an outbreak in French Polynesia, November 2013 to February 2014

(2014) D Musso et al.   Eurosurveillance

Detection of a Sexually Transmitted Hepatitis C Virus Protease Inhibitor-Resistance Variant in a Human Immunodeficiency Virus–Infected Homosexual Man

(2014) Sandra Franco et al.   GASTROENTEROLOGY

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

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

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

Shift of HIV Tropism in Stem-Cell Transplantation with CCR5 Delta32 Mutation

(2014) Lambros Kordelas et al.   NEW ENGLAND JOURNAL OF MEDICINE

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

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

Prevalence and Evolution of Low Frequency HIV Drug Resistance Mutations Detected by Ultra Deep Sequencing in Patients Experiencing First Line Antiretroviral Therapy Failure

(2014) Marie-Anne Vandenhende et al.   PLoS One

Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

(2014) Kyriakos Tsangaras et al.   PLoS One

Antiviral drug resistance in herpesviruses other than cytomegalovirus

(2014) Jocelyne Piret et al.   REVIEWS IN MEDICAL VIROLOGY

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

False-Positive Results in Metagenomic Virus Discovery: A Strong Case for Follow-Up Diagnosis

(2014) T. Rosseel et al.   Transboundary and Emerging Diseases

Molecular diagnosis and treatment of drug-resistant hepatitis B virus

(2014) Jeong Han Kim   WORLD JOURNAL OF GASTROENTEROLOGY

Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion

(2014) A. Lamelas et al.   mBio

The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening

(2014) Marc Lecuit et al.   Frontiers in Cellular and Infection Microbiology

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

(2013) Samit Kundu et al.   CLINICAL INFECTIOUS DISEASES

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

Mode of Virus Rescue Determines the Acquisition of VHS Mutations in VP22-Negative Herpes Simplex Virus 1

(2013) K. Ebert et al.   JOURNAL OF VIROLOGY

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

(2013) Josephine M Bryant et al.   LANCET

Deep Sequencing of Viral Genomes Provides Insight into the Evolution and Pathogenesis of Varicella Zoster Virus and Its Vaccine in Humans

(2013) Daniel P. Depledge et al.   MOLECULAR BIOLOGY AND EVOLUTION

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Autologous Antibody Capture to Enrich Immunogenic Viruses for Viral Discovery

(2013) Bas B. Oude Munnink et al.   PLoS One

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

(2013) George R. Feehery et al.   PLoS One

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

(2013) István Bartha et al.   eLife

Molecular surveillance of hepatitis C

(2012) Yury Khudyakov   ANTIVIRAL THERAPY

Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants

(2012) Ruchi M. Newman et al.   JOURNAL OF INFECTIOUS DISEASES

Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity

(2012) Poornima Parameswaran et al.   JOURNAL OF VIROLOGY

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

(2012) Karen E. Ocwieja et al.   NUCLEIC ACIDS RESEARCH

Next-generation sequencing to assess HIV tropism

(2012) Luke C. Swenson et al.   Current Opinion in HIV and AIDS

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

Outbreak of Infections by Hepatitis B Virus Genotype A and Transmission of Genetic Drug Resistance in Patients Coinfected with HIV-1 in Japan

(2011) S. Fujisaki et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Direct Sequencing and Characterization of a Clinical Isolate of Epstein-Barr Virus from Nasopharyngeal Carcinoma Tissue by Using Next-Generation Sequencing Technology

(2011) P. Liu et al.   JOURNAL OF VIROLOGY

Microbial sequences benefit health now

(2011) Edward J. P. Cartwright et al.   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

(2011) Daniel P. Depledge et al.   PLoS One

Disease-associated XMRV sequences are consistent with laboratory contamination

(2011) Stephane Hue et al.   Retrovirology

Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants

(2011) Nicholas Renzette et al.   PLoS Pathogens

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery

(2010) Soo-Yon Rhee et al.   ANTIVIRAL RESEARCH

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

Genetic Makeup of Amantadine-Resistant and Oseltamivir-Resistant Human Influenza A/H1N1 Viruses

(2010) H. Zaraket et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Clinical management of HIV-1 resistance

(2009) Roger Paredes et al.   ANTIVIRAL RESEARCH

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

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

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

Long-Term Control of HIV byCCR5Delta32/Delta32 Stem-Cell Transplantation

(2009) Gero Hütter et al.   NEW ENGLAND JOURNAL OF MEDICINE

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

(2008) M. Solmone et al.   JOURNAL OF VIROLOGY