Next-Generation Sequencing for Confronting Virus Pandemics

Evaluation of SARS-CoV-2 entry, inflammation and new therapeutics in human lung tissue cells

(2022) Judith Grau-Expósito et al.   PLoS Pathogens

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

(2021) Jennifer Gribble et al.   PLoS Pathogens

Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

(2021) Supaporn Wacharapluesadee et al.   Nature Communications

Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects

(2021) Selene Garcia-Garcia et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Next-generation sequencing technologies: An overview

(2021) Taishan Hu et al.   HUMAN IMMUNOLOGY

Resistance‐associated substitutions after sofosbuvir/velpatasvir/voxilaprevir triple therapy failure

(2021) Damir Garcia‐Cehic et al.   JOURNAL OF VIRAL HEPATITIS

New Approaches to Anticipate the Risk of Reverse Zoonosis

(2021) Peng Jia et al.   TRENDS IN ECOLOGY & EVOLUTION

Perspectives on RNA Vaccine Candidates for COVID-19

(2021) Pobitra Borah et al.   Frontiers in Molecular Biosciences

Characterization of nucleic acids from extracellular vesicle-enriched human sweat

(2021) Geneviève Bart et al.   BMC GENOMICS

Novel Canine Coronavirus Isolated from a Hospitalized Pneumonia Patient, East Malaysia

(2021) Anastasia N Vlasova et al.   CLINICAL INFECTIOUS DISEASES

Viral populations of SARS-CoV-2 in upper respiratory tract, placenta, amniotic fluid and umbilical cord blood support viral replication in placenta

(2021) Maria Piñana et al.   CLINICAL MICROBIOLOGY AND INFECTION

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

(2021) Fernando González-Candelas et al.   INFECTION GENETICS AND EVOLUTION

Science, not speculation, is essential to determine how SARS-CoV-2 reached humans

(2021) Charles H Calisher et al.   LANCET

The total number and mass of SARS-CoV-2 virions

(2021) Ron Sender et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines

(2021) David Brandt et al.   Viruses-Basel

The Emergence and Spread of Novel SARS-CoV-2 Variants

(2021) Huaimin Yi et al.   Frontiers in Public Health

Heavily mutated Omicron variant puts scientists on alert

(2021) Ewen Callaway   NATURE

Omicron emerges

(2021) Adam Vaughan   NEW SCIENTIST

Where did ‘weird’ Omicron come from?

(2021) Kai Kupferschmidt   SCIENCE

Urinary genome detection and tracking of Hantaan virus from hemorrhagic fever with renal syndrome patients using multiplex PCR-based next-generation sequencing

(2021) Seungchan Cho et al.   PLoS Neglected Tropical Diseases

A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)

(2021) Cristina Andrés et al.   Emerging Microbes & Infections

Covid-19 — Navigating the Uncharted

(2020) Anthony S. Fauci et al.   NEW ENGLAND JOURNAL OF MEDICINE

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

(2020) Daniel Kiselev et al.   Viruses-Basel

Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles

(2020) Iván Andreu-Moreno et al.   mBio

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

(2020) Hong Zhou et al.   CURRENT BIOLOGY

Whole‐genome next‐generation sequencing and phylogenetic characterization of viral haemorrhagic septicaemia virus in Korea

(2020) Jee Youn Hwang et al.   JOURNAL OF FISH DISEASES

Infection of dogs with SARS-CoV-2

(2020) Thomas H. C. Sit et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

Conservation and variability of hepatitis B core at different chronic hepatitis stages

(2020) Marçal Yll et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

(2020) Salvatore Di Giorgio et al.   Science Advances

COVID-19 vaccines: breaking record times to first-in-human trials

(2020) Young Chan Kim et al.   npj Vaccines

Natural transmission of bat-like SARS-CoV-2PRRA variants in COVID-19 patients

(2020) Yik Chun Wong et al.   CLINICAL INFECTIOUS DISEASES

Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

(2020) Santiago Ávila-Ríos et al.   Viruses-Basel

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

(2020) Daniele Mercatelli et al.   Frontiers in Microbiology

Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

(2020) Cristina Andres et al.   Emerging Microbes & Infections

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

The role of genetic sequencing and analysis in the polio eradication programme

(2020) David Jorgensen et al.   Virus Evolution

Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

(2020) Barnaby E Young et al.   LANCET

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

(2020) Caroline Charre et al.   Virus Evolution

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

SARS-CoV-2 and the human-animal interface: outbreaks on mink farms

(2020) Marion Koopmans   LANCET INFECTIOUS DISEASES

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

(2020) Xavier Fernandez-Cassi et al.   Viruses-Basel

Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy

(2020) E. I. Patterson et al.   Nature Communications

A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

(2019) John A. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How host genetics dictates successful viral zoonosis

(2019) Cody J. Warren et al.   PLOS BIOLOGY

Viral Metagenomics on Cerebrospinal Fluid

(2019) Edridge et al.   Genes

Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

(2019) Tasha M. Santiago-Rodriguez et al.   Viruses-Basel

A Structure-Informed Atlas of Human-Virus Interactions

(2019) Gorka Lasso et al.   CELL

Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers

(2019) Hanna Jerome et al.   JOURNAL OF INFECTION

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

(2019) Qian Chen et al.   ANTIVIRAL RESEARCH

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

Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses

(2018) Anouk Willemsen et al.   HEREDITY

New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors

(2018) Laura Ordeig et al.   JOURNAL OF GENERAL VIROLOGY

Identification of a Novel Hepatitis C Virus Genotype From Punjab, India: Expanding Classification of Hepatitis C Virus Into 8 Genotypes

(2018) Sergio M Borgia et al.   JOURNAL OF INFECTIOUS DISEASES

Complexities of Viral Mutation Rates

(2018) Kayla M. Peck et al.   JOURNAL OF VIROLOGY

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Defective RNA particles derived from Tomato black ring virus genome interfere with the replication of parental virus

(2018) Beata Hasiów-Jaroszewska et al.   VIRUS RESEARCH

Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

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

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission

(2018) Doreen Muth et al.   Scientific Reports

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

Baseline hepatitis C virus resistance-associated substitutions present at frequencies lower than 15% may be clinically significant

(2018) Celia Perales et al.   Infection and Drug Resistance

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

(2017) Yuelong Shu et al.   Eurosurveillance

Zika virus evolution and spread in the Americas

(2017) Hayden C. Metsky et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Clinical and biological insights from viral genome sequencing

(2017) Charlotte J. Houldcroft et al.   NATURE REVIEWS MICROBIOLOGY

First Cases of Severe Flaccid Paralysis Associated With Enterovirus D68 Infection in Spain, 2015–2016

(2017) María Cabrerizo et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Improving the selection and development of influenza vaccine viruses – Report of a WHO informal consultation on improving influenza vaccine virus selection, Hong Kong SAR, China, 18–20 November 2015

(2017) Alan Hampson et al.   VACCINE

Deep sequencing in the management of hepatitis virus infections

(2017) Josep Quer et al.   VIRUS RESEARCH

High Throughput Sequencing for Detection of Foodborne Pathogens

(2017) Camilla Sekse et al.   Frontiers in Microbiology

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

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

Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data

(2016) John Lednicky et al.   PLoS Neglected Tropical Diseases

Viral Hemorrhagic Fever Diagnostics

(2015) Lori D. Racsa et al.   CLINICAL INFECTIOUS DISEASES

Enhanced virome sequencing using targeted sequence capture

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

Phylogenetic Demonstration of Hepatitis E Infection Transmitted by Pork Meat Ingestion

(2015) Mar Riveiro-Barciela et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Molecular Evidence of Sexual Transmission of Ebola Virus

(2015) Suzanne E. Mate et al.   NEW ENGLAND JOURNAL OF MEDICINE

Third generation sequencing: technology and its potential impact on evolutionary biodiversity research

(2015) Christoph Bleidorn   SYSTEMATICS AND BIODIVERSITY

Hepatitis B virus quasispecies evolution after liver transplantation in patients under long-term lamivudine prophylaxis with or without hepatitis B immune globulin

(2015) M. Buti et al.   Transplant Infectious Disease

Double-stranded RNA-specific adenosine deaminase 1 (ADAR1) promotes EIAV replication and infectivity

(2015) Yan-Dong Tang et al.   VIROLOGY

Inference with viral quasispecies diversity indices: clonal and NGS approaches

(2014) Josep Gregori et al.   BIOINFORMATICS

A conversation with Don Ganem

(2014) Ushma S. Neill   JOURNAL OF CLINICAL INVESTIGATION

Exploring the Potential of Next-Generation Sequencing in Detection of Respiratory Viruses

(2014) S. Prachayangprecha et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

(2014) Josep Quer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

An RNA Editor, Adenosine Deaminase Acting on Double-Stranded RNA (ADAR1)

(2014) Cyril X. George et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Is Virology Dead?

(2014) D. DiMaio   mBio

Acute Viral Infections of the Central Nervous System in Immunocompetent Adults: Diagnosis and Management

(2013) Marie Studahl et al.   DRUGS

Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

(2013) Donald B. Smith et al.   HEPATOLOGY

Hilary Koprowski, MD

(2013) Don Gilden   JOURNAL OF NEUROVIROLOGY

A Leaderless Genome Identified during Persistent Bovine Coronavirus Infection Is Associated with Attenuation of Gene Expression

(2013) Ting-Yung Ke et al.   PLoS One

A Strategy To Estimate Unknown Viral Diversity in Mammals

(2013) S. J. Anthony et al.   mBio

Coronaviruses as DNA Wannabes: A New Model for the Regulation of RNA Virus Replication Fidelity

(2013) Everett Clinton Smith et al.   PLoS Pathogens

Adenovirus 36 as an Obesity Agent Maintains the Obesity State by Increasing MCP-1 and Inducing Inflammation

(2012) Ha-Na Na et al.   JOURNAL OF INFECTIOUS DISEASES

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Error threshold in RNA quasispecies models with complementation

(2010) Josep Sardanyés et al.   JOURNAL OF THEORETICAL BIOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

(2010) Lance D. Eckerle et al.   PLoS Pathogens

Infectious Encephalitis in France in 2007: A National Prospective Study

(2009) Alexandra Mailles et al.   CLINICAL INFECTIOUS DISEASES

Divergent adaptation of hepatitis C virus genotypes 1 and 3 to human leukocyte antigen-restricted immune pressure

(2009) Andri Rauch et al.   HEPATOLOGY

Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection

(2009) Margherita Doria et al.   NUCLEIC ACIDS RESEARCH

Lack of Evidence for the Role of Human Adenovirus-36 in Obesity in a European Cohort

(2009) Valère J. Goossens et al.   Obesity

Hepatitis C virus drug resistance and immune-driven adaptations: Relevance to new antiviral therapy

(2008) Silvana Gaudieri et al.   HEPATOLOGY

Double-Stranded RNA Adenosine Deaminases Enhance Expression of Human Immunodeficiency Virus Type 1 Proteins

(2008) A. Phuphuakrat et al.   JOURNAL OF VIROLOGY

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Single-molecule DNA sequencing technologies for future genomics research

(2008) Pushpendra K. Gupta   TRENDS IN BIOTECHNOLOGY