Genome-Wide Variation in Betacoronaviruses

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

(2021) Kevin R. McCarthy et al.   SCIENCE

Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS

(2020) Yushun Wan et al.   JOURNAL OF VIROLOGY

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

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

(2020) Peng Zhou et al.   NATURE

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

(2020) Jasper Fuk-Woo Chan et al.   Emerging Microbes & Infections

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

(2020) B. Coutard et al.   ANTIVIRAL RESEARCH

Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies

(2020) Daniel Wrapp et al.   CELL

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

(2020) Shuai Xia et al.   CELL RESEARCH

SARS‐CoV‐2 viral spike G614 mutation exhibits higher case fatality rate

(2020) Manuel Becerra‐Flores et al.   INTERNATIONAL JOURNAL OF CLINICAL PRACTICE

Human leukocyte antigen susceptibility map for SARS-CoV-2

(2020) Austin Nguyen et al.   JOURNAL OF VIROLOGY

An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

(2020) LaRinda A. Holland et al.   JOURNAL OF VIROLOGY

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

Phylogenetic network analysis of SARS-CoV-2 genomes

(2020) Peter Forster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

(2020) Yan Gao et al.   SCIENCE

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Evolution of viral quasispecies during SARS-CoV-2 infection

(2020) A. Jary et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genetic diversity and evolution of SARS-CoV-2

(2020) Tung Phan   INFECTION GENETICS AND EVOLUTION

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico

(2020) Blanca Taboada et al.   JOURNAL OF VIROLOGY

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

(2020) Alina Baum et al.   SCIENCE

Distinct conformational states of SARS-CoV-2 spike protein

(2020) Yongfei Cai et al.   SCIENCE

Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2

(2020) Yvonne C. F. Su et al.   mBio

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

(2020) Daniele Mercatelli et al.   Frontiers in Microbiology

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   INFECTION GENETICS AND EVOLUTION

Genomic evidence for reinfection with SARS-CoV-2: a case study

(2020) Richard L Tillett et al.   LANCET INFECTIOUS DISEASES

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

The UCSC SARS-CoV-2 Genome Browser

(2020) Jason D. Fernandes et al.   NATURE GENETICS

Swine acute diarrhea syndrome coronavirus replication in primary human cells reveals potential susceptibility to infection

(2020) Caitlin E. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

(2020) Joana Damas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

(2020) Ludovico Cantuti-Castelvetri et al.   SCIENCE

The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway

(2020) Jin-Yan Li et al.   VIRUS RESEARCH

SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant

(2020) Yoriyuki Konno et al.   Cell Reports

Anti-spike, Anti-nucleocapsid and Neutralizing Antibodies in SARS-CoV-2 Inpatients and Asymptomatic Individuals

(2020) Etienne Brochot et al.   Frontiers in Microbiology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

(2020) Erik Volz et al.   CELL

Viral quasispecies

(2019) Esteban Domingo et al.   PLoS Genetics

Genome-Wide Variation in Potyviruses

(2019) Deepti Nigam et al.   Frontiers in Plant Science

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus

(2018) William J. Fitzsimmons et al.   PLOS BIOLOGY

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

Why are RNA virus mutation rates so damn high?

(2018) Siobain Duffy   PLOS BIOLOGY

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process

(2017) Justine Charon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human Immunodeficiency Virus Immune Cell Receptors, Coreceptors, and Cofactors: Implications for Prevention and Treatment

(2016) Andrew W. Woodham et al.   AIDS PATIENT CARE AND STDS

Mechanisms of viral mutation

(2016) Rafael Sanjuán et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Structure, Function, and Evolution of Coronavirus Spike Proteins

(2016) Fang Li   Annual Review of Virology

The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds

(2015) Yahira M. Báez-Santos et al.   ANTIVIRAL RESEARCH

Severe Acute Respiratory Syndrome Coronavirus ORF7a Inhibits Bone Marrow Stromal Antigen 2 Virion Tethering through a Novel Mechanism of Glycosylation Interference

(2015) Justin K. Taylor et al.   JOURNAL OF VIROLOGY

Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis

(2015) Jean Kaoru Millet et al.   VIRUS RESEARCH

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

T Cell Responses to Whole SARS Coronavirus in Humans

(2014) C. K.-f. Li et al.   JOURNAL OF IMMUNOLOGY

One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities

(2014) Lorenzo Subissi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses

(2014) Everett Clinton Smith et al.   Annual Review of Virology

Receptor recognition and cross-species infections of SARS coronavirus

(2013) Fang Li   ANTIVIRAL RESEARCH

Identification of Residues of SARS-CoV nsp1 That Differentially Affect Inhibition of Gene Expression and Antiviral Signaling

(2013) Andrew R. Jauregui et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

(2010) Marcin J. Mizianty et al.   BIOINFORMATICS

A structural analysis of M protein in coronavirus assembly and morphology

(2010) Benjamin W. Neuman et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural Flexibility Allows the Functional Diversity of Potyvirus Genome-Linked Protein VPg

(2010) K. I. Rantalainen et al.   JOURNAL OF VIROLOGY

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Quasispecies Theory and the Behavior of RNA Viruses

(2010) Adam S. Lauring et al.   PLoS Pathogens

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 2 Interacts with a Host Protein Complex Involved in Mitochondrial Biogenesis and Intracellular Signaling

(2009) C. T. Cornillez-Ty et al.   JOURNAL OF VIROLOGY

Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses

(2009) Eugénie Hébrard et al.   Virology Journal