SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis

(2021) Bryan A. Johnson et al.   NATURE

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

(2021) Tyler N. Starr et al.   SCIENCE

Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

(2021) Lewis F. Buss et al.   SCIENCE

Dose-dependent response to infection with SARS-CoV-2 in the ferret model and evidence of protective immunity

(2021) Kathryn A. Ryan et al.   Nature Communications

SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells

(2021) Michihito Sasaki et al.   PLoS Pathogens

SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site

(2021) Anna Z Mykytyn et al.   eLife

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

(2021) Emma C. Thomson et al.   CELL

Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

(2021) Zhuoming Liu et al.   Cell Host & Microbe

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

(2021) Allison J. Greaney et al.   Cell Host & Microbe

Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies

(2021) Jie Hu et al.   Cellular & Molecular Immunology

Emergence of a Novel SARS-CoV-2 Variant in Southern California

(2021) Wenjuan Zhang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The polybasic cleavage site in the SARS-CoV-2 spike modulates viral sensitivity to Type I interferon and IFITM2

(2021) Helena Winstone et al.   JOURNAL OF VIROLOGY

SARS-CoV-2 spike D614G change enhances replication and transmission

(2021) Bin Zhou et al.   NATURE

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

(2021) Dami A. Collier et al.   NATURE

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

(2021) Houriiyah Tegally et al.   NATURE

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

(2021) Donald J. Benton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2021) Kevin R. McCarthy et al.   SCIENCE

A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry

(2021) Yunkai Zhu et al.   Nature Communications

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

(2021) Seiya Ozono et al.   Nature Communications

Covid-19: The E484K mutation and the risks it poses

(2021) Jacqui Wise   BMJ-British Medical Journal

The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

(2021) Zharko Daniloski et al.   eLife

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

(2021) Alex Graudenzi et al.   iScience

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

(2020) Peng Zhou et al.   NATURE

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

(2020) Daniel Wrapp et al.   SCIENCE

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

Infection and Rapid Transmission of SARS-CoV-2 in Ferrets

(2020) Young-Il Kim et al.   Cell Host & Microbe

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

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

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

(2020) Tran Thi Nhu Thao et al.   NATURE

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

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

(2020) Salvatore Di Giorgio et al.   Science Advances

Emergence of SARS-CoV-2 through recombination and strong purifying selection

(2020) Xiaojun Li et al.   Science Advances

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

(2020) Qianqian Li et al.   CELL

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

(2020) Bette Korber et al.   CELL

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

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

Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

(2020) Amin Addetia et al.   JOURNAL OF CLINICAL VIROLOGY

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

(2020) Natacha S. Ogando et al.   JOURNAL OF GENERAL VIROLOGY

Identification of common deletions in the spike protein of SARS-CoV-2

(2020) Zhe Liu 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

Coronavirus rips through Dutch mink farms, triggering culls

(2020) Martin Enserink   SCIENCE

Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy

(2020) Hongjing Gu 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

SARS-CoV-2 is transmitted via contact and via the air between ferrets

(2020) Mathilde Richard et al.   Nature Communications

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

(2020) Andrew D. Davidson et al.   Genome Medicine

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

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

(2020) P. Simmonds   mSphere

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected hospitalized COVID-19 patients

(2020) William B. Klimstra et al.   JOURNAL OF GENERAL VIROLOGY

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

(2020) Francesca Benedetti et al.   Journal of Translational Medicine

The enzymatic activity of the nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2

(2020) Natacha S. Ogando et al.   JOURNAL OF VIROLOGY

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

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

(2020) Donald J. Benton et al.   NATURE

Structures and distributions of SARS-CoV-2 spike proteins on intact virions

(2020) Zunlong Ke et al.   NATURE

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

(2020) Katharina Schubert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic

(2020) Leszek J. Klimczak et al.   PLoS One

SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling

(2020) Lisa Miorin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

(2020) Shona C. Moore et al.   Viruses-Basel

Host Immune Response Driving SARS-CoV-2 Evolution

(2020) Rui Wang et al.   Viruses-Basel

Point mutation bias in SARS-CoV-2 variants results in increased ability to stimulate inflammatory responses

(2020) Masato Kosuge et al.   Scientific Reports

Evasion of Type I Interferon by SARS-CoV-2

(2020) Hongjie Xia et al.   Cell Reports

A SARS-CoV-2 variant with the 12-bp deletion at E gene

(2020) Yi-Sheng Sun et al.   Emerging Microbes & Infections

Temporal signal and the phylodynamic threshold of SARS-CoV-2

(2020) Sebastian Duchene et al.   Virus Evolution

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

(2020) Erik Volz et al.   CELL

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

(2020) Victoria A. Avanzato et al.   CELL

D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization

(2020) Drew Weissman et al.   Cell Host & Microbe

Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects

(2020) Hanh T. Nguyen et al.   JOURNAL OF VIROLOGY

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome

(2020) Ballamoole Krishna Kumar et al.   VIRUS RESEARCH

Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

(2020) Khajohn Joonlasak et al.   VIRUS RESEARCH

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

(2020) Lizhou Zhang et al.   Nature Communications

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   Nature Communications

The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

(2020) Carina Conceicao et al.   PLOS BIOLOGY

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles

(2020) Akshamal M. Gamage et al.   PLoS Pathogens

A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways

(2020) Ramon Lorenzo-Redondo et al.   EBioMedicine

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands

(2018) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Within-Host Evolution of Human Influenza Virus

(2018) Katherine S. Xue et al.   TRENDS IN MICROBIOLOGY

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

The molecular basis of antigenic variation among A(H9N2) avian influenza viruses

(2018) Thomas P. Peacock et al.   Emerging Microbes & Infections

Immune Escape Variants of H9N2 Influenza Viruses Containing Deletions at the Hemagglutinin Receptor Binding Site Retain Fitness In Vivo and Display Enhanced Zoonotic Characteristics

(2017) Thomas P. Peacock et al.   JOURNAL OF VIROLOGY

Vaccination against infectious bronchitis virus: A continuous challenge

(2017) Brian Jordan   VETERINARY MICROBIOLOGY

Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin

(2017) Naganori Nao et al.   mBio

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission

(2016) Zhao Zhang et al.   Scientific Reports

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

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

(2015) Miles W. Carroll et al.   NATURE

Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine

(2015) Jose M. Jimenez-Guardeño et al.   PLoS Pathogens

Receptor Recognition Mechanisms of Coronaviruses: a Decade of Structural Studies

(2014) Fang Li   JOURNAL OF VIROLOGY

Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein

(2014) Jean Kaoru Millet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of a Highly Conserved Domain within the Severe Acute Respiratory Syndrome Coronavirus Spike Protein S2 Domain with Characteristics of a Viral Fusion Peptide

(2009) I. G. Madu et al.   JOURNAL OF VIROLOGY

Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites

(2009) S. Belouzard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hemagglutinin Receptor Binding Avidity Drives Influenza A Virus Antigenic Drift

(2009) S. E. Hensley et al.   SCIENCE