The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

SARS-CoV-2 spillover events

(2021) Peng Zhou et al.   SCIENCE

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

(2021) Russell Y. Neches et al.   mBio

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

(2021) Jennifer Gribble et al.   PLoS Pathogens

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

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Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera

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Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2

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

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

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SARS-CoV-2 evolution during treatment of chronic infection

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

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Antibody evasion by the P.1 strain of SARS-CoV-2

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Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses

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Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

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Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain

(2021) Mohamed Raef Smaoui et al.   Scientific Reports

Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor

(2021) Jin-Gu Lee et al.   Cell and Bioscience

SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization

(2021) Markus Hoffmann et al.   Cell Reports

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

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The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets

(2021) Thomas P. Peacock et al.   Nature Microbiology

A Synthetic Peptide CTL Vaccine Targeting Nucleocapsid Confers Protection from SARS-CoV-2 Challenge in Rhesus Macaques

(2021) Paul E. Harris et al.   Vaccines

Designing a SARS-CoV-2 T-Cell-Inducing Vaccine for High-Risk Patient Groups

(2021) Hans-Georg Rammensee et al.   Vaccines

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

(2021) Ben Jackson et al.   CELL

The origins of SARS-CoV-2: A critical review

(2021) Edward C. Holmes et al.   CELL

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

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

Cutting Edge: Nucleocapsid Vaccine Elicits Spike-Independent SARS-CoV-2 Protective Immunity

(2021) William E. Matchett et al.   JOURNAL OF IMMUNOLOGY

A novel potentially recombinant rodent coronavirus with a polybasic cleavage site in the spike protein

(2021) Xin Li et al.   JOURNAL OF VIROLOGY

Prevention of host-to-host transmission by SARS-CoV-2 vaccines

(2021) Darius Mostaghimi et al.   LANCET INFECTIOUS DISEASES

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

(2021) Han Mei et al.   MOLECULAR BIOLOGY AND EVOLUTION

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

Molnupiravir: coding for catastrophe

(2021) Brandon Malone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pan-Sarbecovirus Neutralizing Antibodies in BNT162b2-Immunized SARS-CoV-1 Survivors

(2021) Chee-Wah Tan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cross-reactive CD4+ T cells enhance SARS-CoV-2 immune responses upon infection and vaccination

(2021) Lucie Loyal et al.   SCIENCE

Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice

(2021) David R. Martinez et al.   SCIENCE

Evolutionary trajectory of SARS-CoV-2 and emerging variants

(2021) Jalen Singh et al.   Virology Journal

Functions of Coronavirus Accessory Proteins: Overview of the State of the Art

(2021) Puxian Fang et al.   Viruses-Basel

Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains

(2021) Simon A. Rella et al.   Scientific Reports

Combining spike- and nucleocapsid-based vaccines improves distal control of SARS-CoV-2

(2021) Tanushree Dangi et al.   Cell Reports

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

(2021) Juan Ángel Patiño-Galindo et al.   Genome Medicine

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

(2021) Lukasz Jaroszewski et al.   PLoS Computational Biology

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

(2021) Agnieszka M. Szemiel et al.   PLoS Pathogens

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

(2021) Frank Konings et al.   Nature Microbiology

Recombinant SARS-CoV-2 Genomes Circulated at Low Levels Over The First Year of The Pandemic

(2021) David VanInsberghe et al.   Virus Evolution

The spike protein of SARS-CoV-2 variant A.30 is heavily mutated and evades vaccine-induced antibodies with high efficiency

(2021) Prerna Arora et al.   Cellular & Molecular Immunology

A focused review on technologies, mechanisms, safety, and efficacy of available COVID-19 vaccines

(2021) Parisa Ghasemiyeh et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses

(2021) Saathvik R. Kannan et al.   JOURNAL OF AUTOIMMUNITY

The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes

(2021) Marios Nikolaidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

(2021) Elisabetta Cameroni et al.   NATURE

How COVID vaccines shaped 2021 in eight powerful charts

(2021) Smriti Mallapaty et al.   NATURE

Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2

(2021) Leo Swadling et al.   NATURE

Interspecies Jumping of Bat Coronaviruses

(2021) Antonio C. P. Wong et al.   Viruses-Basel

Emerging coronaviruses: Genome structure, replication, and pathogenesis

(2020) Yu Chen et al.   JOURNAL OF MEDICAL VIROLOGY

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

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

(2020) Peng Zhou et al.   NATURE

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

(2020) Alba Grifoni et al.   CELL

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

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Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

(2020) Kangpeng Xiao et al.   NATURE

The proximal origin of SARS-CoV-2

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

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice

(2020) Timothy P. Sheahan et al.   Science Translational Medicine

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

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

(2020) Bette Korber et al.   CELL

The ORF3a protein of SARS-CoV-2 induces apoptosis in cells

(2020) Yujie Ren et al.   Cellular & Molecular Immunology

The molecular virology of Coronaviruses

(2020) Ella Hartenian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Nucleocapsid Protein of SARS–CoV-2: a Target for Vaccine Development

(2020) Noton K. Dutta et al.   JOURNAL OF VIROLOGY

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

(2020) Ayal B. Gussow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

(2020) Maciej F. Boni et al.   Nature Microbiology

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

(2020) Luca Piccoli et al.   CELL

Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses

(2020) Michelle Wille et al.   FEMS MICROBIOLOGY REVIEWS

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

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

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus

(2020) Arinjay Banerjee et al.   JOURNAL OF GENERAL VIROLOGY

Recombination should not be an afterthought

(2020) Russell Y. Neches et al.   NATURE REVIEWS MICROBIOLOGY

Coronavirus hemagglutinin-esterase and spike proteins coevolve for functional balance and optimal virion avidity

(2020) Yifei Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

(2020) David E. Gordon et al.   SCIENCE

The emergence of SARS-CoV-2 in Europe and North America

(2020) Michael Worobey et al.   SCIENCE

Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats

(2020) Kevin J. Olival et al.   PLoS Pathogens

Extensive Genetic Diversity And Host Range Of Rodent-Borne Coronaviruses

(2020) Wen Wang et al.   Virus Evolution

SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

(2020) Sameer Mohammad et al.   Pathogens

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

(2020) Erik Volz et al.   CELL

Phylogenetic analysis of SARS-CoV-2 data is difficult

(2020) Benoit Morel et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

(2020) Omer Ziv et al.   MOLECULAR CELL

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

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

Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera

(2020) Diego Forni et al.   Viruses-Basel

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

(2020) Carina Conceicao et al.   PLOS BIOLOGY

Recombination events are concentrated in the spike protein region of Betacoronaviruses

(2020) Louis-Marie Bobay et al.   PLoS Genetics

Bat Coronaviruses in China

(2019) Yi Fan et al.   Viruses-Basel

Global Epidemiology of Bat Coronaviruses

(2019) Antonio Wong et al.   Viruses-Basel

Interaction of coronavirus nucleocapsid protein with the 5′‐ and 3′‐ends of the coronavirus genome is involved in genome circularization and negative‐strand RNA synthesis

(2019) Chen‐Yu Lo et al.   FEBS Journal

Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV) - Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV

(2019) Pascual-Iglesias et al.   Viruses-Basel

Porcine Torovirus (PToV)—A Brief Review of Etiology, Diagnostic Assays and Current Epidemiology

(2019) Zhang-Min Hu et al.   Frontiers in Veterinary Science

Diversity of dromedary camel coronavirus HKU23 in African camels revealed multiple recombination events among closely related Betacoronaviruses of the subgenus Embecovirus.

(2019) Ray T. Y. So et al.   JOURNAL OF VIROLOGY

Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved

(2019) Chrysa Ntountoumi et al.   NUCLEIC ACIDS RESEARCH

Viral quasispecies

(2019) Esteban Domingo et al.   PLoS Genetics

Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication

(2019) Suttipun Sungsuwan et al.   VIROLOGY

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Discovery and Sequence Analysis of Four Deltacoronaviruses from Birds in the Middle East Reveal Interspecies Jumping with Recombination as a Potential Mechanism for Avian-to-Avian and Avian-to-Mammalian Transmission

(2018) Susanna K. P. Lau et al.   JOURNAL OF VIROLOGY

Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility

(2018) Wentao Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses

(2018) Marios Nikolaidis et al.   VIROLOGY

A planarian nidovirus expands the limits of RNA genome size

(2018) Amir Saberi et al.   PLoS Pathogens

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

(2017) Yuelong Shu et al.   Eurosurveillance

A Naturally Occurring Recombinant Enterovirus Expresses a Torovirus Deubiquitinase

(2017) Pengcheng Shang et al.   JOURNAL OF VIROLOGY

Molecular Evolution of Human Coronavirus Genomes

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Time-Dependent Rate Phenomenon in Viruses

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SARS-like WIV1-CoV poised for human emergence

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Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

(2016) Shuo Su et al.   TRENDS IN MICROBIOLOGY

A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene

(2016) Canping Huang et al.   PLoS Pathogens

Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

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A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

(2015) Vineet D Menachery et al.   NATURE MEDICINE

Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses

(2015) Silvia Caprari et al.   Viruses-Basel

Continuous and Discontinuous RNA Synthesis in Coronaviruses

(2015) Isabel Sola et al.   Annual Review of Virology

Emergence of Pathogenic Coronaviruses in Cats by Homologous Recombination between Feline and Canine Coronaviruses

(2014) Yutaka Terada et al.   PLoS One

Recombination among human non-polio enteroviruses: implications for epidemiology and evolution

(2014) Zaharoula Kyriakopoulou et al.   VIRUS GENES

Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria

(2013) C. C. Burns et al.   JOURNAL OF VIROLOGY

Discovery of a Novel Bottlenose Dolphin Coronavirus Reveals a Distinct Species of Marine Mammal Coronavirus in Gammacoronavirus

(2013) P. C. Y. Woo et al.   JOURNAL OF VIROLOGY

Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study

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Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor

(2013) Xing-Yi Ge et al.   NATURE

The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

(2013) Chris Lauber et al.   PLoS Pathogens

Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses

(2012) Chris Lauber et al.   ARCHIVES OF VIROLOGY

Risks associated with the use of live-attenuated vaccine poliovirus strains and the strategies for control and eradication of paralytic poliomyelitis

(2012) Vaia Pliaka et al.   Expert Review of Vaccines

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

(2012) C. Lauber et al.   JOURNAL OF VIROLOGY

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY

RNA-RNA and RNA-protein interactions in coronavirus replication and transcription

(2011) Isabel Sola et al.   RNA Biology

Viral Mutation Rates

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

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

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Recombinant Canine Coronaviruses Related to Transmissible Gastroenteritis Virus of Swine Are Circulating in Dogs

(2008) N. Decaro et al.   JOURNAL OF VIROLOGY

Identification of a Novel Coronavirus from a Beluga Whale by Using a Panviral Microarray

(2008) K. A. Mihindukulasuriya et al.   JOURNAL OF VIROLOGY

Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution

(2008) Qinghong Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA