Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF

Exploring the natural origins of SARS-CoV-2 in the light of recombination

(2022) Spyros Lytras et al.   Genome Biology and Evolution

The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate

(2022) John H Tay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

(2022) Mahan Ghafari et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2022) Elisabetta Cameroni et al.   NATURE

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

(2022) Sarah Temmam et al.   NATURE

Where did Omicron come from? Three key theories

(2022) Smriti Mallapaty   NATURE

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

(2022) Grigorios D. Amoutzias et al.   Viruses-Basel

N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition

(2022) Ruangang Pan et al.   mBio

Regional and temporal coordinated mutation patterns in SARS-CoV-2 spike protein revealed by a clustering and network analysis

(2022) Surendra S. Negi et al.   Scientific Reports

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

(2021) Emma C. Thomson et al.   CELL

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

(2021) Bin Zhou 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

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Nicholas G. Davies et al.   SCIENCE

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

(2021) Oscar A. MacLean et al.   PLOS BIOLOGY

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

(2021) Wanwisa Dejnirattisai et al.   CELL

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Erik Volz et al.   NATURE

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

(2021) Ales Varabyou et al.   GENETICS

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

(2021) Ben Jackson et al.   CELL

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

(2021) Darren P. Martin et al.   CELL

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

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

Ongoing global and regional adaptive evolution of SARS-CoV-2

(2021) Nash D. Rochman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary trajectory of SARS-CoV-2 and emerging variants

(2021) Jalen Singh et al.   Virology Journal

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

Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination

(2021) Serafeim C. Chaintoutis 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

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole 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

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

(2021) Changshuo Wei et al.   Journal of Genetics and Genomics

Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion

(2021) Veronique Nussenblatt et al.   JOURNAL OF INFECTIOUS DISEASES

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

Beyond Omicron: what’s next for COVID’s viral evolution

(2021) Ewen Callaway   NATURE

PDBsum extras: SARS‐CoV ‐2 and AlphaFold models

(2021) Roman A. Laskowski et al.   PROTEIN SCIENCE

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19

(2021) Dafydd R. Owen et al.   SCIENCE

Where did ‘weird’ Omicron come from?

(2021) Kai Kupferschmidt   SCIENCE

Omicron variant and booster COVID-19 vaccines

(2021) Talha Khan Burki   Lancet Respiratory Medicine

Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring

(2021) Sofya K. Garushyants et al.   Communications Biology

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

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

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

(2020)   Nature Microbiology

The proximal origin of SARS-CoV-2

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

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

(2020) Bette Korber et al.   CELL

Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames

(2020) Yong Wang et al.   Scientific Reports

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

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

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

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

(2020) Michael Worobey et al.   SCIENCE

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

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

(2020) Lizhou Zhang et al.   Nature Communications

Recombination events are concentrated in the spike protein region of Betacoronaviruses

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

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

(2019) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the feasibility of saltational evolution

(2019) Mikhail I. Katsnelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

APOBEC3-mediated restriction of RNA virus replication

(2018) Aleksandra Milewska et al.   Scientific Reports

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

(2017) Yuelong Shu et al.   Eurosurveillance

Time-Dependent Rate Phenomenon in Viruses

(2016) Pakorn Aiewsakun et al.   JOURNAL OF VIROLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION