Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic

Clinical characteristics of 50466 hospitalized patients with 2019‐nCoV infection

(2020) Pengfei Sun et al.   JOURNAL OF MEDICAL VIROLOGY

Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures

(2020) Yixuan Wang et al.   JOURNAL OF MEDICAL VIROLOGY

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

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

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

(2020)   Nature Microbiology

Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy

(2020) Domenico Benvenuto et al.   JOURNAL OF INFECTION

The proximal origin of SARS-CoV-2

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

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

(2020) Carla Mavian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving COVID-19 conundrum and its impact

(2020) Thanat Chookajorn   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

(2020) Santiago J. Sánchez-Pacheco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

(2020) Erik Alm et al.   Eurosurveillance

Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus

(2019) Hongyue Zu et al.   PLoS One

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

(2018) Steven Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

Neutral Theory and Rapidly Evolving Viral Pathogens

(2018) Simon D W Frost et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Increased Virulence of an Epidemic Strain of Vesicular Stomatitis Virus Is Associated With Interference of the Innate Response in Pigs

(2018) Lauro Velazquez-Salinas et al.   Frontiers in Microbiology

Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA

(2017) François Ferron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Evolution of Human Coronavirus Genomes

(2017) Diego Forni et al.   TRENDS IN MICROBIOLOGY

A biologist’s guide to Bayesian phylogenetic analysis

(2017) Fabrícia F. Nascimento et al.   Nature Ecology & Evolution

First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype

(2016) M. Salmona et al.   CLINICAL MICROBIOLOGY AND INFECTION

Both Epistasis and Diversifying Selection Drive the Structural Evolution of the Ebola Virus Glycoprotein Mucin-Like Domain

(2016) Neke Ibeh et al.   JOURNAL OF VIROLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

(2016) B. M. vonHoldt et al.   Science Advances

Coronavirus NSP6 restricts autophagosome expansion

(2014) Eleanor M Cottam et al.   Autophagy

The nsp3 Macrodomain Promotes Virulence in Mice with Coronavirus-Induced Encephalitis

(2014) Anthony R. Fehr et al.   JOURNAL OF VIROLOGY

Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing

(2013) Robert Scott Cornman et al.   BMC GENOMICS

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Role of Severe Acute Respiratory Syndrome (SARS)-Coronavirus Accessory Proteins in Virus Pathogenesis

(2012) Ruth McBride et al.   Viruses-Basel

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses

(2009) Chi Wai Yip et al.   INFECTION GENETICS AND EVOLUTION

Genetic diversity and population structure of rice stripe virus in China

(2009) T.-Y. Wei et al.   JOURNAL OF GENERAL VIROLOGY

A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus

(2008) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION