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

Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: ignore at your own peril

(2020) Sadie R Wisotsky et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

(2020) Qun Li et al.   NEW ENGLAND JOURNAL OF MEDICINE

CpG Frequency in the 5′ Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein

(2020) Dorota Kmiec et al.   mBio

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

(2020) Michael Letko et al.   Nature Microbiology

We shouldn’t worry when a virus mutates during disease outbreaks

(2020) Nathan D. Grubaugh et al.   Nature Microbiology

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

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

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

The proximal origin of SARS-CoV-2

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

Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses

(2020) Spyros Lytras et al.   Viruses-Basel

Estimates of the severity of coronavirus disease 2019: a model-based analysis

(2020) Robert Verity et al.   LANCET INFECTIOUS DISEASES

Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2

(2020) David D Pollock et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

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

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

Inference of Adaptive Shifts for Multivariate Correlated Traits

(2018) Paul Bastide et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

The phylogenomics of evolving virus virulence

(2018) Jemma L. Geoghegan et al.   NATURE REVIEWS GENETICS

CG dinucleotide suppression enables antiviral defence targeting non-self RNA

(2017) Matthew A. Takata et al.   NATURE

Extensive diversity of coronaviruses in bats from China

(2017) Xian-Dan Lin et al.   VIROLOGY

Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus

(2017) S. J. Anthony et al.   mBio

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses

(2016) Diego Forni et al.   JOURNAL OF VIROLOGY

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A synchronized global sweep of the internal genes of modern avian influenza virus

(2014) Michael Worobey et al.   NATURE

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the accumulation of deleterious mutations during range expansions

(2013) S. Peischl et al.   MOLECULAR ECOLOGY

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

(2013) Xing-Yi Ge et al.   NATURE

Virulence attenuation during an influenza A/H5N1 pandemic

(2013) M. F. Boni et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

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

(2009) R. L. Graham et al.   JOURNAL OF VIROLOGY

Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases

(2008) C. R. Parrish et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

(2008) Benjamin D. Greenbaum et al.   PLoS Pathogens