Evolution of the SARS-CoV-2 Mutational Spectrum

Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2

(2022) Johan Ringlander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a

(2022) Luiza Mamigonian Bessa et al.   Science Advances

A natural mutator allele shapes mutation spectrum variation in mice

(2022) Thomas A. Sasani et al.   NATURE

Genetic and chemotherapeutic influences on germline hypermutation

(2022) Joanna Kaplanis et al.   NATURE

SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1

(2022) Sin-Yee Fung et al.   Cell and Bioscience

Evolution, geographic spreading, and demographic distribution of Enterovirus D68

(2022) Emma B. Hodcroft et al.   PLoS Pathogens

Ubiquitination of SARS-CoV-2 ORF7a promotes antagonism of interferon response

(2021) Zengguo Cao et al.   Cellular & Molecular Immunology

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

(2021) Nicholas C. Huston et al.   MOLECULAR CELL

Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution

(2021) Jeremy Ratcliff et al.   VIROLOGY

Targeting novel structural and functional features of coronavirus protease nsp5 (3CLpro, Mpro) in the age of COVID-19

(2021) Molly K. Roe et al.   JOURNAL OF GENERAL VIROLOGY

Mutational signatures of replication timing and epigenetic modification persist through the global divergence of mutation spectra across the great ape phylogeny

(2021) Michael E Goldberg et al.   Genome Biology and Evolution

Mutation rates and selection on synonymous mutations in SARS-CoV-2

(2021) Nicola De Maio et al.   Genome Biology and Evolution

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

(2021) Yatish Turakhia et al.   NATURE GENETICS

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

(2021) Darren P. Martin et al.   CELL

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

(2021) Jakob McBroome et al.   MOLECULAR BIOLOGY AND EVOLUTION

SARS-CoV-2 Nsp5 Demonstrates Two Distinct Mechanisms Targeting RIG-I and MAVS To Evade the Innate Immune Response

(2021) Yongzhen Liu et al.   mBio

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae

(2021) Pengyao Jiang et al.   eLife

Increased somatic mutation burdens in normal human cells due to defective DNA polymerases

(2021) Philip S. Robinson et al.   NATURE GENETICS

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

(2021) James J. Davis et al.   Microbiology Spectrum

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Biased mutation and selection in RNA viruses

(2020) Talia Kustin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stability of SARS-CoV-2 phylogenies

(2020) Yatish Turakhia et al.   PLoS Genetics

Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors

(2019) Robert N. Kirchdoerfer et al.   Nature Communications

The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity

(2019) Natacha S. Ogando et al.   Frontiers in Microbiology

Similarities and differences in patterns of germline mutation between mice and humans

(2019) Sarah J. Lindsay et al.   Nature Communications

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

(2019) James Hadfield et al.   PLoS Pathogens

Differences in the rare variant spectrum among human populations

(2017) Iain Mathieson et al.   PLoS Genetics

Rapid evolution of the human mutation spectrum

(2017) Kelley Harris et al.   eLife

Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity

(2017) Matthew D. Pauly et al.   mSphere

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Background Mutational Features of the Radiation-Resistant BacteriumDeinococcus radiodurans

(2015) Hongan Long et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for recent, population-specific evolution of the human mutation rate

(2015) Kelley Harris   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Analysis of the Murine Coronavirus Genomic RNA Packaging Signal

(2013) L. Kuo et al.   JOURNAL OF VIROLOGY

Mutational Spectrum Drives the Rise of Mutator Bacteria

(2013) Alejandro Couce et al.   PLoS Genetics

ASSESSING PHYLOGENETIC SIGNAL WITH MEASUREMENT ERROR: A COMPARISON OF MANTEL TESTS, BLOMBERG ET AL.'S K, AND PHYLOGENETIC DISTOGRAMS

(2012) Olivier J. Hardy et al.   EVOLUTION

Extraordinary genome stability in the ciliate Paramecium tetraurelia

(2012) W. Sung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drift-barrier hypothesis and mutation-rate evolution

(2012) W. Sung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

(2012) Antoinette C van der Kuyl et al.   Retrovirology

Coronaviruses

(2011) Mark R. Denison et al.   RNA Biology

APOBEC3G Contributes to HIV-1 Variation through Sublethal Mutagenesis

(2010) H. A. Sadler et al.   JOURNAL OF VIROLOGY

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

(2010) Lance D. Eckerle et al.   PLoS Pathogens

Engineering attenuated virus vaccines by controlling replication fidelity

(2008) Marco Vignuzzi et al.   NATURE MEDICINE