A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes

[1]  M. Nowak,et al.  Evolutionary safety of lethal mutagenesis driven by antiviral treatment , 2023, PLoS biology.

[2]  P. Simmonds,et al.  The evolution of SARS-CoV-2 , 2023, Nature Reviews Microbiology.

[3]  William T. Harvey,et al.  SARS-CoV-2 variant biology: immune escape, transmission and fitness , 2023, Nature Reviews Microbiology.

[4]  Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients , 2022, medRxiv.

[5]  M. Meschiari,et al.  A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients , 2022, Communications biology.

[6]  Nigel de Kare-Silver,et al.  Molnupiravir plus usual care versus usual care alone as early treatment for adults with COVID-19 at increased risk of adverse outcomes (PANORAMIC): an open-label, platform-adaptive randomised controlled trial , 2022, The Lancet.

[7]  R. Neher,et al.  Evolution of the SARS-CoV-2 mutational spectrum , 2022, bioRxiv.

[8]  T. Sanderson Taxonium, a web-based tool for exploring large phylogenetic trees , 2022, bioRxiv.

[9]  Jonathon P. Baker,et al.  Molnupiravir versus placebo in unvaccinated and vaccinated patients with early SARS-CoV-2 infection in the UK (AGILE CST-2): a randomised, placebo-controlled, double-blind, phase 2 trial , 2022, The Lancet Infectious Diseases.

[10]  Russell B. Corbett-Detig,et al.  BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees , 2022, J. Open Source Softw..

[11]  Brendan R. Jackson,et al.  Dispensing of Oral Antiviral Drugs for Treatment of COVID-19 by Zip Code-Level Social Vulnerability - United States, December 23, 2021-May 21, 2022. , 2022, MMWR. Morbidity and mortality weekly report.

[12]  A. Telenti,et al.  The Evolution and Biology of SARS-CoV-2 Variants. , 2022, Cold Spring Harbor perspectives in medicine.

[13]  N. Loman,et al.  The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK , 2022, bioRxiv.

[14]  A. Stern,et al.  Drivers of adaptive evolution during chronic SARS-CoV-2 infections , 2022, Nature Medicine.

[15]  M. Kraemer,et al.  Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa , 2021, Nature.

[16]  J. Butterton,et al.  Molnupiravir for Oral Treatment of Covid-19 in Nonhospitalized Patients , 2021, The New England journal of medicine.

[17]  T. Sanderson Chronumental: time tree estimation from very large phylogenies , 2021, bioRxiv.

[18]  R. Schinazi,et al.  Molnupiravir promotes SARS-CoV-2 mutagenesis via the RNA template , 2021, Journal of Biological Chemistry.

[19]  Russell B. Corbett-Detig,et al.  Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic , 2021, Nature Genetics.

[20]  Russell B. Corbett-Detig,et al.  A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees , 2021, bioRxiv.

[21]  D. Tegunov,et al.  Mechanism of SARS-CoV-2 polymerase stalling by remdesivir , 2021, Nature communications.

[22]  William L. Hamilton,et al.  Patterns of within-host genetic diversity in SARS-CoV-2 , 2020, bioRxiv.

[23]  Xiaotao Lu,et al.  An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice , 2020, Science Translational Medicine.

[24]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[25]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[26]  Richard A Neher,et al.  TreeTime: Maximum-likelihood phylodynamic analysis , 2017, bioRxiv.

[27]  Guangchuang Yu,et al.  ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data , 2017 .

[28]  Stefan Elbe,et al.  Data, disease and diplomacy: GISAID's innovative contribution to global health , 2017, Global challenges.

[29]  Shenghao Xu,et al.  Supplementary Information , 2014, States at War, Volume 3.

[30]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2010, Nucleic Acids Res..

[31]  Samuel Litwin,et al.  Examining The Theory of Error Catastrophe , 2006, Journal of Virology.

[32]  M. Eigen Selforganization of matter and the evolution of biological macromolecules , 1971, Naturwissenschaften.

[33]  R. Neher,et al.  Nextclade: clade assignment, mutation calling and quality control for viral genomes , 2021, J. Open Source Softw..

[34]  C. Mcnulty,et al.  English surveillance programme for antimicrobial utilisation and resistance (ESPAUR) 2010 to 2014: report 2015 , 2015 .