A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients

[1]  Tokiko Watanabe,et al.  Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene , 2020, bioRxiv.

[2]  W. Greenhalf,et al.  Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial , 2022, Nature Communications.

[3]  P. Maes,et al.  The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir , 2022, bioRxiv.

[4]  K. Rosenke,et al.  Combined Molnupiravir and Nirmatrelvir Treatment Improves the Inhibitory Effect on SARS-CoV-2 in Rhesus Macaques , 2022, bioRxiv.

[5]  Seo Jung Hong,et al.  Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir , 2022, bioRxiv.

[6]  E. Lau,et al.  Real-world effectiveness of early molnupiravir or nirmatrelvir–ritonavir in hospitalised patients with COVID-19 without supplemental oxygen requirement on admission during Hong Kong's omicron BA.2 wave: a retrospective cohort study , 2022, The Lancet Infectious Diseases.

[7]  E. Zarenezhad,et al.  Paxlovid: Mechanism of Action, Synthesis, and In Silico Study , 2022, BioMed research international.

[8]  M. Zazzi,et al.  The Combination of Molnupiravir with Nirmatrelvir or GC376 Has a Synergic Role in the Inhibition of SARS-CoV-2 Replication In Vitro , 2022, Microorganisms.

[9]  J. Bukh,et al.  Nirmatrelvir Resistant SARS-CoV-2 Variants with High Fitness in Vitro , 2022, bioRxiv.

[10]  L. Giaquinto,et al.  The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle , 2022, Nature.

[11]  Junfen Fan,et al.  Molnupiravir and Its Antiviral Activity Against COVID-19 , 2022, Frontiers in Immunology.

[12]  H. Harapan,et al.  Molnupiravir: A lethal mutagenic drug against rapidly mutating severe acute respiratory syndrome coronavirus 2—A narrative review , 2022, Journal of medical virology.

[13]  Yvette N. Lamb Nirmatrelvir Plus Ritonavir: First Approval , 2022, Drugs.

[14]  Sameer Phalke,et al.  SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines , 2022, Frontiers in Medicine.

[15]  M. Baniecki,et al.  Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19 , 2022, The New England journal of medicine.

[16]  G. Nucci,et al.  Innovative Randomized Phase I Study and Dosing Regimen Selection to Accelerate and Inform Pivotal COVID‐19 Trial of Nirmatrelvir , 2022, medRxiv.

[17]  R. Schinazi,et al.  Lethal mutagenesis as an antiviral strategy , 2022, Science.

[18]  R. Rottier,et al.  SARS-CoV-2 Omicron variant is highly sensitive to molnupiravir, nirmatrelvir, and the combination , 2022, Cell Research.

[19]  Cameron R. Wolfe,et al.  A phase 2a clinical trial of molnupiravir in patients with COVID-19 shows accelerated SARS-CoV-2 RNA clearance and elimination of infectious virus , 2021, Science Translational Medicine.

[20]  Abida,et al.  Discovery, Development, and Patent Trends on Molnupiravir: A Prospective Oral Treatment for COVID-19 , 2021, Molecules.

[21]  A. Kwan,et al.  A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐2 , 2021, Proteins.

[22]  David W. Gray,et al.  Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies , 2021, PloS one.

[23]  J. Liu,et al.  The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι , 2021, Proceedings of the National Academy of Sciences.

[24]  C. Dienemann,et al.  Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis , 2021, Nature Structural & Molecular Biology.

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

[26]  Sudhir Kumar,et al.  MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , 2021, Molecular biology and evolution.

[27]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[28]  Rommie E. Amaro,et al.  Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN , 2021, bioRxiv.

[29]  Chase W. Nelson,et al.  Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution , 2021, Virology.

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

[31]  Giuseppina Mariano,et al.  Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be , 2020, Frontiers in Molecular Biosciences.

[32]  H. Yassine,et al.  Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities , 2020, Frontiers in Cellular and Infection Microbiology.

[33]  R. Fumagalli,et al.  Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients , 2020, PloS one.

[34]  G. Hummer,et al.  Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity , 2020, Nature.

[35]  J. Garcia-Diaz,et al.  Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies , 2020, medRxiv.

[36]  Dimitry Tegunov,et al.  Structure of replicating SARS-CoV-2 polymerase , 2020, Nature.

[37]  MingKun Li,et al.  Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[38]  MingKun Li,et al.  Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

[40]  R. Baric,et al.  Small-Molecule Antiviral β-d-N4-Hydroxycytidine Inhibits a Proofreading-Intact Coronavirus with a High Genetic Barrier to Resistance , 2019, Journal of Virology.

[41]  Ernst Houtgast,et al.  Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths , 2018, Comput. Biol. Chem..

[42]  R. Plemper,et al.  Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses , 2018, Antimicrobial Agents and Chemotherapy.

[43]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[44]  Rolf Hilgenfeld,et al.  Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein , 2017, Antiviral Research.

[45]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[46]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[47]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[48]  Michael Nelson,et al.  A quantitative model of error accumulation during PCR amplification , 2006, Comput. Biol. Chem..

[49]  Piero Fariselli,et al.  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..

[50]  Sergei L. Kosakovsky Pond,et al.  Not so different after all: a comparison of methods for detecting amino acid sites under selection. , 2005, Molecular biology and evolution.

[51]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[52]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.