Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes

Global landscape of SARS-CoV-2 mutations and conserved regions

(2023) Mohammad Hadi Abbasian et al.   Journal of Translational Medicine

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

(2022) Kathryn E. Kistler et al.   Cell Host & Microbe

Search and sequence analysis tools services from EMBL-EBI in 2022

(2022) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host

(2022) Sissy Therese Sonnleitner et al.   Nature Communications

Drivers of adaptive evolution during chronic SARS-CoV-2 infections

(2022) Sheri Harari et al.   NATURE MEDICINE

Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics

(2022) Aleksandr V. Kudriavtsev et al.   Viruses-Basel

Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis

(2022) Bryan A. Johnson et al.   PLoS Pathogens

Transient RNA structures cause aberrant influenza virus replication and innate immune activation

(2022) Hollie French et al.   Science Advances

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

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

(2021) Kevin R. McCarthy et al.   SCIENCE

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

(2021) Gennady M. Verkhivker et al.   BIOCHEMISTRY

Key Factors That Enable the Pandemic Potential of RNA Viruses and Inter-Species Transmission: A Systematic Review

(2021) Santiago Alvarez-Munoz et al.   Viruses-Basel

Ongoing global and regional adaptive evolution of SARS-CoV-2

(2021) Nash D. Rochman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene

(2021) Alyssa T. Pyke et al.   Viruses-Basel

The influenza virus RNA polymerase as an innate immune agonist and antagonist

(2021) Elizaveta Elshina et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

(2021) Deepali Gupta et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The N501Y spike substitution enhances SARS-CoV-2 infection and transmission

(2021) Yang Liu et al.   NATURE

Transmission dynamics and evolutionary history of 2019‐nCoV

(2020) Xingguang Li et al.   JOURNAL OF MEDICAL VIROLOGY

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase

(2020) Joanna M. Wandzik et al.   CELL

Mutation-Simulator: Fine-grained simulation of random mutations in any genome

(2020) M A Kühl et al.   BIOINFORMATICS

Immune escape adaptive mutations in the H7N9 avian influenza hemagglutinin protein increase virus replication fitness and decrease pandemic potential

(2020) Pengxiang Chang et al.   JOURNAL OF VIROLOGY

Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

(2020) Andrea Vandelli et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis

(2020) Liming Yan et al.   CELL

The phylogenetic relationship within SARS-CoV-2s: An expanding basal clade

(2020) Steve Shen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Structural snapshots of actively transcribing influenza polymerase

(2019) Tomas Kouba et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The structure of the influenza A virus genome

(2019) Bernadeta Dadonaite et al.   Nature Microbiology

Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection

(2019) Irina Baranovskaya et al.   Virology Journal

RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference

(2019) Julita Piasecka et al.   Molecular Therapy-Nucleic Acids

Non-Uniform and Non-Random Binding of Nucleoprotein to Influenza A and B Viral RNA

(2018) Valerie Le Sage et al.   Viruses-Basel

Mini viral RNAs act as innate immune agonists during influenza virus infection

(2018) Aartjan J. W. te Velthuis et al.   Nature Microbiology

A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses

(2017) Matthew D Pauly et al.   eLife

Influenza: The Once and Future Pandemic

(2017) Jeffery K. Taubenberger et al.   PUBLIC HEALTH REPORTS

Modulation of the pH Stability of Influenza Virus Hemagglutinin: A Host Cell Adaptation Strategy

(2016) Santiago Di Lella et al.   BIOPHYSICAL JOURNAL

Pandemic influenza - including a risk assessment of H5N1

(2016) J.K. TAUBENBERGER et al.   REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES

The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot

(2015) Salvatore F. Priore et al.   BIOCHEMISTRY

The Avian-Origin PB1 Gene Segment Facilitated Replication and Transmissibility of the H3N2/1968 Pandemic Influenza Virus

(2015) Isabel Wendel et al.   JOURNAL OF VIROLOGY

PB2 Mutations D701N and S714R Promote Adaptation of an Influenza H5N1 Virus to a Mammalian Host

(2014) V. Czudai-Matwich et al.   JOURNAL OF VIROLOGY

Accumulation of Human-Adapting Mutations during Circulation of A(H1N1)pdm09 Influenza Virus in Humans in the United Kingdom

(2014) R. A. Elderfield et al.   JOURNAL OF VIROLOGY

Identification of Adaptive Mutations in the Influenza A Virus Non-Structural 1 Gene That Increase Cytoplasmic Localization and Differentially Regulate Host Gene Expression

(2014) Nicole Forbes et al.   PLoS One

Newly Emerging Mutations in the Matrix Genes of the Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses Reduce the Detection Sensitivity of Real-Time Reverse Transcription-PCR

(2013) J.-R. Yang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Adaptation of Avian Influenza A Virus Polymerase in Mammals To Overcome the Host Species Barrier

(2013) B. Manz et al.   JOURNAL OF VIROLOGY

Analysis of Adaptation Mutants in the Hemagglutinin of the Influenza A(H1N1)pdm09 Virus

(2013) Alicia Jiménez-Alberto et al.   PLoS One

Influenza A Virus Coding Regions Exhibit Host-Specific Global Ordered RNA Structure

(2012) Salvatore F. Priore et al.   PLoS One

Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing

(2012) Mohammed Selman et al.   Emerging Microbes & Infections

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Evolution of the influenza A virus untranslated regions

(2011) Yuki Furuse et al.   INFECTION GENETICS AND EVOLUTION

The 2009 Pandemic H1N1 and Triple-Reassortant Swine H1N1 Influenza Viruses Replicate Efficiently but Elicit an Attenuated Inflammatory Response in Polarized Human Bronchial Epithelial Cells

(2010) H. Zeng et al.   JOURNAL OF VIROLOGY

Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains

(2010) Olivo Miotto et al.   PLoS One

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Incorporation of influenza A virus genome segments does not absolutely require wild-type sequences

(2009) K. Fujii et al.   JOURNAL OF GENERAL VIROLOGY

Characterisation of influenza A viruses with mutations in segment 5 packaging signals

(2009) Edward C. Hutchinson et al.   VACCINE

The biology of influenza viruses

(2008) Nicole M. Bouvier et al.   VACCINE