Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses

[1]  E. Fodor,et al.  Role of the PB2 627 Domain in Influenza A Virus Polymerase Function , 2017, Journal of Virology.

[2]  T. Takagi,et al.  Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeons. , 2017, The Journal of general virology.

[3]  Andrew Rambaut,et al.  Origins of the 2009 H1N1 influenza pandemic in swine in Mexico , 2016, eLife.

[4]  K. Tsao,et al.  Genomic Signatures for Avian H7N9 Viruses Adapting to Humans , 2016, PloS one.

[5]  Wenjun Ma,et al.  PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses , 2016, Scientific Reports.

[6]  Andrew Rambaut,et al.  Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.

[7]  David K. Smith,et al.  Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models , 2015, Scientific Reports.

[8]  Kendra A Bussey,et al.  Identification of Influenza A Virus PB2 Residues Involved in Enhanced Polymerase Activity and Virus Growth in Mammalian Cells at Low Temperatures , 2015, Journal of Virology.

[9]  Y. Kawaoka,et al.  Identification of PB2 Mutations Responsible for the Efficient Replication of H5N1 Influenza Viruses in Human Lung Epithelial Cells , 2015, Journal of Virology.

[10]  Honglin Chen,et al.  The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication , 2014, Nature Communications.

[11]  C. Macken,et al.  Novel residues in avian influenza virus PB2 protein affect virulence in mammalian hosts , 2014, Nature Communications.

[12]  H. Klenk,et al.  PB2 Mutations D701N and S714R Promote Adaptation of an Influenza H5N1 Virus to a Mammalian Host , 2014, Journal of Virology.

[13]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[14]  R. Webster,et al.  Evolution and ecology of influenza A viruses. , 1992, Current topics in microbiology and immunology.

[15]  Huanchun Chen,et al.  PB2-588I Enhances 2009 H1N1 Pandemic Influenza Virus Virulence by Increasing Viral Replication and Exacerbating PB2 Inhibition of Beta Interferon Expression , 2013, Journal of Virology.

[16]  P. Chan,et al.  Replication and Transcription Activities of Ribonucleoprotein Complexes Reconstituted from Avian H5N1, H1N1pdm09 and H3N2 Influenza A Viruses , 2013, PloS one.

[17]  Cristina Marino Buslje,et al.  MISTIC: mutual information server to infer coevolution , 2013, Nucleic Acids Res..

[18]  Marc A Suchard,et al.  Stability-mediated epistasis constrains the evolution of an influenza protein , 2013, eLife.

[19]  M. Laub,et al.  Using analyses of amino Acid coevolution to understand protein structure and function. , 2013, Methods in enzymology.

[20]  W. Barclay,et al.  Unstable Polymerase-Nucleoprotein Interaction Is Not Responsible for Avian Influenza Virus Polymerase Restriction in Human Cells , 2012, Journal of Virology.

[21]  You-Qiang Song,et al.  A functional variation in CD55 increases the severity of 2009 pandemic H1N1 influenza A virus infection. , 2012, The Journal of infectious diseases.

[22]  Jinhua Liu,et al.  Mouse-Adapted H9N2 Influenza A Virus PB2 Protein M147L and E627K Mutations Are Critical for High Virulence , 2012, PloS one.

[23]  Tong Wang,et al.  Amino acids 473V and 598P of PB1 from an avian-origin influenza A virus contribute to polymerase activity, especially in mammalian cells. , 2012, The Journal of general virology.

[24]  Adolfo García-Sastre,et al.  Hemagglutinin stalk antibodies elicited by the 2009 pandemic influenza virus as a mechanism for the extinction of seasonal H1N1 viruses , 2012, Proceedings of the National Academy of Sciences.

[25]  R. Webby,et al.  Combination of PB2 271A and SR Polymorphism at Positions 590/591 Is Critical for Viral Replication and Virulence of Swine Influenza Virus in Cultured Cells and In Vivo , 2011, Journal of Virology.

[26]  A. García-Sastre,et al.  Influenza A viruses: new research developments , 2011, Nature Reviews Microbiology.

[27]  J. Peiris,et al.  Amino Acid Residues 253 and 591 of the PB2 Protein of Avian Influenza Virus A H9N2 Contribute to Mammalian Pathogenesis , 2011, Journal of Virology.

[28]  M. Mura,et al.  Influence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymerase , 2011, The Journal of general virology.

[29]  H. Bussey,et al.  PA Residues in the 2009 H1N1 Pandemic Influenza Virus Enhance Avian Influenza Virus Polymerase Activity in Mammalian Cells , 2011, Journal of Virology.

[30]  J. Dushoff,et al.  Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins , 2011, PLoS genetics.

[31]  E. Brown,et al.  Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence , 2011, Virology Journal.

[32]  D. Spiro,et al.  PB2 Residue 158 Is a Pathogenic Determinant of Pandemic H1N1 and H5 Influenza A Viruses in Mice , 2010, Journal of Virology.

[33]  K. To,et al.  Effect of clinical and virological parameters on the level of neutralizing antibody against pandemic influenza A virus H1N1 2009. , 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[34]  J. Taubenberger,et al.  Influenza virus evolution, host adaptation, and pandemic formation. , 2010, Cell host & microbe.

[35]  Ervin Fodor,et al.  The PB2 Subunit of the Influenza Virus RNA Polymerase Affects Virulence by Interacting with the Mitochondrial Antiviral Signaling Protein and Inhibiting Expression of Beta Interferon , 2010, Journal of Virology.

[36]  Tokiko Watanabe,et al.  Role of host-specific amino acids in the pathogenicity of avian H5N1 influenza viruses in mice. , 2010, The Journal of general virology.

[37]  Baek Kim,et al.  PB2 Residue 271 Plays a Key Role in Enhanced Polymerase Activity of Influenza A Viruses in Mammalian Host Cells , 2010, Journal of Virology.

[38]  T. Tan,et al.  Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains , 2010, PloS one.

[39]  J. Doudna,et al.  Adaptive strategies of the influenza virus polymerase for replication in humans , 2009, Proceedings of the National Academy of Sciences.

[40]  Richard A. Goldstein,et al.  Identifying Changes in Selective Constraints: Host Shifts in Influenza , 2009, PLoS Comput. Biol..

[41]  Andrew A. McCarthy,et al.  The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit , 2009, Nature.

[42]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[43]  John Steel,et al.  Transmission of Influenza Virus in a Mammalian Host Is Increased by PB2 Amino Acids 627K or 627E/701N , 2009, PLoS pathogens.

[44]  Y. Sakoda,et al.  PB2 Protein of a Highly Pathogenic Avian Influenza Virus Strain A/chicken/Yamaguchi/7/2004 (H5N1) Determines Its Replication Potential in Pigs , 2008, Journal of Virology.

[45]  Tin Wee Tan,et al.  Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis , 2008, BMC Bioinformatics.

[46]  Jin Hyun Kim,et al.  Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice , 2007, PLoS pathogens.

[47]  David B. Finkelstein,et al.  Persistent Host Markers in Pandemic and H5N1 Influenza Viruses , 2007, Journal of Virology.

[48]  Guang-Wu Chen,et al.  Genomic Signatures of Human versus Avian Influenza A Viruses , 2006, Emerging infectious diseases.

[49]  H. Klenk,et al.  The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  L. C. Martin,et al.  Using information theory to search for co-evolving residues in proteins , 2005, Bioinform..

[51]  L. Chao,et al.  RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE , 2005, Evolution; international journal of organic evolution.

[52]  R. Watson,et al.  PERSPECTIVE: SIGN EPISTASIS AND GENETIC COSTRAINT ON EVOLUTIONARY TRAJECTORIES , 2005, Evolution; international journal of organic evolution.

[53]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[54]  T. Deng,et al.  A Single Amino Acid Mutation in the PA Subunit of the Influenza Virus RNA Polymerase Inhibits Endonucleolytic Cleavage of Capped RNAs , 2002, Journal of Virology.

[55]  B. Murphy,et al.  A single amino acid in the PB2 gene of influenza A virus is a determinant of host range , 1993, Journal of virology.

[56]  L. Goddard Information Theory , 1962, Nature.