Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs

[1]  E. Holmes,et al.  The origins of SARS-CoV-2: A critical review , 2021, Cell.

[2]  S. Subramaniam,et al.  Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies , 2021, PLoS biology.

[3]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[4]  Sergei L. Kosakovsky Pond,et al.  Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen , 2021, PLoS biology.

[5]  Haiyong Peng,et al.  SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity , 2020, Nature Communications.

[6]  Alice C Hughes,et al.  A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein , 2020, Current Biology.

[7]  James J. Davis,et al.  Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area , 2020, medRxiv.

[8]  J. Epstein,et al.  Origin and cross-species transmission of bat coronaviruses in China , 2020, Nature Communications.

[9]  K. Crandall,et al.  Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity , 2020, Scientific Reports.

[10]  S. Rowland-Jones,et al.  Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus , 2020, Cell.

[11]  J. Epstein,et al.  Origin and cross-species transmission of bat coronaviruses in China , 2020, bioRxiv.

[12]  Sergei L. Kosakovsky Pond,et al.  Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen , 2020, bioRxiv.

[13]  S. Gnanakaran,et al.  Emergence of SARS-CoV-2 through recombination and strong purifying selection , 2020, Science Advances.

[14]  F. Balloux,et al.  No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2 , 2020, Nature Communications.

[15]  Alice C Hughes,et al.  A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein , 2020, Current Biology.

[16]  M. Hoffmann,et al.  A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells , 2020, Molecular Cell.

[17]  Jianping Wu,et al.  Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2 , 2020, Proceedings of the National Academy of Sciences.

[18]  Gintaras Deikus,et al.  Introductions and early spread of SARS-CoV-2 in the New York City area , 2020, Science.

[19]  Colin Renfrew,et al.  Phylogenetic network analysis of SARS-CoV-2 genomes , 2020, Proceedings of the National Academy of Sciences.

[20]  K. Yuen,et al.  Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 , 2020, Cell.

[21]  Andrew Rambaut,et al.  Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic , 2020, Nature Microbiology.

[22]  Elena E. Giorgi,et al.  Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection , 2020, bioRxiv.

[23]  Fabian J Theis,et al.  SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues , 2020, SSRN Electronic Journal.

[24]  E. Holmes,et al.  The proximal origin of SARS-CoV-2 , 2020, Nature Medicine.

[25]  G. Herrler,et al.  SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor , 2020, Cell.

[26]  Peter K. Sorger,et al.  Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2 , 2020, Genome Medicine.

[27]  E. Holmes,et al.  A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[28]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[29]  Jie Dong,et al.  Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study , 2020, Chinese medical journal.

[30]  Ralph S. Baric,et al.  Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus , 2020, Journal of Virology.

[31]  Y. Tseng,et al.  Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution , 2019, Proceedings of the National Academy of Sciences.

[32]  A. Lauring,et al.  Complexities of Viral Mutation Rates , 2018, Journal of Virology.

[33]  M. Suchard,et al.  Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.

[34]  R. Nielsen,et al.  The Evolutionary Pathway to Virulence of an RNA Virus , 2017, Cell.

[35]  R. Sanjuán,et al.  Mechanisms of viral mutation , 2016, Cellular and Molecular Life Sciences.

[36]  J. Thorne,et al.  Relaxing the Molecular Clock to Different Degrees for Different Substitution Types. , 2015, Molecular biology and evolution.

[37]  Sebastián Duchêne,et al.  Molecular‐clock methods for estimating evolutionary rates and timescales , 2014, Molecular ecology.

[38]  E. Holmes,et al.  Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates , 2014, Proceedings of the Royal Society B: Biological Sciences.

[39]  S. Duffy,et al.  Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses , 2014, PLoS pathogens.

[40]  E. Paradis,et al.  QUANTIFYING VARIATION IN SPECIATION AND EXTINCTION RATES WITH CLADE DATA , 2013, Evolution; international journal of organic evolution.

[41]  真田 昌.  骨髄異形成症候群のgenome-wide analysis , 2013 .

[42]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[43]  P. Roques,et al.  Island Biogeography Reveals the Deep History of SIV , 2010, Science.

[44]  M. Suchard,et al.  Bayesian random local clocks, or one rate to rule them all , 2010, BMC Biology.

[45]  R. Sanjuán,et al.  Viral Mutation Rates , 2010, Journal of Virology.

[46]  Rafael Sanjuán,et al.  Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[47]  B. Mahy,et al.  The Evolution and Emergence of RNA Viruses , 2010, Emerging Infectious Diseases.

[48]  E. Holmes.  RNA virus genomics: a world of possibilities. , 2009, The Journal of clinical investigation.

[49]  J. Plotkin,et al.  The Population Genetics of dN/dS , 2008, PLoS genetics.

[50]  D. Bryant,et al.  A general comparison of relaxed molecular clock models. , 2007, Molecular biology and evolution.

[51]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[52]  Santiago F. Elena,et al.  Adaptive Value of High Mutation Rates of RNA Viruses: Separating Causes from Consequences , 2005, Journal of Virology.

[53]  Gerald H Learn,et al.  Molecular clock-like evolution of human immunodeficiency virus type 1. , 2004, Virology.

[54]  S. Elena,et al.  NATURAL SELECTION AND THE ORGAN‐SPECIFIC DIFFERENTIATION OF HIV‐1 V3 HYPERVARIABLE REGION , 2004, Evolution; international journal of organic evolution.

[55]  D. Posada,et al.  Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). , 2001, Molecular biology and evolution.

[56]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[57]  Z. Yang,et al.  Estimation of primate speciation dates using local molecular clocks. , 2000, Molecular biology and evolution.

[58]  H. A. Orr,et al.  The rate of adaptation in asexuals. , 2000, Genetics.

[59]  J. Huelsenbeck,et al.  A compound poisson process for relaxing the molecular clock. , 2000, Genetics.

[60]  H. Kishino,et al.  Estimating the rate of evolution of the rate of molecular evolution. , 1998, Molecular biology and evolution.

[61]  T Gojobori,et al.  Molecular clock of viral evolution, and the neutral theory. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[62]  P. Sharp,et al.  Rates and dates of divergence between AIDS virus nucleotide sequences. , 1988, Molecular biology and evolution.

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

[64]  C. Luo,et al.  A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. , 1985, Molecular biology and evolution.

[65]  S. Jeffery.  Evolution of Protein Molecules , 1979 .

[66]  L. Pauling,et al.  Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.

[67]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[68]  K. Holsinger.  The neutral theory of molecular evolution , 2004 .

[69]  M. Sanderson.  Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.

[70]  J. M. Hannink,et al.  Graphical Abstract. , 2001, Angewandte Chemie.

[71]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[72]  H. Temin.  Retrovirus variation and evolution. , 1989, Genome.

[73]  E. Pesonen,et al.  Compound Poisson process , 1984 .

[74]  M. Kimura.  Estimation of evolutionary distances between homologous nucleotide sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.