4.5 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2

Yinghui Liu et al.

Summary: Epidemiological studies have shown that bats are the natural reservoir of SARS-CoV-2, but the host range and intermediate hosts for transmission are unknown. This study characterized the ability of ACE2 from various species to support viral entry, suggesting a potentially broad host tropism of SARS-CoV-2. Analysis of ACE2 orthologs revealed that New World monkey ACE2 could not support viral entry, with genetic determinants restricting this interaction.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Oscar A. MacLean et al.

Summary: The study suggests that SARS-CoV-2 has undergone limited significant adaptation to humans, with evidence of moderate positive selection concentrated in the early phases of the pandemic. In contrast, bat Sarbecoviruses show evidence of significant positive selection and an adaptive depletion in CpG composition. This indicates that the progenitor of SARS-CoV-2 likely acquired efficient human-human transmission capabilities through evolutionary history in bats, leading to the emergence of a relatively generalist virus.

PLOS BIOLOGY (2021)

Article Multidisciplinary Sciences

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Erik Volz et al.

Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.

NATURE (2021)

Article Biochemistry & Molecular Biology

Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies

Xing Zhu et al.

Summary: The UK variant of SARS-CoV-2 with the N501Y mutation shows increased infectivity due to tighter binding with the ACE2 receptor, but without significant structural changes. Important neutralization epitopes in the spike receptor binding domain are retained.

PLOS BIOLOGY (2021)

Review Biochemistry & Molecular Biology

The origins of SARS-CoV-2: A critical review

Edward C. Holmes et al.

Summary: This article critically reviews the current scientific evidence to help clarify the origin of SARS-CoV-2. Recent debate has centered around two competing ideas: a laboratory escape scenario and zoonotic emergence.
Article Genetics & Heredity

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

Juan Angel Patino-Galindo et al.

Summary: Through phylogenetic and recombination analyses, this study identified evidence of a recombination event in the receptor binding domain (RBD) of both SARS-CoV and SARS-CoV-2, resulting in increased binding affinity to the human ACE2 receptor. Structural modeling suggests that ancestors of SARS-CoV-2 may have acquired the ability to infect humans decades ago, with further mutations in the RBD enhancing binding affinity with the human receptor in SARS-CoV and SARS-CoV-2.

GENOME MEDICINE (2021)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

Qihui Wang et al.

Article Medicine, General & Internal

Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Li-Li Ren et al.

CHINESE MEDICAL JOURNAL (2020)

Article Multidisciplinary Sciences

Phylogenetic network analysis of SARS-CoV-2 genomes

Peter Forster et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Introductions and early spread of SARS-CoV-2 in the New York City area

Ana S. Gonzalez-Reiche et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

Markus Hoffmann et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Emergence of SARS-CoV-2 through recombination and strong purifying selection

Xiaojun Li et al.

SCIENCE ADVANCES (2020)

Letter Biochemistry & Molecular Biology

The proximal origin of SARS-CoV-2

Kristian G. Andersen et al.

NATURE MEDICINE (2020)

Article Multidisciplinary Sciences

Origin and cross-species transmission of bat coronaviruses in China

Alice Latinne et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

M. Rafiul Islam et al.

SCIENTIFIC REPORTS (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

Lizhou Zhang et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

Lucy van Dorp et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution

Jinn-Jy Lin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Virology

Complexities of Viral Mutation Rates

Kayla M. Peck et al.

JOURNAL OF VIROLOGY (2018)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Article Biochemistry & Molecular Biology

The Evolutionary Pathway to Virulence of an RNA Virus

Adi Stern et al.

Review Biochemistry & Molecular Biology

Mechanisms of viral mutation

Rafael Sanjuan et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2016)

Article Biochemistry & Molecular Biology

Relaxing the Molecular Clock to Different Degrees for Different Substitution Types

Hui-Jie Lee et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Biochemistry & Molecular Biology

Molecular-clock methods for estimating evolutionary rates and timescales

Simon Y. W. Ho et al.

MOLECULAR ECOLOGY (2014)

Article Biochemistry & Molecular Biology

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Alexei J. Drummond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Biology

Bayesian random local clocks, or one rate to rule them all

Alexei J. Drummond et al.

BMC BIOLOGY (2010)

Article Virology

Viral Mutation Rates

Rafael Sanjuan et al.

JOURNAL OF VIROLOGY (2010)

Review Biology

Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies

Rafael Sanjuan

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Article Multidisciplinary Sciences

Island Biogeography Reveals the Deep History of SIV

Michael Worobey et al.

SCIENCE (2010)

Review Medicine, Research & Experimental

RNA virus genomics: a world of possibilities

Edward C. Holmes

JOURNAL OF CLINICAL INVESTIGATION (2009)

Article Genetics & Heredity

The Population Genetics of dN/dS

Sergey Kryazhimskiy et al.

PLOS GENETICS (2008)

Article Biochemistry & Molecular Biology

A general comparison of relaxed molecular clock models

Thomas Lepage et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach

MJ Sanderson

MOLECULAR BIOLOGY AND EVOLUTION (2002)

Article Biochemistry & Molecular Biology

Selecting models of nucleotide substitution: An application to human immunodeficiency virus 1 (HIV-1)

D Posada et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Biochemistry & Molecular Biology

Estimation of primate speciation dates using local molecular clocks

AD Yoder et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)

Article Biochemistry & Molecular Biology

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)