Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

Cell - Tập 183 Số 3 - Trang 739-751.e8 - 2020
Leonid Yurkovetskiy1, Handong Wang2, Kristen E. Pascal3, Christopher H. Tomkins-Tinch4,5, Thomas Nyalile1, Yetao Wang1, Alina Baum3, William E. Diehl1, Ann Dauphin1, Claudia Carbone1, Kristen Veinotte1, Shawn B. Egri1, S. F. Schaffner4,5, Jacob E. Lemieux4,6, James B. Munro7,8, Ashique Rafique3, Abhi Barve2, Pardis C. Sabeti4,9,5,10,11, Christos A. Kyratsous3, Natalya V. Dudkina2, Kuang Shen1, Jeremy Luban4,7,11,1
1Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605 USA
2Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
3Regeneron Pharmaceutical, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
4Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
5Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
6Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
7Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA
8Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue, Worcester, MA 01605, USA
9Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, 02115 Boston, MA, USA
10Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
11Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Andersen, 2020, The proximal origin of SARS-CoV-2, Nat. Med., 26, 450, 10.1038/s41591-020-0820-9

Baum, 2020, Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies, Science, 369, 1014, 10.1126/science.abd0831

Boni, 2020, Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic, Nat. Microbiol., 2020, 28

Bos, 1996, The production of recombinant infectious DI-particles of a murine coronavirus in the absence of helper virus, Virology, 218, 52, 10.1006/viro.1996.0165

Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly (Austin), 6, 80, 10.4161/fly.19695

Cock, 2009, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, 25, 1422, 10.1093/bioinformatics/btp163

2020, The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2, Nat. Microbiol., 5, 536, 10.1038/s41564-020-0695-z

Denison, 2011, Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity, RNA Biol., 8, 270, 10.4161/rna.8.2.15013

Diehl, 2016, Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic, Cell, 167, 1088, 10.1016/j.cell.2016.10.014

Drosten, 2003, Identification of a novel coronavirus in patients with severe acute respiratory syndrome, N. Engl. J. Med., 348, 1967, 10.1056/NEJMoa030747

Furuyama, 2020, Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant, arXiv

Grubaugh, 2020, We shouldn’t worry when a virus mutates during disease outbreaks, Nat. Microbiol., 5, 529, 10.1038/s41564-020-0690-4

Gui, 2017, Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding, Cell Res., 27, 119, 10.1038/cr.2016.152

Hadfield, 2018, Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, 34, 4121, 10.1093/bioinformatics/bty407

Hansen, 2020, Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail, Science, 369, 1010, 10.1126/science.abd0827

Hoffmann, 2020, A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells, Mol. Cell, 78, 779, 10.1016/j.molcel.2020.04.022

Holmes, 2003, Error thresholds and the constraints to RNA virus evolution, Trends Microbiol., 11, 543, 10.1016/j.tim.2003.10.006

Huang, 2004, Generation of synthetic severe acute respiratory syndrome coronavirus pseudoparticles: implications for assembly and vaccine production, J. Virol., 78, 12557, 10.1128/JVI.78.22.12557-12565.2004

Huang, 2020, Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, Lancet, 395, 497, 10.1016/S0140-6736(20)30183-5

Hunter, 2007, Matplotlib: A 2D Graphics Environment, Comput. Sci. Eng., 9, 90, 10.1109/MCSE.2007.55

Johnsson, 1991, Immobilization of proteins to a carboxymethyldextran-modified gold surface for biospecific interaction analysis in surface plasmon resonance sensors, Anal. Biochem., 198, 268, 10.1016/0003-2697(91)90424-R

Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010

Korber, 2020, Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus, Cell, 182, 812, 10.1016/j.cell.2020.06.043

Ksiazek, 2003, A novel coronavirus associated with severe acute respiratory syndrome, N. Engl. J. Med., 348, 1953, 10.1056/NEJMoa030781

Lam, 2020, Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins, Nature, 583, 282, 10.1038/s41586-020-2169-0

Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352

Lu, 2020, Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, Lancet, 395, 565, 10.1016/S0140-6736(20)30251-8

Marzi, 2018, Recently Identified Mutations in the Ebola Virus-Makona Genome Do Not Alter Pathogenicity in Animal Models, Cell Rep., 23, 1806, 10.1016/j.celrep.2018.04.027

McNamara, 2020, High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States, bioRxiv

Myszka, 1999, Improving biosensor analysis, J. Mol. Recognit., 12, 279, 10.1002/(SICI)1099-1352(199909/10)12:5<279::AID-JMR473>3.0.CO;2-3

Page, 2016, SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments, Microb. Genom., 2, e000056

Pallesen, 2017, Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen, Proc. Natl. Acad. Sci. USA, 114, E7348, 10.1073/pnas.1707304114

Peters, 2004, J. Virol., 78, 6915, 10.1128/JVI.78.13.6915-6926.2004

Quitadamo, 2018, HIV-1 R5 macrophage-tropic envelope glycoprotein trimers bind CD4 with high affinity, while the CD4 binding site on non-macrophage-tropic, T-tropic R5 envelopes is occluded, J. Virol., 92, 10.1128/JVI.00841-17

Ruedas, 2017, Spontaneous Mutation at Amino Acid 544 of the Ebola Virus Glycoprotein Potentiates Virus Entry and Selection in Tissue Culture, J. Virol., 91, 10.1128/JVI.00392-17

Saberi, 2018, A planarian nidovirus expands the limits of RNA genome size, PLoS Pathog., 14, e1007314, 10.1371/journal.ppat.1007314

Schnell, 2011, HIV-1 replication in the central nervous system occurs in two distinct cell types, PLoS Pathog., 7, e1002286, 10.1371/journal.ppat.1002286

Shang, 2020, Structural basis of receptor recognition by SARS-CoV-2, Nature, 581, 221, 10.1038/s41586-020-2179-y

Shu, 2017, GISAID: Global initiative on sharing all influenza data - from vision to reality, Euro Surveill., 22, 10.2807/1560-7917.ES.2017.22.13.30494

Smith, 2013, Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics, PLoS Pathog., 9, e1003565, 10.1371/journal.ppat.1003565

Smith, 2014, Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses, Annu. Rev. Virol., 1, 111, 10.1146/annurev-virology-031413-085507

Tortorici, 2019, Structural insights into coronavirus entry, Adv. Virus Res., 105, 93, 10.1016/bs.aivir.2019.08.002

Urbanowicz, 2016, Human Adaptation of Ebola Virus during the West African Outbreak, Cell, 167, 1079, 10.1016/j.cell.2016.10.013

Vennema, 1996, Nucleocapsid-independent assembly of coronavirus-like particles by co-expression of viral envelope protein genes, EMBO J., 15, 2020, 10.1002/j.1460-2075.1996.tb00553.x

Volz, 2020, Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity, medRxiv

Wagner, 2020

Walls, 2019, Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion, Cell, 176, 1026, 10.1016/j.cell.2018.12.028

Walls, 2020, Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein, Cell, 181, 281, 10.1016/j.cell.2020.02.058

Wang, 2017, Biochemical Basis for Increased Activity of Ebola Glycoprotein in the 2013-16 Epidemic, Cell Host Microbe, 21, 367, 10.1016/j.chom.2017.02.002

Wrapp, 2020, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 367, 1260, 10.1126/science.abb2507

Wu, 2020, Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China, Cell Host Microbe, 27, 325, 10.1016/j.chom.2020.02.001

Wu, 2020, A new coronavirus associated with human respiratory disease in China, Nature, 579, 265, 10.1038/s41586-020-2008-3

Yan, 2020, Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2, Science, 367, 1444, 10.1126/science.abb2762

Yuan, 2017, Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains, Nat. Commun., 8, 15092, 10.1038/ncomms15092

Zaki, 2012, Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia, N. Engl. J. Med., 367, 1814, 10.1056/NEJMoa1211721

Zhang, 2020, The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity, bioRxiv

Zhou, 2020, A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein, Curr. Biol., 30, 2196, 10.1016/j.cub.2020.05.023

Zhou, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579, 270, 10.1038/s41586-020-2012-7

Zhu, 2020, A Novel Coronavirus from Patients with Pneumonia in China, 2019, N. Engl. J. Med., 382, 727, 10.1056/NEJMoa2001017