IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-28768-w.html
   My bibliography  Save this article

Evolution of the SARS-CoV-2 spike protein in the human host

Author

Listed:
  • Antoni G. Wrobel

    (Structural Biology of Disease Processes Laboratory)

  • Donald J. Benton

    (Structural Biology of Disease Processes Laboratory)

  • Chloë Roustan

    (Structural Biology Science Technology Platform)

  • Annabel Borg

    (Structural Biology Science Technology Platform)

  • Saira Hussain

    (Worldwide Influenza Centre
    RNA Virus Replication Laboratory)

  • Stephen R. Martin

    (Structural Biology of Disease Processes Laboratory)

  • Peter B. Rosenthal

    (Structural Biology of Cells and Viruses Laboratory; Francis Crick Institute)

  • John J. Skehel

    (Structural Biology of Disease Processes Laboratory)

  • Steven J. Gamblin

    (Structural Biology of Disease Processes Laboratory)

Abstract

Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.

Suggested Citation

  • Antoni G. Wrobel & Donald J. Benton & Chloë Roustan & Annabel Borg & Saira Hussain & Stephen R. Martin & Peter B. Rosenthal & John J. Skehel & Steven J. Gamblin, 2022. "Evolution of the SARS-CoV-2 spike protein in the human host," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28768-w
    DOI: 10.1038/s41467-022-28768-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-28768-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-28768-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Zunlong Ke & Joaquin Oton & Kun Qu & Mirko Cortese & Vojtech Zila & Lesley McKeane & Takanori Nakane & Jasenko Zivanov & Christopher J. Neufeldt & Berati Cerikan & John M. Lu & Julia Peukes & Xiaoli X, 2020. "Structures and distributions of SARS-CoV-2 spike proteins on intact virions," Nature, Nature, vol. 588(7838), pages 498-502, December.
    2. Donald J. Benton & Antoni G. Wrobel & Pengqi Xu & Chloë Roustan & Stephen R. Martin & Peter B. Rosenthal & John J. Skehel & Steven J. Gamblin, 2020. "Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion," Nature, Nature, vol. 588(7837), pages 327-330, December.
    3. Lizhou Zhang & Cody B. Jackson & Huihui Mou & Amrita Ojha & Haiyong Peng & Brian D. Quinlan & Erumbi S. Rangarajan & Andi Pan & Abigail Vanderheiden & Mehul S. Suthar & Wenhui Li & Tina Izard & Christ, 2020. "SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    4. Antoni G. Wrobel & Donald J. Benton & Pengqi Xu & Lesley J. Calder & Annabel Borg & Chloë Roustan & Stephen R. Martin & Peter B. Rosenthal & John J. Skehel & Steven J. Gamblin, 2021. "Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    5. Alexandra C. Walls & M. Alejandra Tortorici & Berend-Jan Bosch & Brandon Frenz & Peter J. M. Rottier & Frank DiMaio & Félix A. Rey & David Veesler, 2016. "Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer," Nature, Nature, vol. 531(7592), pages 114-117, March.
    6. Nicholas G. Davies & Christopher I. Jarvis & W. John Edmunds & Nicholas P. Jewell & Karla Diaz-Ordaz & Ruth H. Keogh, 2021. "Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7," Nature, Nature, vol. 593(7858), pages 270-274, May.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Lena Jaki & Sebastian Weigang & Lisa Kern & Stefanie Kramme & Antoni G. Wrobel & Andrea B. Grawitz & Philipp Nawrath & Stephen R. Martin & Theo Dähne & Julius Beer & Miriam Disch & Philipp Kolb & Lisa, 2023. "Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Yuen, Kum Fai & Cai, Lanhui & Wee, Shaun Chuin Kit & Wang, Xueqin, 2024. "Pandemic-driven acceptance of urban drone deliveries," Transport Policy, Elsevier, vol. 146(C), pages 356-370.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Alexander J. Pak & Alvin Yu & Zunlong Ke & John A. G. Briggs & Gregory A. Voth, 2022. "Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Oskar Staufer & Kapil Gupta & Jochen Estebano Hernandez Bücher & Fabian Kohler & Christian Sigl & Gunjita Singh & Kate Vasileiou & Ana Yagüe Relimpio & Meline Macher & Sebastian Fabritz & Hendrik Diet, 2022. "Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Lei Peng & Yingxia Hu & Madeleine C. Mankowski & Ping Ren & Rita E. Chen & Jin Wei & Min Zhao & Tongqing Li & Therese Tripler & Lupeng Ye & Ryan D. Chow & Zhenhao Fang & Chunxiang Wu & Matthew B. Dong, 2022. "Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Rong Zhu & Daniel Canena & Mateusz Sikora & Miriam Klausberger & Hannah Seferovic & Ahmad Reza Mehdipour & Lisa Hain & Elisabeth Laurent & Vanessa Monteil & Gerald Wirnsberger & Ralph Wieneke & Robert, 2022. "Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Sun Jin Kim & Zhong Yao & Morgan C. Marsh & Debra M. Eckert & Michael S. Kay & Anna Lyakisheva & Maria Pasic & Aiyush Bansal & Chaim Birnboim & Prabhat Jha & Yannick Galipeau & Marc-André Langlois & J, 2022. "Homogeneous surrogate virus neutralization assay to rapidly assess neutralization activity of anti-SARS-CoV-2 antibodies," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    6. Gang Ye & Bin Liu & Fang Li, 2022. "Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    7. Taha Y. Taha & Irene P. Chen & Jennifer M. Hayashi & Takako Tabata & Keith Walcott & Gabriella R. Kimmerly & Abdullah M. Syed & Alison Ciling & Rahul K. Suryawanshi & Hannah S. Martin & Bryan H. Bach , 2023. "Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Haisheng Yu & Banghui Liu & Yudi Zhang & Xijie Gao & Qian Wang & Haitao Xiang & Xiaofang Peng & Caixia Xie & Yaping Wang & Peiyu Hu & Jingrong Shi & Quan Shi & Pingqian Zheng & Chengqian Feng & Guofan, 2023. "Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    9. Nikhil Kumar Tulsian & Raghuvamsi Venkata Palur & Xinlei Qian & Yue Gu & Bhuvaneshwari D/O Shunmuganathan & Firdaus Samsudin & Yee Hwa Wong & Jianqing Lin & Kiren Purushotorman & Mary McQueen Kozma & , 2023. "Defining neutralization and allostery by antibodies against COVID-19 variants," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    10. Sheng-Chieh Lee & Ching-Yuan Lin & Ying-Ji Chuang, 2022. "The Study of Alternative Fire Commanders’ Training Program during the COVID-19 Pandemic Situation in New Taipei City, Taiwan," IJERPH, MDPI, vol. 19(11), pages 1-22, May.
    11. Juan Yang & Valentina Marziano & Xiaowei Deng & Giorgio Guzzetta & Juanjuan Zhang & Filippo Trentini & Jun Cai & Piero Poletti & Wen Zheng & Wei Wang & Qianhui Wu & Zeyao Zhao & Kaige Dong & Guangjie , 2021. "Despite vaccination, China needs non-pharmaceutical interventions to prevent widespread outbreaks of COVID-19 in 2021," Nature Human Behaviour, Nature, vol. 5(8), pages 1009-1020, August.
    12. Zhennan Zhao & Yufeng Xie & Bin Bai & Chunliang Luo & Jingya Zhou & Weiwei Li & Yumin Meng & Linjie Li & Dedong Li & Xiaomei Li & Xiaoxiong Li & Xiaoyun Wang & Junqing Sun & Zepeng Xu & Yeping Sun & W, 2023. "Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Rosanna C. Barnard & Nicholas G. Davies & Mark Jit & W. John Edmunds, 2022. "Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    14. Peter J. Halfmann & Kathryn Loeffler & Augustine Duffy & Makoto Kuroda & Jie E. Yang & Elizabeth R. Wright & Yoshihiro Kawaoka & Ravi S. Kane, 2024. "Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    15. Tugba Taskin Tok & Sivakumar J T Gowder, 2020. "An Updated Review on Covid-19 with Special Reference to Structural Elucidation and Functional Properties," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 31(4), pages 24345-24351, November.
    16. Raveen Rathnasinghe & Sonia Jangra & Chengjin Ye & Anastasija Cupic & Gagandeep Singh & Carles Martínez-Romero & Lubbertus C. F. Mulder & Thomas Kehrer & Soner Yildiz & Angela Choi & Stephen T. Yeung , 2022. "Characterization of SARS-CoV-2 Spike mutations important for infection of mice and escape from human immune sera," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    17. Cristina del Álamo & Ángela Vázquez-Calvo & África Sanchiz & Gil Rodríguez-Caravaca & Rocío Martín & Bruno Hernáez & Pablo Méndez-Vigo-Carranza & Juan Sánchez García-Casarrubios & Antonio Alcamí & Jos, 2022. "Fast Air-to-Liquid Sampler Detects Surges in SARS-CoV-2 Aerosol Levels in Hospital Rooms," IJERPH, MDPI, vol. 20(1), pages 1-11, December.
    18. James W. Saville & Dhiraj Mannar & Xing Zhu & Shanti S. Srivastava & Alison M. Berezuk & Jean-Philippe Demers & Steven Zhou & Katharine S. Tuttle & Inna Sekirov & Andrew Kim & Wei Li & Dimiter S. Dimi, 2022. "Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    19. Mitze, Timo & Rode, Johannes, 2022. "Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data," Publications of Darmstadt Technical University, Institute for Business Studies (BWL) 130543, Darmstadt Technical University, Department of Business Administration, Economics and Law, Institute for Business Studies (BWL).
    20. Xuanming Guo & Jianli Cao & Jian-Piao Cai & Jiayan Wu & Jiangang Huang & Pallavi Asthana & Sheung Kin Ken Wong & Zi-Wei Ye & Susma Gurung & Yijing Zhang & Sheng Wang & Zening Wang & Xin Ge & Hiu Yee K, 2022. "Control of SARS-CoV-2 infection by MT1-MMP-mediated shedding of ACE2," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28768-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.