IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-39199-6.html
   My bibliography  Save this article

Predicting the antigenic evolution of SARS-COV-2 with deep learning

Author

Listed:
  • Wenkai Han

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Ningning Chen

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Xinzhou Xu

    (Chinese University of Hong Kong
    Chinese University of Hong Kong)

  • Adil Sahil

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Juexiao Zhou

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Zhongxiao Li

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Huawen Zhong

    (King Abdullah University of Science and Technology (KAUST))

  • Elva Gao

    (The KAUST School, King Abdullah University of Science and Technology (KAUST))

  • Ruochi Zhang

    (Syneron Technology)

  • Yu Wang

    (Syneron Technology)

  • Shiwei Sun

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Peter Pak-Hang Cheung

    (Chinese University of Hong Kong
    Chinese University of Hong Kong)

  • Xin Gao

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

Abstract

The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.

Suggested Citation

  • Wenkai Han & Ningning Chen & Xinzhou Xu & Adil Sahil & Juexiao Zhou & Zhongxiao Li & Huawen Zhong & Elva Gao & Ruochi Zhang & Yu Wang & Shiwei Sun & Peter Pak-Hang Cheung & Xin Gao, 2023. "Predicting the antigenic evolution of SARS-COV-2 with deep learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39199-6
    DOI: 10.1038/s41467-023-39199-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-39199-6
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-39199-6?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. Yunlong Cao & Jing Wang & Fanchong Jian & Tianhe Xiao & Weiliang Song & Ayijiang Yisimayi & Weijin Huang & Qianqian Li & Peng Wang & Ran An & Jing Wang & Yao Wang & Xiao Niu & Sijie Yang & Hui Liang &, 2022. "Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies," Nature, Nature, vol. 602(7898), pages 657-663, February.
    2. Seth J. Zost & Pavlo Gilchuk & James Brett Case & Elad Binshtein & Rita E. Chen & Joseph P. Nkolola & Alexandra Schäfer & Joseph X. Reidy & Andrew Trivette & Rachel S. Nargi & Rachel E. Sutton & Navee, 2020. "Potently neutralizing and protective human antibodies against SARS-CoV-2," Nature, Nature, vol. 584(7821), pages 443-449, August.
    3. Allison J. Greaney & Tyler N. Starr & Christopher O. Barnes & Yiska Weisblum & Fabian Schmidt & Marina Caskey & Christian Gaebler & Alice Cho & Marianna Agudelo & Shlomo Finkin & Zijun Wang & Daniel P, 2021. "Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    4. Lihong Liu & Sho Iketani & Yicheng Guo & Jasper F.-W. Chan & Maple Wang & Liyuan Liu & Yang Luo & Hin Chu & Yiming Huang & Manoj S. Nair & Jian Yu & Kenn K.-H. Chik & Terrence T.-T. Yuen & Chaemin Yoo, 2022. "Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2," Nature, Nature, vol. 602(7898), pages 676-681, February.
    5. Petra Mlcochova & Steven A. Kemp & Mahesh Shanker Dhar & Guido Papa & Bo Meng & Isabella A. T. M. Ferreira & Rawlings Datir & Dami A. Collier & Anna Albecka & Sujeet Singh & Rajesh Pandey & Jonathan B, 2021. "SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion," Nature, Nature, vol. 599(7883), pages 114-119, November.
    6. Jonathan Frazer & Pascal Notin & Mafalda Dias & Aidan Gomez & Joseph K. Min & Kelly Brock & Yarin Gal & Debora S. Marks, 2021. "Disease variant prediction with deep generative models of evolutionary data," Nature, Nature, vol. 599(7883), pages 91-95, November.
    7. Sho Iketani & Lihong Liu & Yicheng Guo & Liyuan Liu & Jasper F.-W. Chan & Yiming Huang & Maple Wang & Yang Luo & Jian Yu & Hin Chu & Kenn K.-H. Chik & Terrence T.-T. Yuen & Michael T. Yin & Magdalena , 2022. "Antibody evasion properties of SARS-CoV-2 Omicron sublineages," Nature, Nature, vol. 604(7906), pages 553-556, April.
    8. Christopher O. Barnes & Claudia A. Jette & Morgan E. Abernathy & Kim-Marie A. Dam & Shannon R. Esswein & Harry B. Gristick & Andrey G. Malyutin & Naima G. Sharaf & Kathryn E. Huey-Tubman & Yu E. Lee &, 2020. "SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies," Nature, Nature, vol. 588(7839), pages 682-687, December.
    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. Haohuai He & Bing He & Lei Guan & Yu Zhao & Feng Jiang & Guanxing Chen & Qingge Zhu & Calvin Yu-Chian Chen & Ting Li & Jianhua Yao, 2024. "De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    2. Tianyu Wu & Min Zhou & Jingcheng Zou & Qi Chen & Feng Qian & Jürgen Kurths & Runhui Liu & Yang Tang, 2024. "AI-guided few-shot inverse design of HDP-mimicking polymers against drug-resistant bacteria," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

    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. Yubin Liu & Ziyi Wang & Xinyu Zhuang & Shengnan Zhang & Zhicheng Chen & Yan Zou & Jie Sheng & Tianpeng Li & Wanbo Tai & Jinfang Yu & Yanqun Wang & Zhaoyong Zhang & Yunfeng Chen & Liangqin Tong & Xi Yu, 2023. "Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Khadija Khan & Farina Karim & Yashica Ganga & Mallory Bernstein & Zesuliwe Jule & Kajal Reedoy & Sandile Cele & Gila Lustig & Daniel Amoako & Nicole Wolter & Natasha Samsunder & Aida Sivro & James Emm, 2022. "Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    3. Markus Hoffmann & Lok-Yin Roy Wong & Prerna Arora & Lu Zhang & Cheila Rocha & Abby Odle & Inga Nehlmeier & Amy Kempf & Anja Richter & Nico Joel Halwe & Jacob Schön & Lorenz Ulrich & Donata Hoffmann & , 2023. "Omicron subvariant BA.5 efficiently infects lung cells," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Biao Zhou & Runhong Zhou & Bingjie Tang & Jasper Fuk-Woo Chan & Mengxiao Luo & Qiaoli Peng & Shuofeng Yuan & Hang Liu & Bobo Wing-Yee Mok & Bohao Chen & Pui Wang & Vincent Kwok-Man Poon & Hin Chu & Ch, 2022. "A broadly neutralizing antibody protects Syrian hamsters against SARS-CoV-2 Omicron challenge," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Leire Campos-Mata & Benjamin Trinité & Andrea Modrego & Sonia Tejedor Vaquero & Edwards Pradenas & Anna Pons-Grífols & Natalia Rodrigo Melero & Diego Carlero & Silvia Marfil & César Santiago & Dàlia R, 2024. "A monoclonal antibody targeting a large surface of the receptor binding motif shows pan-neutralizing SARS-CoV-2 activity," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Emanuele Andreano & Ida Paciello & Silvia Marchese & Lorena Donnici & Giulio Pierleoni & Giulia Piccini & Noemi Manganaro & Elisa Pantano & Valentina Abbiento & Piero Pileri & Linda Benincasa & Ginevr, 2022. "Anatomy of Omicron BA.1 and BA.2 neutralizing antibodies in COVID-19 mRNA vaccinees," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    7. Haofeng Wang & Qi Yang & Xiaoce Liu & Zili Xu & Maolin Shao & Dongxu Li & Yinkai Duan & Jielin Tang & Xianqiang Yu & Yumin Zhang & Aihua Hao & Yajie Wang & Jie Chen & Chenghao Zhu & Luke Guddat & Hong, 2023. "Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    8. Yanqun Wang & An Yan & Deyong Song & Maoqin Duan & Chuangchuang Dong & Jiantao Chen & Zihe Jiang & Yuanzhu Gao & Muding Rao & Jianxia Feng & Zhaoyong Zhang & Ruxi Qi & Xiaomin Ma & Hong Liu & Beibei Y, 2024. "Identification of a highly conserved neutralizing epitope within the RBD region of diverse SARS-CoV-2 variants," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. Alief Moulana & Thomas Dupic & Angela M. Phillips & Jeffrey Chang & Serafina Nieves & Anne A. Roffler & Allison J. Greaney & Tyler N. Starr & Jesse D. Bloom & Michael M. Desai, 2022. "Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    10. Yuanchen Liu & Xiaoyu Zhao & Jialu Shi & Yajie Wang & Huan Liu & Ye-Fan Hu & Bingjie Hu & Huiping Shuai & Terrence Tsz-Tai Yuen & Yue Chai & Feifei Liu & Hua-Rui Gong & Jiayan Li & Xun Wang & Shujun J, 2024. "Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    11. Leander Witte & Viren A. Baharani & Fabian Schmidt & Zijun Wang & Alice Cho & Raphael Raspe & Camila Guzman-Cardozo & Frauke Muecksch & Marie Canis & Debby J. Park & Christian Gaebler & Marina Caskey , 2023. "Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    12. 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.
    13. Hassen Kared & Asia-Sophia Wolf & Amin Alirezaylavasani & Anthony Ravussin & Guri Solum & Trung The Tran & Fridtjof Lund-Johansen & John Torgils Vaage & Lise Sofie Nissen-Meyer & Unni C. Nygaard & Ola, 2022. "Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Juan Liu & Fengfeng Mao & Jianhe Chen & Shuaiyao Lu & Yonghe Qi & Yinyan Sun & Linqiang Fang & Man Lung Yeung & Chunmei Liu & Guimei Yu & Guangyu Li & Ximing Liu & Yuansheng Yao & Panpan Huang & Dongx, 2023. "An IgM-like inhalable ACE2 fusion protein broadly neutralizes SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    15. Rajeshwer S. Sankhala & Kerri G. Lal & Jaime L. Jensen & Vincent Dussupt & Letzibeth Mendez-Rivera & Hongjun Bai & Lindsay Wieczorek & Sandra V. Mayer & Michelle Zemil & Danielle A. Wagner & Samantha , 2024. "Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    16. Xiaolei Wang & Terrence Tsz-Tai Yuen & Ying Dou & Jingchu Hu & Renhao Li & Zheng Zeng & Xuansheng Lin & Huarui Gong & Celia Hoi-Ching Chan & Chaemin Yoon & Huiping Shuai & Deborah Tip-Yin Ho & Ivan Fa, 2023. "Vaccine-induced protection against SARS-CoV-2 requires IFN-γ-driven cellular immune response," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    17. Franziska K. Kaiser & Mariana Gonzalez Hernandez & Nadine Krüger & Ellinor Englund & Wenjuan Du & Anna Z. Mykytyn & Mathijs P. Raadsen & Mart M. Lamers & Francine Rodrigues Ianiski & Tatiana M. Shamor, 2024. "Filamentous fungus-produced human monoclonal antibody provides protection against SARS-CoV-2 in hamster and non-human primate models," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    18. Tomohiro Takano & Takashi Sato & Ryutaro Kotaki & Saya Moriyama & Shuetsu Fukushi & Masahiro Shinoda & Kiyomi Kabasawa & Nagashige Shimada & Mio Kousaka & Yu Adachi & Taishi Onodera & Kazutaka Terahar, 2023. "Heterologous SARS-CoV-2 spike protein booster elicits durable and broad antibody responses against the receptor-binding domain," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    19. Laurent Renia & Yun Shan Goh & Angeline Rouers & Nina Bert & Wan Ni Chia & Jean-Marc Chavatte & Siew‐Wai Fong & Zi Wei Chang & Nicole Ziyi Zhuo & Matthew Zirui Tay & Yi-Hao Chan & Chee Wah Tan & Nicho, 2022. "Lower vaccine-acquired immunity in the elderly population following two-dose BNT162b2 vaccination is alleviated by a third vaccine dose," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    20. Tingting Li & Xiaojian Han & Chenjian Gu & Hangtian Guo & Huajun Zhang & Yingming Wang & Chao Hu & Kai Wang & Fengjiang Liu & Feiyang Luo & Yanan Zhang & Jie Hu & Wang Wang & Shenglong Li & Yanan Hao , 2021. "Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants," Nature Communications, Nature, vol. 12(1), pages 1-11, 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:14:y:2023:i:1:d:10.1038_s41467-023-39199-6. 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.