IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59533-4.html
   My bibliography  Save this article

SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform

Author

Listed:
  • Makoto Kuroda

    (University of Wisconsin)

  • Peter J. Halfmann

    (University of Wisconsin)

  • Ryuta Uraki

    (University of Tokyo
    National Center for Global Health and Medicine Research Institute
    University of Tokyo)

  • Seiya Yamayoshi

    (University of Tokyo
    National Center for Global Health and Medicine Research Institute
    University of Tokyo
    University of Tokyo)

  • Taksoo Kim

    (University of Wisconsin)

  • Tammy A. Armbrust

    (University of Wisconsin)

  • Sam Spyra

    (University of Wisconsin)

  • Randall Dahn

    (University of Wisconsin)

  • Lavanya Babujee

    (University of Wisconsin)

  • Yoshihiro Kawaoka

    (University of Wisconsin
    University of Tokyo
    National Center for Global Health and Medicine Research Institute
    University of Tokyo)

Abstract

To address the need for broadly protective SARS-CoV-2 vaccines, we developed an attenuated a SARS-CoV-2 vaccine virus that lacks the open reading frames of two viral structural proteins: the envelope (E) and membrane (M) proteins. This vaccine virus (ΔEM) replicates in a cell line stably expressing E and M but not in wild-type cells. Vaccination with ΔEM elicits a CD8 T-cell response against the viral spike and nucleocapsid proteins. Two vaccinations with ΔEM provide better protection of the lower respiratory tissues than a single dose against the Delta and Omicron XBB variants in hamsters. Moreover, ΔEM is effective as a booster in hamsters previously vaccinated with an mRNA-based vaccine, providing higher levels of protection in both respiratory tissues compared to the mRNA vaccine booster. Collectively, our data demonstrate the feasibility of a SARS-CoV-2 ΔEM vaccine candidate virus as a vaccine platform.

Suggested Citation

  • Makoto Kuroda & Peter J. Halfmann & Ryuta Uraki & Seiya Yamayoshi & Taksoo Kim & Tammy A. Armbrust & Sam Spyra & Randall Dahn & Lavanya Babujee & Yoshihiro Kawaoka, 2025. "SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59533-4
    DOI: 10.1038/s41467-025-59533-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59533-4
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-59533-4?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. Ryuta Uraki & Peter J. Halfmann & Shun Iida & Seiya Yamayoshi & Yuri Furusawa & Maki Kiso & Mutsumi Ito & Kiyoko Iwatsuki-Horimoto & Sohtaro Mine & Makoto Kuroda & Tadashi Maemura & Yuko Sakai-Tagawa , 2022. "Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents," Nature, Nature, vol. 612(7940), pages 540-545, December.
    2. Alberto A. Amarilla & Julian D. J. Sng & Rhys Parry & Joshua M. Deerain & James R. Potter & Yin Xiang Setoh & Daniel J. Rawle & Thuy T. Le & Naphak Modhiran & Xiaohui Wang & Nias Y. G. Peng & Francisc, 2021. "A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. 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.
    4. Jinyan Liu & Abishek Chandrashekar & Daniel Sellers & Julia Barrett & Catherine Jacob-Dolan & Michelle Lifton & Katherine McMahan & Michaela Sciacca & Haley VanWyk & Cindy Wu & Jingyou Yu & Ai-ris Y. , 2022. "Vaccines elicit highly conserved cellular immunity to SARS-CoV-2 Omicron," Nature, Nature, vol. 603(7901), pages 493-496, March.
    5. Yang Liu & Xianwen Zhang & Jianying Liu & Hongjie Xia & Jing Zou & Antonio E. Muruato & Sivakumar Periasamy & Chaitanya Kurhade & Jessica A. Plante & Nathen E. Bopp & Birte Kalveram & Alexander Bukrey, 2022. "A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Flavia Chiuppesi & Marcela d’Alincourt Salazar & Heidi Contreras & Vu H. Nguyen & Joy Martinez & Yoonsuh Park & Jenny Nguyen & Mindy Kha & Angelina Iniguez & Qiao Zhou & Teodora Kaltcheva & Roman Levy, 2020. "Development of a multi-antigenic SARS-CoV-2 vaccine candidate using a synthetic poxvirus platform," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    7. Wanbo Tai & Shengyong Feng & Benjie Chai & Shuaiyao Lu & Guangyu Zhao & Dong Chen & Wenhai Yu & Liting Ren & Huicheng Shi & Jing Lu & Zhuming Cai & Mujia Pang & Xu Tan & Penghua Wang & Jinzhong Lin & , 2023. "An mRNA-based T-cell-inducing antigen strengthens COVID-19 vaccine against SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    Full references (including those not matched with items on IDEAS)

    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. 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.
    2. 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.
    3. 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.
    4. Wanbo Tai & Chongyu Tian & Huicheng Shi & Benjie Chai & Xinyang Yu & Xinyu Zhuang & Pengyuan Dong & Min Li & Qi Yin & Shengyong Feng & Weixiao Wang & Oujia Zhang & Shibo Liang & Yang Liu & Jianying Li, 2025. "An mRNA vaccine against monkeypox virus inhibits infection by co-activation of humoral and cellular immune responses," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    5. Wanbo Tai & Shengyong Feng & Benjie Chai & Shuaiyao Lu & Guangyu Zhao & Dong Chen & Wenhai Yu & Liting Ren & Huicheng Shi & Jing Lu & Zhuming Cai & Mujia Pang & Xu Tan & Penghua Wang & Jinzhong Lin & , 2023. "An mRNA-based T-cell-inducing antigen strengthens COVID-19 vaccine against SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    6. 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.
    7. Xiang Liu & Wern Hann Ng & Eva Zusinaite & Joseph Freitas & Adam Taylor & Venugopal Yerragunta & Shukra Madhaha Aavula & Sambaiah Gorriparthi & Santhakumar Ponsekaran & Rama Lakshmi Bonda & Priyanka M, 2024. "A single-dose intranasal live-attenuated codon deoptimized vaccine provides broad protection against SARS-CoV-2 and its variants," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Jaime S. Rosa Duque & Xiwei Wang & Daniel Leung & Samuel M. S. Cheng & Carolyn A. Cohen & Xiaofeng Mu & Asmaa Hachim & Yanmei Zhang & Sau Man Chan & Sara Chaothai & Kelvin K. H. Kwan & Karl C. K. Chan, 2022. "Immunogenicity and reactogenicity of SARS-CoV-2 vaccines BNT162b2 and CoronaVac in healthy adolescents," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Jernej Pušnik & Jasmin Zorn & Werner O. Monzon-Posadas & Kathrin Peters & Emmanuil Osypchuk & Sabine Blaschke & Hendrik Streeck, 2024. "Vaccination impairs de novo immune response to omicron breakthrough infection, a precondition for the original antigenic sin," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. 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.
    11. Asolina Braun & Louise C. Rowntree & Ziyi Huang & Kirti Pandey & Nikolas Thuesen & Chen Li & Jan Petersen & Dene R. Littler & Shabana Raji & Thi H. O. Nguyen & Emma Jappe Lange & Gry Persson & Michael, 2024. "Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    12. Peter J. Halfmann & Raj S. Patel & Kathryn Loeffler & Atsuhiro Yasuhara & Lee-Ann Velde & Jie E. Yang & Jordan Chervin & Chloe Troxell & Min Huang & Naiying Zheng & Elizabeth R. Wright & Paul G. Thoma, 2025. "Multivalent S2 subunit vaccines provide broad protection against Clade 1 sarbecoviruses in female mice," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    13. Bruno A. Rodriguez-Rodriguez & Grace O. Ciabattoni & Ralf Duerr & Ana M. Valero-Jimenez & Stephen T. Yeung & Keaton M. Crosse & Austin R. Schinlever & Lucie Bernard-Raichon & Joaquin Rodriguez Galvan , 2023. "A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    14. Maki Kiso & Yuri Furusawa & Ryuta Uraki & Masaki Imai & Seiya Yamayoshi & Yoshihiro Kawaoka, 2023. "In vitro and in vivo characterization of SARS-CoV-2 strains resistant to nirmatrelvir," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    15. Maki Kiso & Seiya Yamayoshi & Shun Iida & Yuri Furusawa & Yuichiro Hirata & Ryuta Uraki & Masaki Imai & Tadaki Suzuki & Yoshihiro Kawaoka, 2023. "In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    16. Nozomi Kuse & Yu Zhang & Takayuki Chikata & Hung The Nguyen & Shinichi Oka & Hiroyuki Gatanaga & Masafumi Takiguchi, 2022. "Long-term memory CD8+ T cells specific for SARS-CoV-2 in individuals who received the BNT162b2 mRNA vaccine," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    17. Rafael R. G. Machado & Jordyn L. Walker & Dionna Scharton & Grace H. Rafael & Brooke M. Mitchell & Rachel A. Reyna & William M. Souza & Jianying Liu & David H. Walker & Jessica A. Plante & Kenneth S. , 2023. "Immunogenicity and efficacy of vaccine boosters against SARS-CoV-2 Omicron subvariant BA.5 in male Syrian hamsters," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    18. Julia M. Adler & Ricardo Martin Vidal & Christine Langner & Daria Vladimirova & Azza Abdelgawad & Daniela Kunecova & Xiaoyuan Lin & Geraldine Nouailles & Anne Voss & Sandra Kunder & Achim D. Gruber & , 2024. "An intranasal live-attenuated SARS-CoV-2 vaccine limits virus transmission," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    19. Robert W. Aldridge & Alexei Yavlinsky & Vincent Nguyen & Max T. Eyre & Madhumita Shrotri & Annalan M. D. Navaratnam & Sarah Beale & Isobel Braithwaite & Thomas Byrne & Jana Kovar & Ellen Fragaszy & Wi, 2022. "SARS-CoV-2 antibodies and breakthrough infections in the Virus Watch cohort," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    20. Shufeng Liu & Charles B. Stauft & Prabhuanand Selvaraj & Prabha Chandrasekaran & Felice D’Agnillo & Chao-Kai Chou & Wells W. Wu & Christopher Z. Lien & Clement A. Meseda & Cyntia L. Pedro & Matthew F., 2022. "Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters," Nature Communications, Nature, vol. 13(1), pages 1-15, 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:16:y:2025:i:1:d:10.1038_s41467-025-59533-4. 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.