Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo

Tessy A H Hick; Corinne Geertsema; Wilson Nguyen; Linda van Oosten; Cameron R Bishop; Sandra R Abbo; Troy Dumenil; Frank J M van Kuppeveld; Martijn A Langereis; Daniel J Rawle; Bing Tang; Kexin Yan; Monique M van Oers; Andreas Suhrbier; Gorben P Pijlman

doi:10.1016/j.ymthe.2024.06.019

Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo

Tessy A H Hick
, Corinne Geertsema
, Wilson Nguyen
, Linda van Oosten
, Cameron R Bishop
, Sandra R Abbo
, Troy Dumenil
, Frank J M van Kuppeveld
, Martijn A Langereis
, Daniel J Rawle
, Bing Tang
, Kexin Yan
, Monique M van Oers
, Andreas Suhrbier^*
, Gorben P Pijlman^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Self-amplifying mRNA (SAM) vaccines can be rapidly deployed in the event of disease outbreaks. A legitimate safety concern is the potential for recombination between alphavirus-based SAM vaccines and circulating viruses. This theoretical risk needs to be assessed in the regulatory process for SAM vaccine approval. Herein, we undertake extensive in vitro and in vivo assessments to explore recombination between SAM vaccine and a wide selection of alphaviruses and a coronavirus. SAM vaccines were found to effectively limit alphavirus co-infection through superinfection exclusion, although some co-replication was still possible. Using sensitive cell-based assays, replication-competent alphavirus chimeras were generated in vitro as a result of rare, but reproducible, RNA recombination events. The chimeras displayed no increased fitness in cell culture. Viable alphavirus chimeras were not detected in vivo in C57BL/6J, Rag1-/- and Ifnar-/- mice, in which high levels of SAM vaccine and alphavirus co-replicated in the same tissue. Furthermore, recombination between a SAM-spike vaccine and a swine coronavirus was not observed. In conclusion we state that although the ability of SAM vaccines to recombine with alphaviruses might be viewed as an environmental safety concern, several key factors substantially mitigate against in vivo emergence of chimeric viruses from SAM vaccine recipients.

Original language	English
Pages (from-to)	2519-2534
Number of pages	16
Journal	Molecular Therapy
Volume	32
Issue number	8
Early online date	17 Jun 2024
DOIs	https://doi.org/10.1016/j.ymthe.2024.06.019
Publication status	Published - 7 Aug 2024

Bibliographical note

Publisher Copyright:
© 2024 The Author(s)

Funding

We thank the TTW RepliSAFE (project 15791) user committee members for their continuous support, suggestions, and insightful discussions. We thank Prof. Dr. Roy Hall (University of Queensland, Brisbane, Australia), Prof. Dr. Michael Diamond (Washington University, USA), and Dr. Byron Martina (Erasmus Medical Center, the Netherlands) for providing alphavirus stocks. We thank Dr. Berend-Jan Bosch (Utrecht University, the Netherlands) for providing PEDV CV777 and PEDV DR13, and the defective PEDV DR13 construct. We thank Prof. Dr. Toos Daemen (University Medical Center Groningen, the Netherlands) for sharing detailed VRP production protocols. We also thank Marleen Henkens, Dr. Julian Bakker, Tessa Visser, and Dr. Athos Oliveira (Wageningen University and Research, the Netherlands) for their contribution to the alphavirus growth curves on the \u0394G3BP cells. We thank Dr. Itaru Anraku (QIMR Berghofer) for managing the PC3 facility, Dr. Viviana Lutzky (QIMR Berghofer) for help with proof reading, and the animal house staff at QIMR Berghofer MRI. This project (TTW RepliSAFE, 15791) was funded by the research program \u201CToward Modernization of Biotechnology and Safety\u201D of the Dutch Research Council (Domain Applied and Engineering Sciences), commissioned by the Dutch Ministry of Infrastructure and Water Management (I&W). A.S. was supported by an Investigator grant awarded to from the National Health and Medical Research Council of Australia (APP1173880). G.P.P. conceived of the work. M.A.L. developed the G3BP knockout cells under the supervision of F.J.M.v.K. The in vitro experiments were performed by T.A.H.H. C.G. and S.R.A. and the resulting data were analyzed by T.A.H.H. under supervision of G.P.P. and M.M.v.O. Mouse work was conducted by T.A.H.H. W.N. B.T. and K.Y. with D.J.R. and A.S. who supervised the work and obtained the regulatory approvals. C.R.B. and T.D undertook the bioinformatic analyses. G.P.P. and A.S. obtained the funding. T.A.H.H. A.S. and G.P.P. wrote the manuscript. All authors reviewed the manuscript. The user committee for the RepliSAFE project included members from MSD Animal Health. MSD Animal Health provided TC-83 replicons and antibodies but otherwise provided no other resources or funding, had no input into the manuscript nor the decision to publish. This project (TTW RepliSAFE, 15791) was funded by the research program \u201CToward Modernization of Biotechnology and Safety\u201D of the Dutch Research Council (Domain Applied and Engineering Sciences), commissioned by the Dutch Ministry of Infrastructure and Water Management (I&W). A.S. was supported by an Investigator grant awarded to from the National Health and Medical Research Council of Australia ( APP1173880 ).

Funders	Funder number
Dr. Berend-Jan Bosch
Ministry of Infrastructure and Water Management
Erasmus Medisch Centrum
University of Queensland
Dutch Research Council
Domain Applied and Engineering Sciences
Marleen Henkens
National Health and Medical Research Council	APP1173880
Utrecht University	CV777

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

RNA recombination
SAM vaccine
alphavirus
chimera
coronavirus
replicon
safety concern
self-amplifying mRNA
superinfection exclusion

Access to Document

10.1016/j.ymthe.2024.06.019Licence: CC BY-NC-ND

mmc2 Final published version, 12.5 MBLicence: CC BY-NC-ND

Cite this

Hick, T. A. H., Geertsema, C., Nguyen, W., van Oosten, L., Bishop, C. R., Abbo, S. R., Dumenil, T., van Kuppeveld, F. J. M., Langereis, M. A., Rawle, D. J., Tang, B., Yan, K., van Oers, M. M., Suhrbier, A., & Pijlman, G. P. (2024). Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo. Molecular Therapy, 32(8), 2519-2534. https://doi.org/10.1016/j.ymthe.2024.06.019

@article{81ad2292503543558da94adf3d513e51,

title = "Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo",

abstract = "Self-amplifying mRNA (SAM) vaccines can be rapidly deployed in the event of disease outbreaks. A legitimate safety concern is the potential for recombination between alphavirus-based SAM vaccines and circulating viruses. This theoretical risk needs to be assessed in the regulatory process for SAM vaccine approval. Herein, we undertake extensive in vitro and in vivo assessments to explore recombination between SAM vaccine and a wide selection of alphaviruses and a coronavirus. SAM vaccines were found to effectively limit alphavirus co-infection through superinfection exclusion, although some co-replication was still possible. Using sensitive cell-based assays, replication-competent alphavirus chimeras were generated in vitro as a result of rare, but reproducible, RNA recombination events. The chimeras displayed no increased fitness in cell culture. Viable alphavirus chimeras were not detected in vivo in C57BL/6J, Rag1-/- and Ifnar-/- mice, in which high levels of SAM vaccine and alphavirus co-replicated in the same tissue. Furthermore, recombination between a SAM-spike vaccine and a swine coronavirus was not observed. In conclusion we state that although the ability of SAM vaccines to recombine with alphaviruses might be viewed as an environmental safety concern, several key factors substantially mitigate against in vivo emergence of chimeric viruses from SAM vaccine recipients.",

keywords = "RNA recombination, SAM vaccine, alphavirus, chimera, coronavirus, replicon, safety concern, self-amplifying mRNA, superinfection exclusion",

author = "Hick, \{Tessy A H\} and Corinne Geertsema and Wilson Nguyen and \{van Oosten\}, Linda and Bishop, \{Cameron R\} and Abbo, \{Sandra R\} and Troy Dumenil and \{van Kuppeveld\}, \{Frank J M\} and Langereis, \{Martijn A\} and Rawle, \{Daniel J\} and Bing Tang and Kexin Yan and \{van Oers\}, \{Monique M\} and Andreas Suhrbier and Pijlman, \{Gorben P\}",

note = "Publisher Copyright: {\textcopyright} 2024 The Author(s)",

year = "2024",

month = aug,

day = "7",

doi = "10.1016/j.ymthe.2024.06.019",

language = "English",

volume = "32",

pages = "2519--2534",

journal = "Molecular Therapy",

issn = "1525-0016",

publisher = "Cell Press",

number = "8",

}

Hick, TAH, Geertsema, C, Nguyen, W, van Oosten, L, Bishop, CR, Abbo, SR, Dumenil, T, van Kuppeveld, FJM, Langereis, MA, Rawle, DJ, Tang, B, Yan, K, van Oers, MM, Suhrbier, A & Pijlman, GP 2024, 'Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo', Molecular Therapy, vol. 32, no. 8, pp. 2519-2534. https://doi.org/10.1016/j.ymthe.2024.06.019

TY - JOUR

T1 - Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo

AU - Hick, Tessy A H

AU - Geertsema, Corinne

AU - Nguyen, Wilson

AU - van Oosten, Linda

AU - Bishop, Cameron R

AU - Abbo, Sandra R

AU - Dumenil, Troy

AU - van Kuppeveld, Frank J M

AU - Langereis, Martijn A

AU - Rawle, Daniel J

AU - Tang, Bing

AU - Yan, Kexin

AU - van Oers, Monique M

AU - Suhrbier, Andreas

AU - Pijlman, Gorben P

PY - 2024/8/7

Y1 - 2024/8/7

N2 - Self-amplifying mRNA (SAM) vaccines can be rapidly deployed in the event of disease outbreaks. A legitimate safety concern is the potential for recombination between alphavirus-based SAM vaccines and circulating viruses. This theoretical risk needs to be assessed in the regulatory process for SAM vaccine approval. Herein, we undertake extensive in vitro and in vivo assessments to explore recombination between SAM vaccine and a wide selection of alphaviruses and a coronavirus. SAM vaccines were found to effectively limit alphavirus co-infection through superinfection exclusion, although some co-replication was still possible. Using sensitive cell-based assays, replication-competent alphavirus chimeras were generated in vitro as a result of rare, but reproducible, RNA recombination events. The chimeras displayed no increased fitness in cell culture. Viable alphavirus chimeras were not detected in vivo in C57BL/6J, Rag1-/- and Ifnar-/- mice, in which high levels of SAM vaccine and alphavirus co-replicated in the same tissue. Furthermore, recombination between a SAM-spike vaccine and a swine coronavirus was not observed. In conclusion we state that although the ability of SAM vaccines to recombine with alphaviruses might be viewed as an environmental safety concern, several key factors substantially mitigate against in vivo emergence of chimeric viruses from SAM vaccine recipients.

AB - Self-amplifying mRNA (SAM) vaccines can be rapidly deployed in the event of disease outbreaks. A legitimate safety concern is the potential for recombination between alphavirus-based SAM vaccines and circulating viruses. This theoretical risk needs to be assessed in the regulatory process for SAM vaccine approval. Herein, we undertake extensive in vitro and in vivo assessments to explore recombination between SAM vaccine and a wide selection of alphaviruses and a coronavirus. SAM vaccines were found to effectively limit alphavirus co-infection through superinfection exclusion, although some co-replication was still possible. Using sensitive cell-based assays, replication-competent alphavirus chimeras were generated in vitro as a result of rare, but reproducible, RNA recombination events. The chimeras displayed no increased fitness in cell culture. Viable alphavirus chimeras were not detected in vivo in C57BL/6J, Rag1-/- and Ifnar-/- mice, in which high levels of SAM vaccine and alphavirus co-replicated in the same tissue. Furthermore, recombination between a SAM-spike vaccine and a swine coronavirus was not observed. In conclusion we state that although the ability of SAM vaccines to recombine with alphaviruses might be viewed as an environmental safety concern, several key factors substantially mitigate against in vivo emergence of chimeric viruses from SAM vaccine recipients.

KW - RNA recombination

KW - SAM vaccine

KW - alphavirus

KW - chimera

KW - coronavirus

KW - replicon

KW - safety concern

KW - self-amplifying mRNA

KW - superinfection exclusion

UR - https://www.scopus.com/pages/publications/85199076988

U2 - 10.1016/j.ymthe.2024.06.019

DO - 10.1016/j.ymthe.2024.06.019

M3 - Article

C2 - 38894543

SN - 1525-0016

VL - 32

SP - 2519

EP - 2534

JO - Molecular Therapy

JF - Molecular Therapy

IS - 8

ER -

Safety concern of recombination between self-amplifying mRNA vaccines and viruses is mitigated in vivo

Abstract

Bibliographical note

Funding

UN SDGs

Keywords

Access to Document

Other files and links

Fingerprint

Cite this