SaRNA (self-amplifying RNA) vaccines are created with the dual purpose of reducing the amount of genetic material inoculated with the vaccination and simultaneously generating large amounts of viral antigens to achieve a strong immune system response. The platform of these vaccines is based on the genome of a specific, suitably modified alphavirus: the Venezuelan equine encephalitis virus VEEV, consisting of a positive single-stranded RNA of about 11 Kbases. It is organized into two open reading frames (ORFs); the first encodes for 4 non-structural proteins that constitute an RNA-dependent RNA polymerase (replicase), the second encodes for the virus’ structural proteins, which make-up the capsid and envelope glycoproteins. Once assembled, the viral replicase is able to replicate the entire genome (called replicon, i.e. a sequence of genetic material able to replicate itself) in thousands of copies and the researchers thought to exploit this feature by modifying the genome of appropriate strains of VEEV preserving the non-structural replicase genes and by replacing the structural proteins genes with the sequence of a protein of a specific virus, called gene of interest (GOI), capable of behaving like an antigen and triggering a strong immune system response. The self-amplification of this structure within the host cell results in the synthesis of very large amounts of reference antigen, much higher than those synthesized by current mRNA vaccines, thus allowing the inoculation of smaller amounts of encapsulated genetic material carried in lipid nanoparticles (LNPs). In view of the current spread of SARS-CoV-2, the first saRNA vaccine produced and approved worldwide involved the insertion of the RNA sequence encoding for the spike protein as a GOI within the replicon. However, concerns have been raised in the international scientific world regarding the self-amplification mechanism of saRNA vaccines: the aim of this paper is to demonstrate that the self-replication mechanism of the saRNA vaccines is controlled and self-limiting.
References
[1]
Paul-Chima, U.O., Ben, O.M., Fabian, C.O., Nnenna, U.J. and Chinyere, N.U. (2026) Self-Amplifying RNA (saRNA) and Circular RNA (circRNA) Vaccines: Progress, Evidence Gaps, and Translational Pathways for Durable and Scalable Immunization. HumanVaccines&Immunotherapeutics, 22, Article ID: 2661120. https://doi.org/10.1080/21645515.2026.2661120
[2]
Pietil?, M.K., Hellstr?m, K. and Ahola, T. (2017) Alphavirus Polymerase and RNA Replication. VirusResearch, 234, 44-57. https://doi.org/10.1016/j.virusres.2017.01.007
[3]
H?, N.T., Hughes, S.G., Ta, V.T., Phan, L.T., ??, Q., Nguy?n, T.V., et al. (2024) Safety, Immunogenicity and Efficacy of the Self-Amplifying mRNA ARCT-154 COVID-19 Vaccine: Pooled Phase 1, 2, 3a and 3b Randomized, Controlled Trials. NatureCommunications, 15, Article No. 4081. https://doi.org/10.1038/s41467-024-47905-1
[4]
Shin, G., Yost, S.A., Miller, M.T., Elrod, E.J., Grakoui, A. and Marcotrigiano, J. (2012) Structural and Functional Insights into Alphavirus Polyprotein Processing and Pathogenesis. ProceedingsoftheNationalAcademyofSciences, 109, 16534-16539. https://doi.org/10.1073/pnas.1210418109
[5]
Kinney, R.M., Johnson, B.J.B., Welch, J.B., Tsuchiya, K.R. and Trent, D.W. (1989) The Full-Length Nucleotide Sequences of the Virulent Trinidad Donkey Strain of Venezuelan Equine Encephalitis Virus and Its Attenuated Vaccine Derivative, Strain TC-83. Virology, 170, 19-30. https://doi.org/10.1016/0042-6822(89)90347-4
[6]
Casmil, I.C., Jin, J., Won, E., Huang, C., Liao, S., Cha-Molstad, H., et al. (2025) The Advent of Clinical Self-Amplifying RNA Vaccines. MolecularTherapy, 33, 2565-2582. https://doi.org/10.1016/j.ymthe.2025.03.060
[7]
Tassinari, V., Cerboni, C. and Soriani, A. (2022) Self or Non-Self? It Is Also a Matter of RNA Recognition and Editing by ADAR1. Biology, 11, Article No. 568. https://doi.org/10.3390/biology11040568
[8]
Wolf, J. and Passmore, L.A. (2014) mRNA Deadenylation by Pan2-Pan3. BiochemicalSocietyTransactions, 42, 184-187. https://doi.org/10.1042/bst20130211
[9]
Ferreira-Ramos, A.S., Li, C., Eydoux, C., Contreras, J.M., Morice, C., Quérat, G., et al. (2019) Approved Drugs Screening against the nsP1 Capping Enzyme of Venezuelan Equine Encephalitis Virus Using an Immuno-Based Assay. AntiviralResearch, 163, 59-69. https://doi.org/10.1016/j.antiviral.2019.01.003
[10]
Bowie, A.G. and Fitzgerald, K.A. (2007) RIG-I: Tri-Ing to Discriminate between Self and Non-Self RNA. TrendsinImmunology, 28, 147-150. https://doi.org/10.1016/j.it.2007.02.002
[11]
Miedziak, B., Dobie?yńska, A., Dar?ynkiewicz, Z.M., Bartkowska, J., Miszkiewicz, J., Kowalska, J., et al. (2019) Kinetic Analysis of IFIT1 and IFIT5 Interactions with Different Native and Engineered RNAs and Its Consequences for Designing mRNA-Based Therapeutics. RNA, 26, 58-68. https://doi.org/10.1261/rna.073304.119
[12]
Kumar, P., Sweeney, T.R., Skabkin, M.A., Skabkina, O.V., Hellen, C.U.T. and Pestova, T.V. (2013) Inhibition of Translation by IFIT Family Members Is Determined by Their Ability to Interact Selectively with the 5’-Terminal Regions of cap0-, cap1-and 5’ppp-mRNAs. NucleicAcidsResearch, 42, 3228-3245. https://doi.org/10.1093/nar/gkt1321
[13]
Abbas, Y.M., Laudenbach, B.T., Martínez-Montero, S., Cencic, R., Habjan, M., Pichlmair, A., et al. (2017) Structure of Human IFIT1 with Capped RNA Reveals Adaptable mRNA Binding and Mechanisms for Sensing N1 and N2 Ribose 2’-O Methylations. ProceedingsoftheNationalAcademyofSciences, 114, E2106-E2115. https://doi.org/10.1073/pnas.1612444114
[14]
de Alwis, R., Gan, E.S., Chen, S., Leong, Y.S., Tan, H.C., Zhang, S.L., et al. (2021) A Single Dose of Self-Transcribing and Replicating RNA-Based SARS-CoV-2 Vaccine Produces Protective Adaptive Immunity in Mice. MolecularTherapy, 29, 1970-1983. https://doi.org/10.1016/j.ymthe.2021.04.001
[15]
Uehata, T. and Takeuchi, O. (2020) RNA Recognition and Immunity-Innate Immune Sensing and Its Posttranscriptional Regulation Mechanisms. Cells, 9, Article No. 1701. https://doi.org/10.3390/cells9071701
[16]
Santhakumar, D., Rohaim, M.A.M.S., Hussein, H.A., Hawes, P., Ferreira, H.L., Behboudi, S., et al. (2018) Chicken Interferon-Induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses. ScientificReports, 8, Article No. 6794. https://doi.org/10.1038/s41598-018-24905-y
[17]
Chattopadhyay, S. and Sen, G.C. (2014) dsRNA-Activation of TLR3 and RLR Signaling: Gene Induction-Dependent and Independent Effects. JournalofInterferon&CytokineResearch, 34, 427-436. https://doi.org/10.1089/jir.2014.0034
[18]
Kunyk, D., Plotnikova, M., Bespalov, M., Shevyrev, D., Klotchenko, S., Ivanov, R., et al. (2025) The Interplay between Therapeutic Self-Amplifying RNA and the Innate Immune System: Balancing Efficiency and Reactogenicity. InternationalJournalofMolecularSciences, 26, Article No. 8986. https://doi.org/10.3390/ijms26188986
[19]
Blakney, A.K., Ip, S. and Geall, A.J. (2021) An Update on Self-Amplifying mRNA Vaccine Development. Vaccines, 9, Article No. 97. https://doi.org/10.3390/vaccines9020097
[20]
Swiecki, M., McCartney, S.A., Wang, Y. and Colonna, M. (2011) TLR7/9 versus TLR3/MDA5 Signaling during Virus Infections and Diabetes. JournalofLeukocyteBiology, 90, 691-701. https://doi.org/10.1189/jlb.0311166
[21]
Wang, F., Wang, L., Zou, X., Duan, S., Li, Z., Deng, Z., et al. (2019) Advances in CRISPR-Cas Systems for RNA Targeting, Tracking and Editing. BiotechnologyAdvances, 37, 708-729. https://doi.org/10.1016/j.biotechadv.2019.03.016
[22]
Lundstrom, K. (2016) Self-Replicating RNA Viral Vectors in Vaccine Development and Gene Therapy. FutureVirology, 11, 345-356. https://doi.org/10.2217/fvl-2016-0028
[23]
Currier, R.B., Calvete, J.J., Sanz, L., Harrison, R.A., Rowley, P.D. and Wagstaff, S.C. (2012) Unusual Stability of Messenger RNA in Snake Venom Reveals Gene Expression Dynamics of Venom Replenishment. PLOSONE, 7, e41888. https://doi.org/10.1371/journal.pone.0041888
[24]
Gu, Y., Choi, J., Mutha, D., Wu, C., Ganem, N.J., Grinstaff, M.W. and Wong, W.W. (2026) Self-Amplifying RNA-Based CAR T Cell Therapy with Enhanced Duration and Multi-Genic Logic Functions. https://pmc.ncbi.nlm.nih.gov/articles/PMC12934621/
[25]
Kamat, A., Joseph, A.M., Rathour, D. and Badrinarayanan, A. (2025) Variability in Intrinsic Promoter Strength Underlies the Temporal Hierarchy of the Caulobacter SOS Response Induction. PLOSBiology, 23, e3003557. https://doi.org/10.1371/journal.pbio.3003557
[26]
Waterhouse, P.M., Wang, M. and Finnegan, E.J. (2001) Role of Short RNAs in Gene Silencing. TrendsinPlantScience, 6, 297-301. https://doi.org/10.1016/s1360-1385(01)01989-6
[27]
Federico, M. (2025) The Potential of Extracellular Vesicle-Mediated Spread of Self-Amplifying RNA and a Way to Mitigate It. InternationalJournalofMolecularSciences, 26, Article No. 5118. https://doi.org/10.3390/ijms26115118
[28]
Beissert, T., Koste, L., Perkovic, M., Walzer, K.C., Erbar, S., Selmi, A., et al. (2017) Improvement of inVivo Expression of Genes Delivered by Self-Amplifying RNA Using Vaccinia Virus Immune Evasion Proteins. HumanGeneTherapy, 28, 1138-1146. https://doi.org/10.1089/hum.2017.121
[29]
Curcio, J.S.d., Silva, L.d.C., Novaes, E. and Silveira-Lacerda, E.d.P. (2026) Differential Expression of miRNAs in Vero Cells after Mayaro Virus Infection. MemóriasdoInstitutoOswaldoCruz, 121, e250177. https://doi.org/10.1590/0074-02760250177
[30]
Aufiero, S., Reckman, Y.J., Pinto, Y.M. and Creemers, E.E. (2019) Circular RNAs Open a New Chapter in Cardiovascular Biology. NatureReviewsCardiology, 16, 503-514. https://doi.org/10.1038/s41569-019-0185-2
[31]
Ying, H., Zaks, T.Z., Wang, R., Irvine, K.R., Kammula, U.S., Marincola, F.M., et al. (1999) Cancer Therapy Using a Self-Replicating RNA Vaccine. NatureMedicine, 5, 823-827. https://doi.org/10.1038/10548
[32]
Han, D., Zhang, B., Wang, Z. and Mi, Y. (2025) Cell-Autonomous Immunity: From Cytosolic Sensing to Self-Defense. InternationalJournalofMolecularSciences, 26, Article No. 4025. https://doi.org/10.3390/ijms26094025
[33]
Chan, Y.K. and Gack, M.U. (2016) Viral Evasion of Intracellular DNA and RNA Sensing. NatureReviewsMicrobiology, 14, 360-373. https://doi.org/10.1038/nrmicro.2016.45
[34]
Opyrchal, M., Anderson, J.R., Sokoloski, K.J., Wilusz, C.J. and Wilusz, J. (2005) A Cell-Free mRNA Stability Assay Reveals Conservation of the Enzymes and Mechanisms of mRNA Decay between Mosquito and Mammalian Cell Lines. InsectBiochemistryandMolecularBiology, 35, 1321-1334. https://doi.org/10.1016/j.ibmb.2005.08.004
[35]
Mata, J., Marguerat, S. and B?hler, J. (2005) Post-Transcriptional Control of Gene Expression: A Genome-Wide Perspective. TrendsinBiochemicalSciences, 30, 506-514. https://doi.org/10.1016/j.tibs.2005.07.005
[36]
Ma?dziarz, M.A., Krawczyk, K., Lepiarczyk, E., Paukszto, ?., Makowczenko, K.G., Moczulska, B., et al. (2025) Poly(A) Tail Dynamics, Non-Adenine Incorporation and Alternative Polyadenylation Shape the Host Transcriptome in COVID-19 Pathogenesis. ScientificReports, 15, Article No. 37986. https://doi.org/10.1038/s41598-025-21969-5
[37]
Gaglia, M.M. and Glaunsinger, B.A. (2010) Viruses and the Cellular RNA Decay Machinery. WIREsRNA, 1, 47-59. https://doi.org/10.1002/wrna.3
[38]
White, E.J.F., Brewer, G. and Wilson, G.M. (2013) Post-Transcriptional Control of Gene Expression by AUF1: Mechanisms, Physiological Targets, and Regulation. BiochimicaetBiophysicaActa (BBA)—GeneRegulatoryMechanisms, 1829, 680-688. https://doi.org/10.1016/j.bbagrm.2012.12.002
[39]
Serdyuk, A. and Allers, T. (2025) DNA Replication in Time and Space: The Archaeal Dimension. DNA, 5, Article No. 24. https://doi.org/10.3390/dna5020024
[40]
Loan Young, T., Chang Wang, K., James Varley, A. and Li, B. (2023) Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development. AdvancedDrugDeliveryReviews, 197, Article ID: 114826. https://doi.org/10.1016/j.addr.2023.114826
[41]
Della Santina, C.M., Ploessl, D.S., Lindsay-Mosher, N., et al. (2025) Self-Amplifying RNA Enables Rapid, Durable, Integration-Free Programming of hiPSCs. https://doi.org/10.1101/2025.10.24.684179
[42]
Roux, C., Etienne, T.A., Hajnsdorf, E., Ropers, D., Carpousis, A.J., Cocaign-Bousquet, M., et al. (2022) The Essential Role of mRNA Degradation in Understanding and Engineering E. coli Metabolism. BiotechnologyAdvances, 54, Article ID: 107805. https://doi.org/10.1016/j.biotechadv.2021.107805