Self-Amplifying RNA: A Second Revolution of mRNA Vaccines against COVID-19

Abstract

SARS-CoV-2 virus, the causative agent of COVID-19, has produced the largest pandemic in the 21st century, becoming a very serious health problem worldwide. To prevent COVID-19 disease and infection, a large number of vaccines have been developed and approved in record time, including new vaccines based on mRNA encapsulated in lipid nanoparticles. While mRNA-based vaccines have proven to be safe and effective, they are more expensive to produce compared to conventional vaccines. A special type of mRNA vaccine is based on self-amplifying RNA (saRNA) derived from the genome of RNA viruses, mainly alphaviruses. These saRNAs encode a viral replicase in addition to the antigen, usually the SARS-CoV-2 spike protein. The replicase can amplify the saRNA in transfected cells, potentially reducing the amount of RNA needed for vaccination and promoting interferon I responses that can enhance adaptive immunity. Preclinical studies with saRNA-based COVID-19 vaccines in diverse animal models have demonstrated the induction of robust protective immune responses, similar to conventional mRNA but at lower doses. Initial clinical trials have confirmed the safety and immunogenicity of saRNA-based vaccines in individuals that had previously received authorized COVID-19 vaccines. These findings have led to the recent approval of two of these vaccines by the national drug agencies of India and Japan, underscoring the promising potential of this technology.

Keywords: COVID-19 vaccines; alphavirus; clinical trials; mRNA vaccine; self-amplifying RNA.

Figure 1

Alphavirus-based self-amplifying RNA vector expressing SARS-CoV-2 antigens for vaccination. The upper diagram represents the saRNA, which is a single strand positive-sense RNA containing a 5′ methylguanylate cap structure (cap) and a 3′ polyadenylate sequence (polyA). The saRNA vector contains two open reading frames (ORFs): the first one codes for the viral replicase, containing four subunits, or non-structural proteins (nsP); the second ORF codes for the SARS-CoV-2 antigen(s). saRNA also includes sequences necessary for replication (5′and 3′ untranslated regions, UTR), a packaging signal (PS), and a subgenomic promoter (sgPr) between both ORFs. The lower left part of the figure represents the replication and expression of saRNA in transduced/transfected cells. Once the saRNA reaches the cytoplasm of a target cell, the replicase is translated from the first ORF. The replicase synthesizes the complementary negative-sense strand of the saRNA (− saRNA), which is later used by the replicase as template to generate more saRNA (+ saRNA) in a self-amplification process. In addition, the replicase can recognize the sgPr in the negative saRNA strand, synthesizing a smaller subgenomic RNA (sgRNA) of positive polarity containing the second ORF, which will be translated to produce the desired antigen (represented on the surface of the cell). With this system, high levels of expression of the vaccine antigen(s) are achieved, as well as induction of type I interferon (IFN-I) responses and apoptosis due to saRNA replication. In addition, this approach can induce specific humoral (antibodies) and cellular immune responses (CD4⁺ and CD8⁺ T cells) against SARS-CoV-2, mediated by the presentation of antigens both on the surface of transduced/transfected cells and by antigen presenting cells (APCs), which can uptake antigens from apoptotic cells (right part of lower figure).

Figure 2

Modalities to deliver saRNA vaccines. Delivery methods include nanoparticles (upper panel), biological vectors (Biologics, lower left panel), and delivery of naked RNA (Naked delivery, lower central panel). The components of each delivery vehicle are indicated in each modality, as well as the main animal models in which they have been tested (animal icons). Preclinical models include Golden Syrian Hamsters, non-human primates (NHP), and transgenic mice either expressing hACE2 or transduced with adeno-associated virus or adenoviral vectors encoding hACE2 (hACE2 mice) (lower right panel). A human icon indicates that the vaccine has also been tested in clinical trials. LNPs (lipid nanoparticles), LION (Lipid InOrganic Nanoparticle), LPR (liposome-protamine-RNA nanoparticle), NLCs (nanostructured lipid carrier), VRPs (viral replicon particles). Created with BioRender.com.