Nature of viruses and pandemics: Coronaviruses

Abstract

Coronaviruses (CoVs) have the largest genome among RNA viruses and store large amounts of information without genome integration as they replicate in the cell cytoplasm. The replication of the virus is a continuous process, whereas the transcription of the subgenomic mRNAs is a discontinuous one, involving a template switch, which resembles a high frequency recombination mechanism that may favor virus genome variability. The origin of the three deadly human CoVs SARS-CoV, MERS-CoV and SARS-CoV-2 are zoonotic events. SARS-CoV-2 has incorporated in its spike protein a furine proteolytic site that facilitates the activation of the virus in any tissue, making this CoV strain highly polytropic and pathogenic. Using MERS-CoV as a model, a propagation-deficient RNA replicon was generated by removing E protein gene (essential for viral morphogenesis and involved in virulence), and accessory genes 3, 4a, 4b and 5 (responsible for antagonism of the innate immune response) to attenuate the virus: MERS-CoV-Δ[3,4a,4b,5,E]. This RNA replicon is strongly attenuated and elicits sterilizing protection after a single immunization in transgenic mice with the receptor for MERS-CoV, making it a promising vaccine candidate for this virus and an interesting platform for vector-based vaccine development. A strategy could be developed for the design of RNA replicon vaccines for other human pathogenic coronaviruses.

Keywords: Coronavirus; MERS-CoV; RNA replicon; SARS-CoV-2; Transcription; Vaccine.

Graphical abstract

Fig. 1

CoV genome. Genome organization of the three highly pathogenic human CoVs: SARS-CoV, MERS-CoV and SARS-CoV-2. The letters above the boxes indicate the viral genes. Leader sequence (L), replicase genes (ORF1a, ORF1b), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes. Accessory genes are indicated by numbers and are different for each CoV. An, poly A sequence.

Fig. 2

CoV RNA synthesis. (A) Upper panel represents the MERS-CoV genome as in Fig. 1. During infection, the viral polymerase produces a series of viral RNAs (lower panel), of positive (+) polarity and other complementary RNAs of negative (−) polarity. The dark blue line indicates the portion of the gRNA or mRNA that is translated. Numbers and letter in the right indicated the viral proteins translated from each viral mRNA. (B) CoV transcription. The coding gRNA of positive polarity is shown as a dark blue line, in which leader sequence (red) and TRSs from leader (TRS-L) and body (TRS-B) are indicated, highlighting the core sequences in each case (yellow). The negative polarity RNA is shown as a light blue line, were complementary sequences (cL, cTRS-B and cCS-B) are indicated. RNA-RNA and RNA-protein interactions (represented by the RNA folding and grey ovals, respectively) control the template switch (red arrow). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Human CoVs origin. The three pathogenic human CoVs, SARS-CoV, MERS-CoV and SARS-CoV-2 were derived from natural reservoirs in bats (black), using intermediate hosts (orange) before jumping to humans (blue). Wild and domestic animals (grey) can be infected by SARS-CoV-2 or its variants, with possibility of virus circulating and adapting to these animal species, and posing the thread of creating novel virus reservoirs from which the virus could emerge to infect humans (dashed lines). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

VLPs containing CoV-derived RNA replicons. (A) RNA replicon is introduced in packaging cell lines, providing the missing proteins (protein X) required for VLP formation. Then cells produce VLPs encapsulating the RNA replicon. (B) Upper panel: when cells are infected with WT virus, membrane vesicles containing virions were observed (EM image) and progeny viruses were produced. In contrast (lower panel), when replicon VLPs enter into the cells, some membrane rearrangements with VLPs were observed (EM image), but no infectious virus is produced.