sgRNAs: A SARS-CoV-2 emerging issue

Abstract

Like for other coronaviruses, SARS-CoV-2 gene expression strategy is based on the synthesis of a nested set of subgenomic mRNA species (sgRNAs). These sgRNA are synthesized using a "discontinuous transcription" mechanism that relies on template switching at Transcription Regulatory Sequences (TRS). Both canonical (c-sgRNA) and non-canonical (nc-sgRNA, less numerous) subgenomic RNA species can be produced. Currently, sgRNAs are investigated on the basis of sequence data obtained through next generation sequencing (NGS), and bioinformatic tools are crucial for their identification, characterization and quantification. To date, few software have been developed to this aim, whose reliability and applicability to all the available NGS platforms need to be established, to build confidence on the information resulting from such tools. In fact, these information may be crucial for the in depth elucidation of viral expression strategy, particularly in respect of the significance of nc-sgRNAs, and for the possible use of sgRNAs as potential markers of virus replicative activity in infected patients.

Keywords: Bioinformatics; Coronavirus; Next-generation sequencing; SARS-CoV2; Viruses; sgRNAs.

Fig. 1

Transcription mechanisms that lead to the generation of sgRNAs in the replication cycle of coronaviruses. A: the structure of the SARS-CoV-2 genome, along with the location of Transcript Regulatory Sequences (TRS). B: the discontinuous transcription of ORF N, where the replicase-transcriptase complex (RTC) generates a negative RNA molecule until a TRS-B is reached. At this point, the RNA template forms a hairpin structure and the RTC switches to the TRS-L template and proceeds until the 5′ UTR, omitting the transcription of the hairpin content. As a result, the neo-synthesized antisense RNA sequences lack parts of the positive RNA template, resulting in sgRNAs. C: the various types of discontinuous viral genome transcription (negative RNA synthesis), including those caused by concomitant involvement of TRS-L and TRS-B (TRS-L – TRS-B interactions, red lines), by only TRS-L involvement (TRS-B independent, green lines), and by neither of them (non-TRS dependent, purple lines). The TRS-B independent transcription generates the complete negative RNA copies of the genomic RNA template that are used to produce the genomic RNA progeny. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)