sgRNAs: A SARS-CoV-2 emerging issue

Abstract

sgRNAs: A SARS-CoV-2 emerging issue Antonio Mori 1, Denise Lavezzari 1, Elena Pomari, Michela Deiana, Chiara Piubelli, Maria Rosaria Capobianchi *, Concetta Castilletti Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024, Verona, Italy A R T I C L E I N F O Handling Editor: Prof A Angelo Azzi Keywords: sgRNAs SARS-CoV2 Bioinformatics Next-generation sequencing Viruses Coronavirus A B S T R A C T 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 (csgRNA) 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 ncsgRNAs, and for the possible use of sgRNAs as potential markers of virus replicative activity in infected patients.