In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles

Martin Bartas; Václav Brázda; Natália Bohálová; Alessio Cantara; Adriana Volná; Tereza Stachurová; Katerina Malachová; Eva B. Jagelská; Otília Porubiaková; Jirí Cerven; Petr Pecinka

Local DNA structures have been shown to play important roles in basic biological processes, including replication and transcription Travers and Muskhelishvili, 2015; Surovtsev and Jacobs-Wagner, 2018) . PQS analyses of human viruses have clearly demonstrated that these sequences are conserved also in the viral genomes (Lavezzo et al., 2018) and could be targets for antiviral therapies (Wang et al., 2015; Krafčíková et al., 2017; Ruggiero and Richter, 2018) . For example, the conserved PQS sequence present in the L gene of Zaire ebolavirus and related to its replication is inhibited by interaction with G-quadruplex ligand TMPyP4, and this finding has led to suggestions that G-quadruplex RNA stabilization could constitute a new strategy against Ebola virus disease (Wang et al., 2016) . Our results found only one PQS in the genomic sequence of SARS-CoV-2, that having an absolute (Fehr and Perlman, 2015) . It would be of great value to know whether TMPyP4 or other G-quadruplex stabilizing compounds can inhibit replication processes of SARS-CoV-2. RNA hairpins, which are formed by IRs, are basic structural elements of RNA and play crucial roles in gene expression and intermolecular recognition. Conserved palindromic RNA structures have been found in many viral genomes, including HIV-1, and play a crucial role in their replication (Liu et al., 2018) . We have found an abundance of IRs inside 5′UTR in Nidovirales genomes. In general, 5′UTR is an important locus for regulation of viral replication and gene expression. It has been demonstrated that stem integrity of phylogenetically conserved stem-loop structure located in 5′UTR of the PRRSV virus from the Arteriviridae family is crucial for viral replication and subgenomic mRNA synthesis. Similar secondary structures have been proposed for several viruses from the Arteriviridae and Coronaviridae families (Lu et al., 2011) . Our analyses of annotated features in Figure 5 therefore support this report.