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

All PQSs found in ranges of G4Hunter score intervals and precomputed PQS frequencies per 1,000 nt are summarized in Table 2 . The relationship between observed PQS frequency per 1,000 nucleotides and GC content in all analyzed Nidovirales sequences is depicted in Figure 3 , the Beihai Nido-like virus has both the highest GC content and highest PQS frequency. Within Nidovirales with Humans as host, however, the highest PQS frequency was found in Breda virus, which does not have the highest GC content in the dataset. This is a provisional file, not the final typeset article Figure 4 shows the differences in PQS frequency by annotated loci. We downloaded features for every virus genome and analyzed the presence of PQS in each annotated sequence and in its proximity (before and after). The most notable enrichment of PQSs was located before 3′UTR, inside 5′UTR, before mRNA, and after miscellaneous RNA. The lowest PQS frequencies were found after 3′UTR, before 5′UTR, before and inside miscellaneous RNA, and in miscellaneous features.