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

TABLE 3 | Genomic sequence sizes, IRs frequencies and total counts. Seq (total number of sequences), Median (median length of sequences), Short (shortest sequence), Long (longest sequence), GC% (mean GC content), IRs (total number of predicted IRs), Mean f (mean frequency of predicted IRs per 1,000 nt), Min f (lowest frequency of predicted IRs per 1,000 nt), and Max f (highest frequency of predicted PQS per 1,000 nt) are shown for all 109 Nidovirales sequences, families, host groups, and for SARS-CoV-2 alone. This is a provisional file, not the final typeset article A summary of all IRs found in ranges of different IR sizes and precomputed IR frequencies per 1,000 nt is shown in Table 4 . Although generally the frequency of IR presence decreases with the IR length, there are notable differences between groups and also between viruses with different hosts. The most as well as longest IRs occur in the Coronaviridae group and in viruses having humans as a host. IRs 12 bp long and longer are very rare in the Ronidovirineae group. The relationship between IRs length and stability of resulting secondary structure is not simple. While some authors believe that longer IRs are more stable, others suggest that there is an energy optimum defined by arm and spacer length (Sinden et al., 1991; Brázda et al., 2016; Georgakopoulos-Soares et al., 2018) . Differences in IR frequency according to annotated loci are shown in Figure 5 . The most notable enrichment of IRs was found inside 5′UTR for IRs of size 12+ nt, and this is the most frequently occurring location of 12+ IRs in Nidovirales genomes. Noteworthy is that there are no 12+ IRs around 5′UTR loci, but there is an abundance of IRs 10+ nt long in these locations. The 5′UTR are abundant for 12+ IR, but there are no 12+ IRs within 3′UTR. This points to functional relevance of these IRs in viral genomes.