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

Novel human coronavirus SARS-CoV-2 has relatively high IR frequency per 1,000 nt, in comparison with other Nidovirales. To test if the frequency of IRs per 1,000 nt in SARS-CoV-2 is significantly greater than in random sequence, we generated 10 random sequences with length and GC content the same as in SARS-CoV-2. The mean frequency of IRs per 1,000 nt was 30.23, with standard deviation 0.22. We applied Wilcoxon signed-rank test with continuity correction to find that p-value was equal to 0.0029. Thus, the IR frequency per 1,000 nt in SARS-CoV-2 (40.23) is significantly higher than expected. When we inspected differences of IR frequencies according to hosts, we found the highest mean IR frequency per 1,000 nt to be in Nidovirales infecting Humans (38.13), then in Vertebrates (34.25), and the lowest mean frequency is in Invertebrates (31.77).