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

Genomic sequence sizes, total IR counts, and IR frequencies characteristics are summarized in Table 3 . In total, 93,369 IRs were found and the mean IRs frequency was 33.90 per 1,000 nt. The maximal IR frequency was found in Planarian secretory cell nidovirus (56.17), the species with the largest genome among Nidovirales. It has been suggested that Planarian secretory cell nidovirus diverged early The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.031252 doi: bioRxiv preprint from multi-ORF Nidovirales and acquired additional genes, including those typical of large DNA viruses or hosts (RNAse T2, Ankyrin, and Fibronectin type II), which might modulate virus-host interactions (Saberi et al., 2018) . The lowest IR frequency was noticed in Beihai Nido-like virus 1 (19.23). Noteworthy is that this is the species of Nidovirales with the highest GC content and PQS frequency. Differences in IR frequency by annotated locus are depicted in Figure 5 . By families, the highest mean IRs frequency was found in Coronaviridae (37.08) and lowest in Ronidovirineae (26.37).