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

We analyzed the occurrence of PQSs using G4Hunter in all 109 known genomes of Nidovirales. The length of genomes in the dataset varies from 12,704 nt (Equine arteritis virus) to 41,178 nt (Planarian secretory cell nidovirus). The mean GC content is 42.15%, the minimum is 27.50% for Planarian secretory cell nidovirus (Mononiviridae family), and the maximum is 57.35% for Beihai Nido-like virus 1 (Mesnidovirineae family). Using standard values for the G4Hunter algorithm (i.e., window size 25 and G4Hunter score above 1.2), we found 1,021 PQSs among all 109 Nidovirales genomes. The most abundant PQSs are those with G4Hunter scores of 1.2-1.4 (98.24% of all PQS), much less abundant are PQSs with G4Hunter scores 1.4-1.6 (1.76% of all PQS), and there were no PQSs above the 1.6 G4Hunter score threshold. In general, a higher G4Hunter score means a higher probability of G-quadruplexes forming inside the PQS (Bedrat et al., 2016) . Genomic sequence sizes, total PQS counts, and PQS frequencies characteristics are summarized in Table 1. TABLE 1 | Genomic sequence sizes, PQS frequencies, and total counts. Seq (total number of sequences), Median (median length of sequences), Short (shortest sequence), Long (longest sequence), PQS (total number of predicted PQSs), Mean f (mean frequency of predicted PQS per 1,000 nt), Min f (lowest frequency of predicted PQS per 1,000 nt), Max f (highest frequency of predicted PQS per 1,000 nt), GC% (mean GC content). Note that 132 PQSs were in Nidovirales with Undefined host.