Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses

A rough phylogenetic tree of the Genus beta of the Coronaviridae with the main subgenus species (for more details, see Supplemental Fig. S1A). The consensus sequences derived here for the first 80 nt of the 5′ leader are shown on each branch, with the SL1 nomenclature indicated on the right. The color code is the same as in the alignments (green, SL2; yellow and cyan, SL3). TRS sequences are in bold. In italics are shown potential alternative pairings. In red are shown nucleotides that vary between types I, II, and III in the 5′ segment upstream of SL2.