Fig. 1

Modified carboxyl-termini of ORF8 protein predicted to be encoded by 5′-UTR sequence insertions in SARS-CoV-2. A. The largest 5′-UTR segment that was duplicated and translocated as an insertion to the carboxyl terminus of ORF8 is shown at the nucleotide and amino acid levels (latter underlined). All translocated 5′-UTR nucleotide sequence segments include TRS-L (dark blue box) with variable extents of SL3 (blue) and SL2 (red). Examples are shown, and corresponding similar sequences in GenBank as of February 20, 2022, are listed in the Additional file 1: legend to Fig. S1. The C-terminus of ORF8 in the Wuhan reference strain is depicted using orange letters with mutations in ochre; the asterisks over the C-terminus sequence designate residues contributing to the covalent dimer interface (Arg115, Asp119, Phe120, Iso121; [80]). The 5′-UTR insertions are shown as underlined letters in black with mutations, deletions, and insertions within them highlighted in green. B. Secondary structures of ORF8 RNA in reference strain and in that with longest 5′-UTR sequence intragenomic rearrangement. Nucleotide and amino acid sequences of the carboxyl termini of ORF8 from Wuhan reference (NC_0445512) and from isolate QUP34336 (USA/Minnesota, 2021-04-05) with the longest 5′-UTR sequence. ORF8 protein from the latter has modified carboxyl terminus and is therefore designated ORF8x. Amino acid sequence from the reference strain is highlighted in yellow while that encoded by the duplicated and translocated 5′-UTR segment is highlighted in green. Stop codon of ORF8 protein is depicted with a red asterisk, and initiation codon of N is in green letters. TRS-B core sequence and complementary TRS-Bs in ORF8 and in ORF8x are highlighted in blue; and the uridine/adenosine tracks, including the torovirus-like attenuation sequence [56] are highlighted in fuchsia. 5′-UTR nucleotide and predicted translated amino acid sequences in ORF8X are in bold letters and highlighted in green