Fig. 4

A. Insertions of a 5′-UTR sequence into two sites within the nucleotide segment encoding the Nidovirus RdRp associated nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (nsp12) of SARS-CoV-2. Examples of isolates with 5′-UTR sequences at the proximal and distal sites are provided in the figure and a full listing is provided in the Additional file 1: legend to Fig. S4, as is a listing of variants with single amino acid changes relative to the Wuhan reference strain in the segment corresponding to the insertion. The Wuhan reference strain sequence corresponding to the insertion areas is the most abundant among SARS-CoV-2 isolates. The nsp12-nsp9 interface regions are shown with yellow bars and key residues therein with ochre letters, while the contact regions with GDP are indicated with blue boxes and key residues therein in ochre. B. Secondary structures for RNAs in the proximal sites in nsp12 and nsp12x. Color scheme is as in previous figures. The site for -1 frameshifting is also highlighted