Fig. 8

Intragenomic rearrangement in nsp2 of rodent alphacoronaviruses subgenus Luchacovirus, N of bat alphacoronaviruses subgenus Nyctacovirus (A) and ORF5b or ORF4b of bat alphacoronaviruses subgenus Decacovirus. Nucleotide and amino acid sequences of intragenomic rearrangements are shown. 5′-UTR sequence (negative strand) is highlighted in green. Conservative amino acid substitutions are highlighted in blue while non-conservative ones are highlighted in red. For the intragenomic rearrangement in nsp2 of rodent alphacoronaviruses subgenus Luchacovirus, two examples of isolates (listed by rodent of origin) with nsp2 nucleotide sequences up to 75% similar to the 5′-UTR sequences are shown. There appears to be a temporal gradient with the most similar sequence (99%) in isolate KX964649 (China, 2011-10) to the least similar (59%) in isolate OK655840 (USA, 2018). The temporal gradient holds within animals from the same genus, which would suggest that the translocated sequence is the oldest and the rest reflect more recent mutations. For the predicted secondary structures of the RNAs corresponding to the intragenomic rearrangement and adjacent sequences, the minimum free energy increases among variants from those with the most to those with the least similar sequence to the 5′-UTR insertion (Additional file 1: Fig. S3). Color scheme is as in previous figures