Fig 4.

Base pairings between the inter-stem-loop and partnering domains for 10 betacoronaviruses. (A) Alignment of the inter-stem-loop domains for MHV-like, HCoV-HKU1, and BCoV-like betacoronaviruses. Shading identifies bases that are in common with MHV-A59. The inter-stem-loop domains are identified with a hatched box. (B) Base pairings as predicted by Mfold. Shaded areas identify regions of base pairing common to the whole group. Underlined bases within the shaded areas are variant bases relative to those in MHV-A59 that maintain base pairing at the same position. Note that the number of base pairings within the inter-stem-loop domain for any given virus ranges from 25 to 27. (C) Potential 5′-end-proximal long-range RNA-RNA interaction derived by Mfold analysis of the 5′ region of the SCoV-Tor2 genome. This folding prediction is identical to that named for stem-loop 5 by Chen and Olsthoorn (10). The AUG start codon for the Nsp1 coding region is identified with a hatched box.