An inter-genotypically conserved RNA secondary structure models of the 5'-proximal genomic region of PRRSV, based on the consensus sequences generated by sequence lineup (Lasergene Package). (A) Predicted RNA structure by MFold for different genotypes and chimeric sequences. (i) RNA secondary structure prediction of the consensus 5'-proximal 280 nt of type I PRRSV genome from five available type I PRRSV sequences. (ii) Predicted RNA secondary structure of the consensus 5'-proximal 246 nt generated by comparison of nine type II PRRSV genomes. Stem-loop 2 (SL2) in both models are highlighted by the dashed box. The leader TRS and start codon for ORF1a in two models are shown by gray shading and solid boxes separately. Stem-loop structures are designated as E-SL1-5 for type I PRRSV and N-SL1-5 for type II, respectively. (iii) Predicted secondary structure of the 5'-proximal 246 nt of mutant EX generated by substituting N-SL2 with E-SL2. The mutant region in EX is highlighted by solid box and lowercase. (B) Schematic drawing sequence location of type II PRRSV stem-loops, represented by black boxes. Parental (WT) N-SL2 sequence from nt 46-70 (GQ330474) was shown, based on which mutations (lowercase) were made. Dashed lines represent stem base-pair deletions in the mutant plasmids D1-D6.