FIG 1.

Generation of codon pair-optimized (CPO) rRSVs. (A) Gene maps of the CPO rRSVs Max A, Max B, Max L, and Max FLC. The wt and CPO ORFs are shown as gray and black boxes, respectively. Restriction sites used for the constructions are indicated. The red bar in the L ORF indicates the positions of the Δ1313 codon deletion and I1314L missense mutations. For simplicity, “Δ1313/I1314L” was not included in the names of the CPO viruses. (B) Codon pair bias (CPB) values plotted against ORF lengths in codons, shown for wt RSV ORFs (red circles), CPO RSV ORFs (blue circles), and a set of 14,795 National Center for Biotechnology Information (NCBI)-annotated human protein-coding sequences (Consensus Coding Sequence [CCDS] database published March 2005) (open circles). As described previously (1, 6), the CPB score for each ORF is the mean of the codon pair scores (CPSs) for all of its codon pairs. In turn, the CPS for each codon pair is the natural log of the ratio of the observed versus expected frequency of that codon pair in the human ORFeome. (C) Total numbers of CpG and UpA dinucleotides in the wt and CPO viral genomes.