Table 2.

Genomic analysis of CpG-recoded ZIKV variants.

Genome region	Sequence	G+C content, %	GC3, %	ENca	CAIb	CPBc (human)
E	Wild-type	49.8	53.0	52.7	0.756	0.032
	Permuted	49.8	53.0	53.9	0.759	0.020
	E+32CpG	49.9	52.6	54.6	0.728	−0.022
	E+102CpG	49.9	50.6	48.4	0.639	−0.132
	E/NS1+176CpG	49.9	50.6	48.4	0.639	−0.132
NS1	Wild-type	50.1	53.4	51.5	0.784	0.001
	Permuted	50.1	53.4	51.5	0.784	0.001
	E+32CpG	50.1	53.4	51.5	0.784	0.001
	E+102CpG	50.1	53.4	51.5	0.784	0.001
	E/NS1+176CpG	50.8	51.1	51.5	0.705	−0.193
ORFd	Wild-type	51.1	55.1	53.4	0.755	0.021
	Permuted	51.1	55.1	53.6	0.755	0.019
	E+32CpG	51.1	55.0	53.9	0.751	0.013
	E+102CpG	51.1	54.7	55.4	0.736	−0.003
	E/NS1+176CpG	51.2	54.5	56.3	0.728	−0.023

^aENc—Effective Number of Codons (49).

^bCAI—Codon Adaptation Index (50).

^cCodon pair bias was calculated using codon pair scores from Kunec and Osterrider (7).

^dORF, open reading frame.