Molecular evolution of two asymptomatic echovirus 6 strains that constitute a novel branch of recently epidemic echovirus 6 in China

Table 2 Log-likelihood values and parameter estimates for genes which showed increased ω on the nonpathogenic KM branch

Genes	Model^a	ℓ	Parameter estimates^b	Sites with ω2a changed on the KM branch^c
2C	H0	−6933.9	p0 = 0.88, p1 = 0.01, p2a = 0.11, p2b = 0.00	260 V, 307 L, 312 T, 319I, 321R
			Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00
			Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00
	H1	−6933.9	p0 = 0.88, p1 = 0.01, p2a = 0.11, p2b = 0.00
			Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00
			Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00
3AB	H0	−2348.1	p0 = 0.52, p1 = 0.01, p2a = 0.47, p2b = 0.00	15D, 16 T, 29 L, 41 K, 55D
			Background: ω0 = 0.02, ω1 = 1.00, ω2a = 0.02, ω2b = 1.00
			Foreground: ω0 = 0.02, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00
	H1	−2348.1	p0 = 0.52, p1 = 0.01, p2a = 0.47, p2b = 0.00
			Background: ω0 = 0.02, ω1 = 1.00, ω2a = 0.02, ω2b = 1.00
			Foreground: ω0 = 0.02, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00
3C	H0	−3919.5	p0 = 0.85, p1 = 0.01, p2a = 0.15, p2b = 0.00	3P, 16G, 52H, 84 M, 98S
			Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00
			Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00
	H1	−3919.2	p0 = 0.93, p1 = 0.01, p2a = 0.06, p2b = 0.00
			Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00
			Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 3.31, ω2b = 3.31

^aH1 assumed there was positive selection at only some sites on the foreground branch (nonpathogenic branch), and H0 was its null model
^b ω is the ratio of nonsynonymous-synonymous substitutions (d _N/d _S) of sites, and p corresponded to their proportions. These parameters were set according to the branch-site model in the PAML software
^cThe mutations written in bold were only found in the KM branch, and these mutations were named in reference to K727. The amino acid positions are counted separately for each gene

ISSN: 1743-422X