Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups

Table 1 Likelihood values and parameter estimates for 45 S gene sequences from the whole epidemic of SARS from 2002 to 2004.

Model code	lnL	d_N/d_S	Estimates of parameters	2Δl	Positively selected sites
M0 (one-ratio)	-5818.14	0.64	ω = 0.64	51.91	None
M3 (discrete)	-5792.19	0.69	p₀ = 0.43340, p₁ = 0.50712 (p₂ = 0.05948), ω₀ = 0.12, ω₁ = 0.13, ω₂ = 9.68	(13.28)	75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E
M1a (NearlyNeutral)	-5807.78	0.36	p₀ = 0.63944 (p₁ = 0.36056)	31.25	Not allowed
M2a (PositiveSelection)	-5792.16	0.69	p₀ = 0.78594, p₁ = 0.16251 (p₂ = 0.05155), ω₂ = 10.29	(9.21)	75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E
M7 (beta)	-5807.92	0.40	p = 0.00568, q = 0.00856	31.51	Not allowed
M8 (beta&v)	-5792.16	0.69	p₀ = 0.94614 (p₁ = 0.05386) p = 0.05787, q = 0.30879, ω = 10.11	(9.21)	75T 239S 244T 311G 479R 609L 613E 743R 765V 778D 1148L 1163E

The values in parentheses represent the significant level of 0.01 with a χ²distribution at d.f. = 4 (M0 vs. M3) or 2 (M1a vs. M2a and M7 vs. M8). The amino acid sequence of strain PC4-13 was used as the sequence reference, and positive selected sites were identified with posterior probability p ≥ 0.9. In boldface, p ≥ 0.95.

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