Molecular clock of HIV-1 envelope genes under early immune selection

Retrovirology

Table 1 The rate of HIV-1 envelope gene sequence diversification with standard errors during the 150 days from the first sample in 15 subjects whose sequence data come from references [27, 30–32]

Subject	Rate of linear diversification with standard errors (× 10⁻⁵ per base per day)	p-value	p-value for departure from the linear neutral rate^a	Rate of diversification in selection sites (× 10⁻⁵ per base per day)	Rate of diversification in non-selection sites (× 10⁻⁵ per base per day)
CAP045	3.24 ± 0.56	<0.0001	0.073	8.74 ± 57.8	3.04 ± 0.50
CH040	1.54 ± 0.39	0.0013	0.13	47.3 ± 35.9	1.16 ± 0.35
CH042	1.96 ± 0.61	0.0061	0.74	28.2 ± 65.8	1.48 ± 0.55
CH058	2.91 ± 0.51	<0.0001	0.16	633.9 ± 50.6	2.03 ± 0.46
CH077	3.91 ± 0.42	<0.0001	0.00097	91.2 ± 39.8	3.09 ± 0.38
CH131	2.21 ± 0.38	<0.0001	0.90	27.1 ± 35.6	1.80 ± 0.34
CH159	2.57 ± 0.42	<0.0001	0.34	22.2 ± 39.4	2.21 ± 0.37
CH162	2.46 ± 0.53	0.0004	0.57	78.0 ± 53.2	1.89 ± 0.47
CH164	2.26 ± 0.64	0.0033	0.88	43.4 ± 71.9	1.83 ± 0.58
CH185	1.86 ± 0.57	0.0053	0.61	47.2 ± 59.0	1.51 ± 0.51
CH198	3.57 ± 0.62	<0.0001	0.039	50.4 ± 68.4	3.09 ± 0.56
CH256	3.58 ± 0.58	<0.0001	0.028	57.3 ± 61.0	2.77 ± 0.52
CH505	2.30 ± 0.27	<0.0001	0.60	45.4 ± 23.7	1.57 ± 0.24
SUMA0874	2.85 ± 0.78	0.0027	0.39	706.8 ± 109.8	2.17 ± 0.70
WEAU0578	3.17 ± 0.79	0.0013	0.22	190.8 ± 113.8	2.39 ± 0.71
Population mean	2.69 ± 0.29	N/A	N/A	138.5 ± 61.7	2.13 ± 0.26

^aLess than 0.05 implies a statistically significant deviation from the neutral evolution rate, 2.16 × 10⁻⁵ per site per day

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