Table 3.

Significantly correlated pairs of HIV-1 Gag mutations with protease major or accessory resistance mutations.

Class	Gag mutations	Frequency (%)a	Covariated mutations	Frequency (%)b	Covariation frequency (%)	phi	p-valued
I	L449F	8 (5.59)	L10F	6 (4.19)	2 (25.00)	0.25	3.69E−02
			V32I	3 (2.09)	2 (25.00)	0.38	8.04E−03
			M46I	22 (15.38)	4 (50.00)	− 0.07	1.98E−02
			I54V	11 (7.69)	3 (37.5)	0.27	1.55E−02
			L90M	4 (2.79)	2 (25.00)	0.32	1.56E−02
	Y484P	10 (6.99)	K20T	4 (2.79)	2 (20.00)	0.28	2.46E−02
			L33F	9 (6.29)	3 (30.00)	0.26	1.68E−02
			I54V	11 (7.69)	4 (40.00)	0.33	3.23E−03
			V82A	9 (6.29)	3 (30.00)	0.26	1.68E−02
			L89V	8 (5.59)	3 (30.00)	0.29	1.16E−02
II	I479G	22 (15.38)	I64M	19 (13.28)	7 (31.81)	− 0.09	1.18E−02
	D480E	36 (25.17)	V82A	9 (6.29)	5 (13.88)	0.18	4.47E−02
III	P453L	22 (15.38)	L10F	6 (4.19)	3 (13.63)	0.20	4.68E−02
			L33F	9 (6.29)	5 (22.72)	0.28	4.62E−03
			M46I	22 (15.38)	9 (40.90)	0.30	1.35E−03
			I54L	2 (1.39)	2 (9.10)	0.27	2.28E−02
			I54V	11 (7.69)	7 (31.81)	0.38	1.79E−04
			Q58E	6 (4.19)	3 (13.63)	0.20	4.68E−02
			V82A	9 (6.29)	4 (18.18)	0.20	3.19E−02
			V82T	2 (1.39)	2 (9.10)	0.27	2.28E−02
			I84V	11 (7.69)	7 (31.81)	0.38	1.79E−04
			L89V	8 (5.59)	5 (22.72)	0.31	2.29E−03
	S465F	24 (16.78)	I54V	11 (7.69)	5 (20.83)	0.22	2.03E−02
			V82A	9 (6.29)	4 (16.67)	0.19	4.35E−02
	Q474P	99 (69.23)	M46I	22 (15.38)	11 (11.11)	− 0.03	4.46E−02
	E482G	74 (51.74)	I54V	11 (7.69)	2 (2.70)	− 0.19	2.71E−02
	T487A	52 (36.36)	M46I	22 (15.38)	3 (5.76)	− 0.21	1.64E−02

^aThe frequency was determined in 143 isolates from PI/r-treated patients.

^bPercentages were calculated for patients containing each specific mutation.

^cAll P values for covariation were significant at a false discovery rate of 0.05. Mutations in bold represents major protease resistance mutations.