Table 3.

Variation in Gag cleavage and non-cleavage sites and protease

	HIV-1 subtype	Treatment outcome	Gag cleavage sites					Gag non-cleavage sites
			MA/CA 128–137 VSQNY/ PIVQN	CA/p2 359–368 KARVL/ AEAMS	p2/NC 373–382 SATIM/ MQRGN	NC/p1 428–437 ERQAN/ FLGKI	p1/p6 444–453 RPGNF/ LQSRP
Pair 1	CRF02_AG	success	-----/-----	-----/-----	-+N--/-----	-----/-----	-----/P----	E12K, R76K, R79F, H219Q, T242N, R409K, T487S
		failure	-----/-----	-----/-----	T +N--/-----	-----/-----	-----/P----	R76K, R79F, T81A, G248A, V370A, R409K, E468K, T487S
Pair 2	G	success	-----/-----	-----/-----	A-A--/-----	-----/----L	-----/--N--	E12K, R76K, R79F, G123E, H219Q, G248A, V370A, R409K, T487S
		failure	-----/-----	-----/-----	---+-/---S-	-----/-----	-----/--N-L	E12K, G62R, R76K, H219Q, V370A, R409K, T487S
Pair 3	G	success	-----/-----	-----/-----	--A--/--KS-	-----/-----	-----/--N-L	E12K, G62R, R76K, H219Q, T242N, G248A, V370A, R409K, T487S
		failure	-----/-----	-----/-----	-+NV-/--K--	-----/-----	-----/P----	E12K, R76K, R79F, H219Q, T242N, V370A, T371del, R409K, T456S, T487S
Pair 4	CRF02_AG	success	+----/-----	-----/-----	T+NV-/--K--	-----/-----	-----/P----	R76K, R409K, T487S
		failure	+----/-----	-----/-----	-+NV-/-K--	-----/-----	-----/P----	E12K, R76K, R79F, G248A, V370A, R409K, T487S
Pair 5	G	success	-----/-----	-----/-----	A-A--/-----	-----/---R-	-----/-----	E12K, R76K, R79F, G123E, V370A, R409K, T487S
		failure	+---F/-----	-----/-----	QPN--/I----	-----/----V	-----/P----	E12K, R76K, R79F, S165N, H219Q, V370A, R409K, T487S
Pair 6	CRF02_AG	success	S----/-----	---I-/-----	ANI--/-----	-----/-----	-----/P----	E12K, R76K, R79F, V370A, R409K, T487S
		failure	+----/-----	-----/-----	T+NV-/--K--	-----/-----	-----/P----	E12K, G248A, V370A, R409K, S451T, T487S

The consensus clonal sequence at each of the Gag cleavage sites is shown for the six pairs using HXB2 numbering. Deletions are represented by +.