Multiple shRNA combinations for near-complete coverage of all HIV-1 strains

Table 2 Percentage conservations for the combinations

		229 sequences				995 sequences				127 sequences				549 sequences
		Clade B ^d				Others ^e				Clade B (LTR) ^f				Others (LTR) ^g
# ^a	Combin.^c	4+	5+	6+	7+	4+	5+	6+	7+	4+	5+	6+	7+	4+	5+	6+	7+
5.1	3.4.7.2.9	89	48	-	-	54	15	-	-	91	53	-	-	58	15	-	-
5.2 ^b	3.4.7.2.0	n/a	n/a	-	-	n/a	n/a	-	-	94	57	-	-	57	23	-	-
5.3	3.8.9.2.7	92	49	-	-	40	13	-	-	94	54	-	-	41	15	-	-
5.4 ^b	3.8.5.9.0	n/a	n/a	-	-	n/a	n/a	-	-	95	64	-	-	58	20	-	-
5.5	3.8.5.2.9	92	53	-	-	48	12	-	-	94	59	-	-	54	13	-	-
5.6 ^b	3.8.5.2.1	n/a	n/a	-	-	n/a	n/a	-	-	97	65	-	-	53	10	-	-
6.2 ^b	3.4.7.2.0.5	n/a	n/a	n/a	-	n/a	n/a	n/a	-	100	89	51	-	81	50	15	-
6.3	3.8.9.2.7.6	100	86	46	-	65	26	4	-	99	89	49	-	67	23	3	-
6.4 ^b	3.8.5.9.0.6	n/a	n/a	n/a	-	n/a	n/a	n/a	-	100	88	60	-	75	38	5	-
6.5 ^b	3.8.5.2.9.0	n/a	n/a	n/a	-	n/a	n/a	n/a	-	99	94	58	-	80	45	13	-
6.6	3.8.5.2.9.7	99	87	43	-	68	31	9	-	98	92	47	-	73	34	10	-
6.7 ^b	3.8.5.2.1.7	n/a	n/a	n/a	-	n/a	n/a	n/a	-	100	94	53	-	75	30	7	-
6.8 ^b	3.4.7.2.0.6	n/a	n/a	n/a	-	n/a	n/a	n/a	-	99	88	52	-	77	40	5	-
6.9	3.4.7.2.9.5	98	84	43	-	75	45	9	-	98	87	47	-	79	50	10	-
7.3 ^b	3.8.9.2.7.6.0	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	100	98	89	48	87	57	22	3
7.5	3.8.5.2.9.7.6	100	99	81	41	84	56	18	3	100	98	84	44	85	58	17	2
7.7	3.4.7.2.9.5.6	100	96	80	40	86	64	31	3	100	94	83	43	86	64	34	2

^a Combination reference number (#) used in this study.
^b As these combinations contained an LTR shRNA (0 or 1) the intersecting conservations calculated on all sequences (where a large number lacked LTR sequence coverage), were not applicable (n/a); only the LTR containing subset were used, as shown.
^c The component shRNAs (in order of arrangement) for each combination.
^d The clade B sequences only.
^e The sequences of all other clades (excluding clade B).
^f The subset of clade B sequences that contain LTR sequence coverage.
^g The subset of all other sequences (non B) that contain LTR sequence coverage.

ISSN: 1742-6405