Table 3. Comparison of amino acid length, number of potential N-linked glycosylation sites, V3 sequences and co-receptor usage between anti-retroviral drug-selected and control-passaged KP-1 variants.

	Passage no.	Genetic diversity*	Mean ENV1–474 length (range)†	Mean V1/V2 length (range)	Mean V3 length (range)	Mean V4 length (range)	Mean PNGs (range)	V3 region		Geno2 pheno (%)§
								Prevalence (%)	Sequence‡
Baseline	0	0.056	472 (461–480)	69 (60–74)	34 (33–34)	30 (29–31)	24 (22–28)	41.9	CTRPNNNTRKGIHIGPGKFYATGAIIGDIRQAHC	41.2
								22.6	.........................V........	41.2
								16.1	....-..I.......T.R..T.RD...N..K...	1.7
								13.0	....-..I.......T.R..T.KT...N.KK...	2.9
								3.2	....-..I..........................	7.4
								3.2	.......................D..........	55.3
Passage control	8	0.0070	463 (462–463)	62	34	29	23 (22–23)	100.0	.........................V........	41.2
RAL-selected virus	8	0.0070	480	74	34	31	28 (26–29)	100.0	..................................	41.2
3TC-selected virus	6	0.020	478 (475–480)	74	34	31 (29–31)	27 (25–28)	83.3	..................................	41.2
SQV-selected virus	11	0.0040	474	71	34	31	26	100.0	..................................	41.2
MVC-selected virus	7	0.0080	469 (468–469)	69	33	29	24 (23–24)	100.0	....-..I....R..T.R..T.KT...N.KK...	1.7

^*Overall mean distance.

^†Sequence from gp120 SP to the V5 region (aa 1–474).

^‡V3 sequences of each variant are shown. Dots denote sequence identity and dashes indicate a deletion mutation.

^§Prediction of viral co-receptor tropism using Geno2pheno based on a selectable ‘false positive rate’.