Defining the fitness of HIV-1 isolates with dual/mixed co-receptor usage

Table 1 Determination of predicted co-receptor usage in the HIV-1 isolate by 454 deep sequencing analyses

Culture	N	Plasmid	N	Plasma	N	Genotype		PSSM results			Geno2Pheno (5 %)
Culture	N	Plasmid	N	Plasma	N	11/25	Prediction	% X4	% R5	Prediction	FPR (%)	Prediction
Predicted co-receptor usage for B19 clones^a
B19 C1	4,070	B19 P1	4,102	B19 R1	2,237	S/E	CCR5	0.11	0.62	CCR5 only	33.90	CCR5
B19 C2	25					S/E	CCR5	0.11	0.59	CCR5 only	10.90	CCR5
B19 C3	5					S/E	CCR5	0	0.1	CCR5 only	55	CCR5
B19 C4	3					S/E	CCR5	0.22	0.82	CCR5 only	41.20	CCR5
		B19 P2	3			S/E	CCR5	0.22	0.89	CCR5 only	50.50	CCR5
				B19 R2	51	S/K	CXCR4	0.24	0.92	CCR5 only	7.80	CCR5
				B19 R3	13	S/E	CCR5	0.22	0.86	CCR5 only	26.90	CCR5
				B19 R4	11	S/E	CCR5	0.11	0.42	CCR5 only	72	CCR5
				B19 R5	7	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R6	7	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R7	6	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R8	6	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R9	6	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R10	5	S/E	CCR5	0.11	0.6	CCR5 only	42.30	CCR5
				B19 R11	4	S/E	CCR5	0.11	0.47	CCR5 only	18.20	CCR5
				B19 R12	4	S/E	CCR5	0.09	0.39	CCR5 only	59.80	CCR5
				B19 R13	3	S/E	CCR5	0.11	0.46	CCR5 only	47.70	CCR5
				B19 R14	3	S/K	CXCR4	0.29	0.95	CXCR4 capable	3.20	CXCR4

Plasmid	N	Culture	N	Genotype		PSSM Results			Geno2Pheno (5 %)
Plasmid	N	Culture	N	11/25	Prediction	% X4	% R5	Prediction	FPR (%)	Prediction
Predicted co-receptor usage for B12 clones^a
B12_P1	3,611	B12_C1	1,405	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
B12_P2	55	B12_C2	19	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
B12_P3	24	B12_C3	10	S/Q	CCR5	0.31	0.96	CCR5 only	20.4	CCR5
B12_P4	21	B12_C4	6	S/Q	CCR5	0.27	0.95	CCR5 only	18.80	CCR5
		B12_C5	6	S/Q	CCR5	0.33	0.96	CCR5 only	22.60	CCR5
		B12_C6	6	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
		B12_C7	5	S/Q	CCR5	0.36	0.98	CCR5 only	10.50	CCR5
		B12_C8	5	S/Q	CCR5	0.36	0.98	CCR5 only	17.10	CCR5
B12_P10	3	B12_C9	5	S/Q	CCR5	0.33	0.96	CCR5 only	20.20	CCR5
B12_P17	3	B12_C10	4	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
		B12_C11	4	S/Q	CCR5	0.47	0.98	CCR5 only	36.90	CCR5
B12_P15	3	B12_C12	3	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
		B12_C13	3	S/Q	CCR5	0.51	0.98	CCR5 only	35.60	CCR5
B12_P8	4	B12_C14	3	S/Q	CCR5	0.33	0.96	CCR5 only	49.70	CCR5
		B12_C5	3	S/Q	CCR5	0.33	0.98	CCR5 only	14.40	CCR5
B12_P5	7	B12_C1	1,405	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
B12_P6	6	B12_C2	19	S/K	CXCR4	0.53	0.99	CXCR4 capable	4.80	CXCR4
B12_P7	4	B12_C3	10	S/E	CCR5	0.36	0.98	CCR5 only	1.70	CXCR4
B12_P9	3	B12_C4	6	S/Q	CCR5	0.29	0.95	CCR5 only	13.10	CCR5
B12_P11	3	B12_C5	6	S/Q	CCR5	0.31	0.96	CCR5 only	20.40	CCR5
B12_P12	3	B12_C6	6	S/Q	CCR5	0.42	0.98	CCR5 only	6.80	CCR5
B12_P13	3	B12_C7	5	S/Q	CCR5	0.31	0.96	CCR5 only	17.80	CCR5
B12_P14	3	B12_C8	5	S/Q	CCR5	0.33	0.96	CCR5 only	7.90	CCR5
B12_P16	3	B12_C9	5	S/Q	CCR5	0.29	0.95	CCR5 only	8.20	CCR5
B12_P18	3	B12_C10	4	S/Q	CCR5	0.51	0.98	CCR5 only	6.80	CCR5

Italics values indicate clones with different amino acids at the 11/25 positions
^aThe C2-V3 coding regions was RT-PCR amplified with barcoded 454 primers from the plasma RNA (only for B12), from the plasmid population following yeast recombination (no RT step), and from RNA of culture supernatant. Amino acid alignments grouped identical clones. Predictive co-receptor algorithms, 11/25, PSSM, and Geno2Pheno were run on the V3 loop amino acid sequences. FPR false positive rate for Geno2Pheno at 5 %.

ISSN: 1742-6405