Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a

Moreau, Isabelle; Levis, John; Crosbie, Orla; Kenny-Walsh, Elizabeth; Fanning, Liam J

doi:10.1186/1743-422X-5-78

Virology Journal

Table 3 Intra- and intersample genetic variability of the HVR1 and outside the HVR1 over time in the two groups of patients

From: Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a

Region	Patient Group	Samples	^aIntrasample variability				Samples	^bIntersample variability
			Ks	Ka	*Ka/Ks*	gd		Ks	Ka	*Ka/Ks*	gd
	SVR	E	0.0195 ± 0.0141	0.0308 ± 0.0130	0.998	0.0283 ± 0.0095
		B	0.0236 ± 0.0175	0.0225 ± 0.0115*	0.850 ^†	0.0233 ± 0.0091	B-B	0.0236 ± 0.0175	0.0225 ± 0.0115*	0.850	0.0233 ± 0.0091
		W1	0.0277 ± 0.0152	0.0302 ± 0.0100	1.067 ^‡	0.0302 ± 0.0087	B-W1	0.0293 ± 0.0160	0.0305 ± 0.0110	1.041	0.0305 ± 0.0095
		W2	0.0050 ± 0.0025	0.0375 ± 0.0155	2.700	0.0280 ± 0.0125	B-W2	0.0070 ± 0.0045	0.0370 ± 0.0205	7.300	0.0285 ± 0.0125
		W3/W4	0.0000 ± 0.0000	0.0135 ± 0.0075	NA	0.0095 ± 0.0045	B-W3/4	0.0015 ± 0.0015	0.0150 ± 0.0085	9.333	0.0110 ± 0.0055
HVR1
	NR	E	0.0292 ± 0.0185	0.0585 ± 0.0207	1.860	0.0492 ± 0.0145
		B	0.0345 ± 0.0192	0.0802 ± 0.0227*	2.427 ^†	0.0667 ± 0.0185	B-B	0.0345 ± 0.0192	0.0802 ± 0.0227*	2.427	0.0667 ± 0.0185
		W1	0.0172 ± 0.0115	0.0507 ± 0.0175	2.033 ^‡	0.0412 ± 0.0135	B-W1	0.0218 ± 0.0125	0.0538 ± 0.0178	2.332	0.0432 ± 0.0130
		W2/4	0.0205 ± 0.0175	0.0320 ± 0.0135	1.574	0.0290 ± 0.0115	B-W2/4	0.0200 ± 0.0100	0.0325 ± 0.0135	1.648	0.0295 ± 0.0120
		L	0.0160 ± 0.0033	0.008 ± 0.0036	0.285	0.0106 ± 0.0043	B-L	0.0153 ± 0.008	0.0133 ± 0.0057	0.873	0.0137 ± 0.0047
Outside
	SVR	E	0.0106 ± 0.005	0.0023 ± 0.0015	0.216	0.0045 ± 0.0016
		B	0.0130 ± 0.0061	0.0036 ± 0.0020	0.277	0.0061 ± 0.0023	B-B	0.0130 ± 0.0061	0.0036 ± 0.0020	0.277	0.0061 ± 0.0023
		W1	0.0052 ± 0.0022	0.0017 ± 0.0015	0.327	0.0027 ± 0.0012	B-W1	0.0050 ± 0.0020	0.0018 ± 0.0018	0.360	0.0025 ± 0.0013
		W2	0.0035 ± 0.0025	0.0025 ± 0.0015	0.714	0.0025 ± 0.0020	B-W2	0.0035 ± 0.0025	0.0025 ± 0.0020	0.714	0.0025 ± 0.0020
		W3/W4	0.0015 ± 0.0015	0.0010 ± 0.0010	0.667	0.0010 ± 0.0010	B-W3/4	0.0015 ± 0.0015	0.0010 ± 0.0010	0.667	0.0010 ± 0.0010
	NR	E	0.0612 ± 0.0205	0.0042 ± 0.0025	0.068	0.0180 ± 0.0052
		B	0.0280 ± 0.0115	0.0017 ± 0.0012	0.061	0.0085 ± 0.0032	B-B	0.0280 ± 0.0115	0.0017 ± 0.0012	0.061	0.0085 ± 0.0032
		W1	0.0132 ± 0.0085	0.0005 ± 0.0005	0.038	0.0040 ± 0.0022	B-W1	0.0148 ± 0.0090	0.0008 ± 0.0008	0.054	0.0043 ± 0.0025
		W2/4	0.0100 ± 0.0060	0.0015 ± 0.0010	0.150	0.0047 ± 0.0026	B-W2/4	0.0095 ± 0.0060	0.0015 ± 0.0010	0.158	0.0035 ± 0.0020
		L	0.0133 ± 0.0060	0.0006 ± 0.0006	0.045	0.0030 ± 0.0020	B-L	0.0140 ± 0.0057	0.0010 ± 0.0010	0.071	0.0043 ± 0.0020

^a The average number of nucleotide substitutions per nonsynonymous site and per synonymous site for all pairwise comparisons within each sampling point. ^b The average number of nucleotide substitutions per nonsynonymous site and per synonymous site for all pairwise comparisons for consensus of baseline for baseline sample (B-B) and follow-up samples (B-W1-2-3/4 and B-L). Ka/Ks indicate the ratio of nonsynonymous to synonymous nucleotide substitutions. All data represent mean ± SEM. The statistical significance of comparisons among individual samples or between the two groups of patients were analysed with non parametric Mann-Whitney U test.*, P = 0.05 for comparison between the two groups of patient. †, P = 0.01 for comparison between the two groups of patient. ‡, P = 0.05 for comparison between the two groups of patient.

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ISSN: 1743-422X

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