Multigene tracking of quasispecies in viral persistence and clearance of hepatitis C virus

Table 1 Molecular, biochemical, and serological characterization of five HCV primary infections.

Subjects	Samples	Age (yr)/sex	Duration ofinfection(mo)	Genotype	Log10 [HCVRNA]1	HCV RNA	ALT level (nkat/L)2	Result of ELISA
A	A1	30/M	0	3b	7.30	++++	1833.70	-
	A2		6		6.20	+++	583.45	+
	A3		14		5.30	+++	616.79	+
B	B1	28/F	0	3b	7.50	++++	1933.72	-
	B2		6		6.40	+++	1150.23	+
	B3		12		6.90	+++	1533.64	+
C	C1	33/M	0	1b	6.41	+++	683.47	+
	C2		24		5.25	+++	383.41	+
	C3		34		4.16	++	166.70	+
E	E1	20/M	0	1a	6.80	+++	4017.47	-
	E2		3.5		4.20	++	766.82	+
	E3		9		0	–	583.45	+
	E4		24		0	–	400.08	-
F	F1	28/M	0	1b	6.00	++++	3067.28	-
	F2		2		5.60	+++	1066.88	+
	F3		7		0	–	666.80	+
	F4		18		0	–	483.43	-

¹Number of HCV RNA molecules per milliliter plasma. Time zero is the time where the first sample was available; others indicate are times after time zero.

²Normal value, <666.80 nkat/L.

Table 2 Primers for amplification of E1 and E2 regions of HCV genome¹.

Region	Designation	Sequence	5’ to 3’ polarity	Position of 5’ base2
C/E2	P1	GCAACAGGGAAYYTDCCCGGTTGCTC	Outer sense	837–862
	P2	TTCATCCASGTRCAVCCRAACCA	Outer antisense	2020–1998
	P3	CCATGTGCTCYTTYTCTATCTTC	Inner sense	855–874
	P4	GTTTAAARCARTACACYGGRCCRCANAC	Inner antisense	1882–1857
C/E1	P3	CCATGTGCTCYTTYTCTATCTTC	Sense	855–874
	P5	GTRGGBGACCAGTTCATCATCAT	Antisense	1333–1311
E2	P6	GGGAYATGATGATGAACTGGTC	Sense	1306–1327
	P4	GTTTAAARCARTACACYGGRCCRCANAC	Antisense	1882–1857

¹Degenerate bases are indicated with standard codes of the international union of Pure and Applied Chemistry.

²Position of 5’ base relative to the HCV genomic sequence of the HCV J6 strain.

Table 3 Comparison of changes in genetic diversity of viral strains in individuals with self -limited and persistent viremia¹.

Patient group	Number of patients	Time points2	Interval (wk)	Change in genetic diversity (×10–2)
				E1	HVR1	E2
Clearance	2	B vs A	3.75±0.35	0.08±0.20	0.30±0.71	–0.37±0.04
Persistence	3	B vs A	12.67±9.86	–0.20±0.14	3.22±0.68a	0.17±0.11
		C vs A	20.0±12.16	0.06±0.23	4.10±2.35	0.21±0.39
		B vs C	7.33±3.03	–0.26±0.11	–0.89±1.81	0.15±0.71

¹Genetic diversity was assessed by using the DNADIST program, maximum-likelihood. The data are represented as mean±SE. Negative values indicate a reduction in genetic diversity of viral strains; positive values indicate an increase in genetic diversity of viral strains.

²The first time point (A) corresponds to the baseline, the second (B) and the third (C) after antibody seroconversion.

^aP<0.05 time points B vs A of self-limited vs persistent viremia by unpaired Welch’s t test.