Characteristics of study population
Among all enrolled participants (n = 243), the median age was 49 years, 64.6% (n = 157) were male, and 48 (19.8%) had a previous history of HCV treatment. Fibrosis assessment by transient elastography (TE) was performed on 66 patients, of whom, 20 (30.3%) had cirrhosis. Among 180 patients with quantifiable VL on Roche, HCV genotypes were successfully determined on 172 samples, with GT1 (108/62.8%) and GT3 (26/15.1%) being the most commonly found, followed by GT2 (20/11.6%), GT4 (17/9.9%) and GT6 in one (0.6%) sample (Table 1).
Table 1 Characteristics of study population (N = 243)
Characteristics
|
n (max, min)
|
%
|
Age (years)a
|
49 (10, 87)
|
|
Male
|
157
|
64.6
|
Fibrosis stageb (n=66)
|
|
|
F0 (<5.1 kPa)
|
3
|
4.5
|
F1 (≥5.1 and <7.2 kPa)
|
4
|
6.1
|
F2 (≥7.2 and <9.6 kPa)
|
19
|
28.8
|
F3 (≥9.6 and <14.1 kPa)
|
20
|
30.3
|
F4 (≥14.1 kPa)
|
20
|
30.3
|
History of HCV treatment (n=48)c
|
|
|
IFN or PegIFN
|
44
|
91.7
|
DAAd
|
7
|
14.6
|
Both IFN/PegIFN and DAA
|
3
|
6.3
|
HCV genotypes (n=172)e
|
|
|
1
|
108
|
62.8
|
1a
|
57
|
33.1
|
1b
|
40
|
23.3
|
Subtype unknown
|
11
|
6.4
|
2
|
20
|
11.6
|
2a/c
|
14
|
8.1
|
Subtype unknown
|
6
|
3.5
|
3
|
26
|
15.1
|
3a
|
15
|
8.7
|
3k
|
11
|
6.4
|
4
|
17
|
9.9
|
4h
|
6
|
3.5
|
Subtype unknown
|
11
|
6.4
|
6
|
1
|
0.6
|
6c
|
1
|
0.6
|
Indeterminate
|
8
|
4.7
|
aMedian (minimum, maximum)
bBy transient elastography (TE) using FibroScan®, cirrhosis was defined as having a TE value of 14.1 kPa or above
(fibrosis stage 4) [31]
cWith previous HCV treatment
dEither daclatasvir/sofosbuvir or sofosbuvir/ledipasvir with or without ribavirin
eGenotypes are among 180 patients with quantifiable viral load by Roche
Sensitivity and specificity of Xpert
Of the 243 patients, 180 (74.1%) had detectable and quantifiable VL above the lower LOQ on both platforms, and 55 (22.6%) had undetectable VL on both platforms (Table 2). One sample was unquantifiable and detectable by Roche but quantifiable by Xpert with a VL of 1.04 log10 IU/mL. This was one of the eight samples with indeterminate HCV genotype. There were no samples quantifiable by Roche but unquantifiable by Xpert. Considering quantifiable VL as positive and unquantifiable VL as negative results, the sensitivity of Xpert was 100% (95% CI 0.98, 1.00) and the specificity was 98.41% (95% CI 0.91, 0.99). VL values and bias between the two tests at percentiles are shown in Table 3.
Table 2 Comparison of Viral Load test results between Xpert and Roche (n = 243)
|
|
Roche Cobas® TaqMan® HCV Test
|
Detectable & Quantifiable
|
Detectable & Unquantifiable
|
Undetectable
|
Total
|
Xpert®
HCV Test
|
Detectable & Quantifiable
|
180
|
1
|
0
|
181
|
Detectable & Unquantifiable
|
0
|
7
|
0
|
7
|
Undetectable
|
0
|
0
|
55
|
55
|
|
Total
|
180
|
8
|
55
|
243
|
Table 3 Viral load values and bias between Xpert and Roche at percentiles
Variable
|
Xpert HCV viral load
(95% CI)
(log10 IU/mL)
|
Roche HCV viral load
(95% CI)
(log10 IU/mL)
|
Bias
(95% CI)
(log10 IU/mL)
|
10th percentile
|
4.56 (3.69, 4.83)
|
4.43 (4.01, 4.88)
|
-0.90 (-1.03, -0.79)
|
25th percentile
|
5.35 (5.14, 5.48)
|
5.42 (5.13, 5.76)
|
-0.55 (-0.68, -0.49)
|
50th percentile
|
5.95 (5.75, 6.09)
|
6.19 (5.98, 6.37)
|
-0.26 (-0.36, -0.20)
|
75th percentile
|
6.42 (6.34, 6.52)
|
6.76 (6.58, 6.86)
|
0.04 (-0.06, 0.18)
|
90th percentile
|
6.70 (6.62, 6.85)
|
7.24 (7.06, 7.44)
|
0.39 (0.25, 0.54)
|
Concordance between Xpert and Roche
A very good correlation was seen between Xpert and Roche (Pearson’s correlation coefficient (r) = 0.97, P < 0.001). When analyzed separately by HCV genotype, the correlation was significant in GT1 (r = 0.87, P < 0.001), GT2 (r = 0.93, P < 0.001), GT3 (r = 0.87; P < 0.001), GT4 (r = 0.88, P < 0.001), and indeterminate genotype (r = 0.99, P < 0.001). Further analysis by Deming regression for the 180 samples showed the overall Deming regression equation Y = 0.87X + 0.53 (Figure 1A). When analyzed by genotype, the Deming regression equations were Y = 0.88X + 0.50 for GT1, Y = 0.69X + 1.37 for GT2, Y = 0.71X + 1.60 for GT3, Y = 0.97X + 0.13 for GT4, and Y = 0.97X - 0.07 for indeterminate genotype (Figure 2A, 2C, 2E, 2G, 2I). Detailed correlation and Deming regression results are shown in Table 4.
Table 4 Pearson’s correlation and Deming Regression analysis of Xpert against Roche
Genotype
|
N
|
Pearson’s Correlation
|
|
Deming Regression
|
r
|
P value
|
|
Intercept (95% CI)
|
Slope (95% CI)
|
T-value
|
Df
|
All
|
180
|
0.97
|
<0.001
|
|
0.70 (0.32, 1.08)
|
0.84 (0.79, 0.90)
|
1.97
|
178
|
GT1
|
108
|
0.87
|
<0.001
|
|
0.71 (0.11, 1.31)
|
0.84 (0.74, 0.94)
|
1.98
|
106
|
GT2
|
20
|
0.93
|
<0.001
|
|
1.54 (0.84, 2.25)
|
0.66 (0.53, 0.80)
|
2.10
|
18
|
GT3
|
26
|
0.87
|
<0.001
|
|
1.96 (0.59, 3.35)
|
0.65 (0.44, 0.86)
|
2.06
|
24
|
GT4
|
17
|
0.88
|
<0.001
|
|
0.16 (-0.79, 1.11)
|
0.97 (0.79, 1.45)
|
2.13
|
15
|
GT6
|
1
|
n.a.
|
n.a.
|
|
n.a.
|
n.a.
|
|
|
Indeterminate
|
8
|
0.99
|
<0.001
|
|
-0.06 (-1.06, 0.93)
|
0.97 (0.77, 1.17)
|
2.45
|
6
|
CI = confidence interval, Df = N-2 degrees of freedom; n.a = not applicable
By Bland-Altman plot analysis, the mean difference between the two platforms was -0.25 log10 IU/mL (95% CI -0.33, -0.18) with differences between the platforms ranging from −1.62 to 1.56 log10 IU/mL. The lower and upper LOAs were −1.24 log10 IU/mL (95% CI −1.37, −1.12) and 0.74 log10 IU/mL (95% CI 0.61, 0.87), respectively. One hundred sixty-nine (93.9%) samples were within the LOA, while eleven (6.1%) samples (five GT1, one GT2, two GT3, and three GT4) were outside the LOA (Figure 1B). By genotype, the mean differences across the two platforms were -0.26 ± 0.49 (95% CI -0.36, -0.17) log10 IU/mL for GT1, -0.45 ± 0.49 (-0.68, -0.22) log10 IU/mL for GT2, -0.21 ± 0.52 (-0.42, 0.00) log10 IU/mL for GT3, -0.01 ± 0.66 (-0.35, 0.33) log10 IU/mL for GT4, and -0.20 ± 0.27 (-0.43, 0.02) log10 IU/mL for indeterminate genotype. Detailed Bland-Altman analysis results are shown in Figure 2B, 2D, 2F, 2H, 2J, and Table 5.
Table 5 Bland-Altman Plot analysis of Xpert against Roche
Genotype
|
N
|
Mean difference ± SD
(95% CI)
|
Lower LOA
(95% CI)
|
Upper LOA
(95% CI)
|
Inside LOA
|
Outside LOA
|
(log10 IU/mL)
|
(log10 IU/mL)
|
(log10 IU/mL)
|
n (%)
|
n (%)
|
All
|
180
|
-0.25 ± 0.51 (-0.33, -0.18)
|
-1.24 (-1.37, -1.12)
|
0.74 (0.61, 0.87)
|
169 (93.9)
|
11 (6.1)
|
GT1
|
108
|
-0.26 ± 0.49 (-0.36, -0.17)
|
-1.22 (-1.37, -1.06)
|
0.69 (0.53, 0.84)
|
100 (92.6)
|
8 (7.4)
|
GT2
|
20
|
-0.45 ± 0.49 (-0.68, -0.22)
|
-1.40 (-1.81, 1.01)
|
0.51 (0.11, 0.91)
|
19 (95.0)
|
1 (5.0)
|
GT3
|
26
|
-0.21 ± 0.52 (-0.42, 0.00)
|
0.18 (-1.61, 0.88)
|
0.83 (0.45, 1.20)
|
24 (92.3)
|
2 (7.7)
|
GT4
|
17
|
-0.01 ± 0.66 (-0.35, 0.33)
|
-1.30 (-1.89, -0.71)
|
1.28 (0.67, 1.87)
|
16 (94.1)
|
1 (5.9)
|
GT6
|
1
|
n.a.
|
n.a.
|
n.a.
|
n.a.
|
n.a.
|
Indeterminate
|
8
|
-0.20 ± 0.27 (-0.43, 0.02)
|
-0.744 (-1.14, -0.33)
|
0.32 (-0.08, 0.74)
|
8 (100.0)
|
0 (0.0)
|
n.a. = not applicable