TABLE 3.

Performance of the laboratories in HCV genotype determination

Gene region and genotyping technique	Labora- tory	Primers used for PCRa or reference	Primers used for sequencing or reference	Results (no. of samples) for HCV RNA-positive samples (n = 14)				No. of samples with false-positive results (n = 1)	Quality scoree (n = 15) (no. [%] of samples)
				Correct resultsb	Incomplete resultsc	Misclassified samplesd	False-negative results
NS5b
In-house	A	PR3-PR4/PR3-PR5	PR3-PR5	10 (71.4)	0	0	4	0	11 (73.3)
In-house	B	PR1-PR2/PR3-PR5	PR3-PR5	12 (85.7)	0	1	1	0	13 (86.7)
In-house	C1	PR3-PR4/PR3-PR5	PR3-PR5	12 (85.7)	0	0	2	0	13 (86.7)
Trugene	C2	28		13 (92.9)	0	0	1	0	14 (93.3)
In-house	D	1203-1204	123	9 (64.3)	0	0	5	0	10 (66.7)
In-house	E1	1203-1204	1203-1204 (−20 ntf at 3′ end)	11 (78.6)	1	0	2	0	12 (80)
In-house	F1	1203-1204/1203-123	1203-1204	11 (78.6)	1	0	2	0	12 (80)
Trugene	G1	28		12 (85.7)	0	1	1	0	13 (86.7)
In-house	H1	243-242/122-123	122-123	9 (64.3)	0	0	5	0	10 (66.7)
In-house	I	PR3-PR4	PR3-PR4	14 (100)	0	0	0	0	15 (100)
5′ NC
In-house	E2	K80-K78	K80-K78	9 (64.3)	3	0	1	0	10 (66.7)
In-house	F2	K80-K78	DOG1-SF1	9 (64.3)	3	0	1	1	10 (60)
Trugene	G2	32	32	12 (85.7)	1	1	0	0	13 (86.7)
InnoLipa	G3	37		9 (64.3)	2	2	1	0	10 (66.7)
InnoLipa	H2	37		6 (42.7)	7	1	0	0	7 (46.7)
Trugene	J	32	32	6 (42.7)	7	1	0	0	7 (46.7)
InnoLipa	K	37		6 (42.7)	7	1	0	0	7 (46.7)

^aHeminested PCR or nested PCR was used when two pairs of primers are mentioned.

^bPercentage of correct results among the HCV RNA-positive samples. Percent sensitivity is presented in parentheses.

^cCorrect genotype with a subtype not identified.

^dCorrect genotype but incorrect subtype.

^eCorrect results among the 15 samples in the panel.

^fnt, nucleotides.