Table 3.

Concordance for HCV genotype and subtype determination of Sentosa SQ HCV Genotyping Assay and VERSANT HCV Genotype 2.0 LiPA with the reference method, in-house Sanger sequencing of the NS5B region followed by phylogenetic analysis.

HCV genotype (reference methoda)	Patients, n	HCV genotype				HCV subtype
		Sentosa SQ HCV Genotyping Assay		VERSANT HCV Genotype 2.0 LiPA		Sentosa SQ HCV Genotyping Assay		VERSANT HCV Genotype 2.0 LiPA
		Concordant n (%)	Discordant n (%)	Concordant n (%)	Discordant n (%)	Concordant n (%)	Discordant n (%)	Concordant n (%)	Discordant n (%)
1	46	45 (97.8%)	1 (2.2%)	46 (100%)	0 (0%)	34 (73.9%)	12 (24.1%)	39 (84.8%)	7 (15.2%)
2	11	11 (100%)	0 (0%)	11 (100%)	0 (0%)	4 (36.4%)	7 (63.6%)	8 (72.7%)	3 (27.3%)
3	14	14 (100%)	0 (0%)	14 (100%)	0 (0%)	14 (100%)	0 (0%)	13 (92.3%)	1 (7.7%)
4	17	17 (100%)	0 (0%)	17 (100%)	0 (0%)	16 (94.1%)	1 (5.9%)	8 (47.1%)	9 (52.9%)
5	2	2 (100%)	0 (0%)	2 (100%)	0 (0%)	2 (100%)	0 (0%)	2 (100%)	0 (0%)
6	5	5 (100%)	0 (0%)	5 (100%)	0 (0%)	5 (1000%)	0 (0%)	3 (60%)	2 (40%)
2k/1b*	4	4 (100%)	0 (0%)	4 (100%)	0 (0%)	4 (100%)	0 (0%)	0 (0%)	4 (100%)
Total	99	98 (99.0%)	1 (1.0%)	99 (100%)	0 (0%)	79 (79.8%)	20 (20.2%)	73 (73.7%)	26 (26.3%)

^aIn addition to Sanger sequencing of the NS5B region, E1 region sequencing was used in 4 patients infected with a 2k/1b recombinant strain.

^*These strains were identified as recombinant due to the discrepancy between their initial assignment based on the Lipa assay and NS5B sequencing. Recombination was confirmed by sequence analysis of the E1 region spanning the recombining region. Sentosa SQ HCV Genotyping Assay correctly identified genotype 1b in the NS5B region. VERSANT HCV Genotype 2.0 LiPA correctly identified HCV genotype 2 by means of its 5’NCR probes but failed to correctly identify subtype 2k.