Table 1.

Genotyping Results Using Different Assays

Patient	Subtype by Lipa/ Trugene or Abbott RT-PCR Assay	Amplicon Deep Sequencing												Full-Genome Sequencing
		NS3				NS5A				NS5B				Subtype	Nt Homology, %
		nt	H omology, %	aa	Homology, %	nt	Homology, %	aa	Homology, %	nt	Homology, %	aa	Homology, %
1	2a/2c	ND	NA	ND	NA	2j	79	2i	84	2e	86	2d	92	Novel GT2 subtype	82 (2c, 2r, 2d, 2)
2	2a/2c	ND	NA	ND	NA	2d	79	2j	85	2e	86	2k	91	Novel GT2 subtype	82 (2)
3	2	ND	NA	ND	NA	2e	82	2j	86	2e	88	2e	94	Novel GT2 subtype	85 (2)
4	2	2a	82	2c	92	2q	78	2j	80	2e	83	2d	89	Novel GT2 subtype	82 (2)
5	2a/2c	2q	86	2c	96	2q	81	2k	86	2k	88	2k	93	Novel GT2 subtype	84 (2k, 2q)
6	2a/2c	2a	81	2c	94	2a	79	2a	83	2a	86	2a	92	Novel GT2 subtype	82 (2a, 2)
7	2b/2j	2i	75	2j	87	No hit	0	2i	77	2r	80	2r	86	Novel GT2 subtype	83 (2l)
8	2l	2e	75	2i	89	No hit	0	2b	75	2r	79	2r	85	Novel GT2 subtype	81 (2l)
9	2	ND	NA	ND	NA	2d	80	2e	85	2k	86	2d	92	Novel GT2 subtype	83 (2c, 2q)
10	4	4a	83	4a	94	4v	79	4v	85	4l	87	4l	92	Novel GT4 subtype	82 (4v, 4l)
11	4a/4c	4a	88	4a	97	4a	86	4a	92	4c	91	4c	96	Novel GT4 subtype	86 (4a, 4)
12	4l/4t	4t	83	4t	94	4a	79	4t	85	4p	87	4l	93	Novel GT4 subtype	84 (4p)
13	4m/4v	4o	82	4v	95	4v	79	4a	85	4l	86	4m	93	Novel GT4 subtype	82 (4v, 4q, 4l, 4)
14	4a/4c	4c	84	ND	ND	4v	81	ND	ND	ND	ND	4a	89	Novel GT4 subtype	84 (4)
15	6c/6q	6d	78	6c	94	6p	75	6q	87	6q	86	6q	92	Novel GT6 subtype	84 (6q)
16	1b	ND	ND	ND	ND	6w	72	6g	84	No hit	0	6g	88	Novel GT6 subtype	80 (6q)
17	1b	1a	79	1h	91	1c	78	1c	84	1c	86	1c	92	Novel GT1 subtype	81 (1c, 1)
18	3f	NA	NA	NA	NA	3i	79	3g	87	3i	87	3i	94	Novel GT3 subtype	82 (3i)
19	5a	NA	NA	NA	NA	1b	74	5a	84	4v	71	5a	85	Novel GT5 subtype	78 (5a)

Homology, in percentage, was calculated by BLASTN analysis for NS3, NS5A, and NS5B. The subtype with the highest match is shown. BLASTN was performed on the sequences generated by full–HCV genome sequencing; the query nucleotide length was 6567 for GT2, 9334 for GT3, 6576 for GT4, 4098 for GT6, 7270 for GT1, and 4095 for GT5.

Abbreviations: aa, amino acid; GT, genotype; HCV, hepatitis C virus; nt, nucleotide; RT-PCR, reverse transcriptase polymerase chain reaction.