Table 4 Results provided by Sentosa SQ HCV Genotyping Assay in samples that were incorrectly or not classified, as compared to the reference method based on Sanger sequencing of the NS5B region followed by phylogenetic analysis. NS5B contig characteristics provided by the Quality Control Report and Pathology Report in the Sentosa SQ HCV Genotyping Assay are indicated.
From: A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination
Patient number | HCV genotype and subtype with the reference method | HCV RNA level (Log IU/mL) | HCV genotype and subtype using the Sentosa SQ HCV Genotyping Assay | NS5B contig characteristics | ||
|---|---|---|---|---|---|---|
Median coverage | No of reads | Length | ||||
Pt-25 | 1l | 6.20 | 1a | 16,992 | 84,058 | 683 |
Pt-40 | 1d | 5.90 | 1b | 9,585 | 37,291 | 683 |
Pt-61 | 1l | 5.90 | 1a | 27,221 | 102,007 | 683 |
Pt-62 | 1d | 6.60 | 1b | 11,791 | 43,735 | 683 |
Pt-63 | 1l | 5.00 | 1b | 13,186 | 56,316 | 682 |
Pt-64 | 1e | 5.30 | 1g | 25,458 | 99,559 | 683 |
Pt-65 | 1e | 5.80 | 1g | 23,395 | 87,406 | 683 |
Pt-67 | 1d | 5.90 | 1b | 21,565 | 71,120 | 652 |
Pt-17 | 1e | 6.10 | 1g | 5,864 | 23,755 | 681 |
Pt-12 | 1i | 5.40 | 1b | 21,099 | 86,173 | 687 |
Pt-92 | 1a | 2.70 | Not interpretable | 1,191 | 4,473 | 592 |
Pt-97 | 1 | 5.60 | 1b | 10,454 | 40,612 | 677 |
Pt-41 | 2l | 5.20 | 2c | 15,071 | 69,466 | 683 |
Pt-42 | 2 | 4.90 | 2c, 2m | 12,762 | 47,402 | 683 |
Pt-44 | 2l | 6.60 | 2c | 6,189 | 26,579 | 681 |
Pt-45 | 2 | 5.50 | 2a, 2m | 15,325 | 51,871 | 680 |
Pt-74 | 2 | 6.30 | 2b | 12,559 | 55,110 | 684 |
Pt-80 | 2 | 7.00 | 2c | 7,996 | 31,547 | 682 |
Pt-94 | 2 | 5.40 | 2d, 2j | 13,342 | 49,111 | 683 |
Pt-46 | 4 | 5.00 | 4a, 4c | 11,472 | 43,868 | 682 |
