TABLE 2.
NS3/4A, NS5A, and NS5B PCR amplification results and comparison between LiPA 2.0 and BLAST-based subtyping methods
| LiPA 2.0 subtype | Result for gene: |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NS3/4A |
NS5A |
NS5B |
|||||||||||||
| Patients (n) | Nucleotide coverage (start position-end position) | Concordanta (no. [%]) | Refinementb (no. [%]) | BLAST identity range (%) | Patients (n) | Nucleotide coverage (start position-end position) | Concordanta (no. [%]) | Refinementb (no. [%]) | BLAST identity range (%) | Patients (n) | Nucleotide coverage (start position-end position) | Concordanta (no. [%]) | Refinementb (no. [%]) | BLAST identity range (%) | |
| 5a | 6 | 1–685 | 6 (100) | 0 | 89–93 | 7 | 1–450 | 7 (100) | 0 | 87–93 | 7 | 1–591 | 7 (100) | 0 | 92–94 |
| 6 | 1 | 0 | 1 (100) | 95 | 9 | 1–456 | 0 | 9 (100) | 89–96 | 9 | 0 | 9 (100) | 93–97 | ||
| 6a/b | 4 | 0 | 4 (100) | 92–95 | 3 | 1–451 | 0 | 3 (100) | 90–91 | 3 | 0 | 3 (100) | 94–95 | ||
| 6c-l | 3 | 0 | 3 (100) | 89–93 | 8 | 1–456 | 0 | 8 (100) | 84–94 | 7 | 0 | 7 (100) | 89–95 | ||
| Total | 14 | 6 (42.9) | 8 (57.1) | 27 | 7 (25.9) | 20 (74.1) | 26 | 7 (26.9) | 19 (73.1) | ||||||
a
The same subtype was assigned by both methods.
b
Indeterminate subtype from LiPA 2.0 was fully determined at subtype level by BLAST sequencing.