|
Single-nucleotide polymorphisms identified by Not-N analysis for the major subtypes of hepatitis C virus. |
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| HCV subtypea |
No. genotypes |
SNP 1 |
SNP 2 |
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|
|
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| Positionb |
Discrimination (%) |
Position |
Discrimination (%) |
||
|
|
|||||
| 1a |
117 |
126* (C or T) |
100 |
- |
- |
| 1b |
382 |
103 (C) |
72.1 |
194* (G)/238* (C) 100% |
100 |
| 2a |
38 |
258 (A or G) 99.7% |
99.7 |
182* (T) |
100 |
| 2b |
53 |
314 (A) |
99.7 |
127 (A) |
100 |
| 2c |
5 |
50 (T) |
99.7 |
39* (G) |
100 |
| 3a |
49 |
295 (G) |
100 |
- |
- |
| 3b |
6 |
307 (T) |
99.8 |
126* (G) |
100 |
| 4a |
26 |
182* (A) |
97.8 |
325* (A) |
100 |
| 4d |
17 |
154 (A) |
100 |
- |
- |
| 4f |
21 |
325* (C) |
99.5 |
194* (T)/238* (A) 100% |
100 |
| 4t |
4 |
338/339 (C) |
100 |
- |
- |
| 5a |
18 |
100 (C) |
100 |
- |
- |
| 6a |
34 |
39* (C or T) |
100 |
- |
- |
|
aSubtypes containing less than four confirmed sequences were not included in the analysis. Sequences were downloaded from the hepatitis C virus (HCV) sequence database [10]. bThe single-nucleotide polymorphism (SNP) position refers to a 340 bp fragment of the RNA-dependent RNA polymerase NS5B spanning nucleotides 8276 to 8615 (GenBank accession AF009606 [48]). NS5B is used to construct phylogenetic trees for HCV, which form the basis of the genotype and subtype nomenclature [40]. *SNP discriminates multiple subtypes. | |||||
Price et al. BMC Bioinformatics 2007 8:278 doi:10.1186/1471-2105-8-278 |
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