Table 2.
HBV genotype and subgenotype determination based on diagnostic SNP signatures in the preS2 region
| Specific SNP | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genotype | 20 | 25 | 27 | 43 | 45 | 76 | 96 | 135 | 150 | |||||||||||
| a. HBV genotype determination | ||||||||||||||||||||
| B | A | T | A | G | C | A | A | C | C | |||||||||||
| C | G | G | T | G | G | C | C | C | C | |||||||||||
| D | A | G | A | A | G | A | C | T | T | |||||||||||
| Specific SNP | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subgenoype | 10 | 31 | 34 | 35 | 46 | 55 | 85 | 87 | 93 | 99 | 100 | 105 | 109 | 110 | 123 | 128 | 148 | |||
| b. HBV/B subgenotyping | ||||||||||||||||||||
| B1 | T | T | C | A | T | T | A | G | C | A | T | T | A | G | T | T | G | |||
| B2 | T | C | A | C | T | G | G | C | A | T | T | T | G | T | T | A | ||||
| B3 | T | C | A | T | T | A | A | T | A | C | C | T | T | T | T | G | ||||
| B4 | T | C | A | T | T | G/A | G/A | C | A | T | C | T | G | C | T | A | ||||
| B5 | T | C | A | T | T | G | A | C | A | C | C | T | T | T | T | A | ||||
| B6 | T | C | A | T | T | G | A | C | T | T | C | T | T | T | C | A | ||||
| B7 | T | C | A/C | T | C/T | G | A | T | C | C | C | T | T | T | T | G | ||||
| B8 | T | G | A | T | T | G | A | T | A | C | C | T | T | C | T | A | ||||
| B9 | C | C | A | T | T | A | A | T | A | C | C | T | T | T | T | A | ||||
| Specific SNP | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subgenotype | 6 | 7 | 8 | 13 | 16 | 27 | 28 | 40 | 46 | 49 | 84 | 99 | 105 | 109 | 111 | 115 | 132 | 147 | 149 | 154 |
| c. HBV/C subgenotyping | ||||||||||||||||||||
| C1 | G | C | A | T | C | T | A | G | C | A | T | C | C | C | C | A | G | C | C | T |
| C2 | C | A/C | A | T | C | T | A | G | C | A | T | C | C | A | C | A | G | C | C | C |
| C3 | C | A | A | T | A | T/A | A/G | G/C | C | A/T | T | C | C | C | T | T | G | T | A | C |
| C4 | C | A | G | T | C | A | G | A | T | G | T | A | T | C | A | C | A | C | T | C |
| C5 | C | A | A | C | T | T | A | A | C | A | C | C | C | C | C | A | G | C | C | C |
| C6 | C | A | G | C/T | C | T | A | G | C | T | T | C | C | C | C | C | G | C | C | C |
| Specific SNPs | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subgenoype | 37 | 105 | 111 | 113 | ||||||||||||||||
| d. HBV/D subgenotyping | ||||||||||||||||||||
| D1 | A | T | A | A | ||||||||||||||||
| D2 | G | C | C | A | ||||||||||||||||
| D3 | A | C | C | T | ||||||||||||||||
| D4 | A | C | C | A | ||||||||||||||||
For genotype assignment, the sequence of the preS2 region of the HBV genome was obtained for each isolate. The genotype was determined from the preS2 sequence employing the nine SNPs (Table 2a) that form the signatures of HBV genotype B (20A, 25T, 27A, 43G, 45C, 76A, 96A, 135C, and 150C), C (20G, 25G, 27A, 43G, 45C, 76A, 96A, 135C, and 150C) and D (20A, 25G, 27A, 43A, 45G, 76A, 96C, 135T, and 150T) as reported previously [30]. Isolates of HBV/B, HBV/C and HBV/D genotypes were further subgenotyped based on the SNP signatures of the preS2 region that define these subgenotypes (Table 2b, 2c and 2d, respectively). Nucleotide numbering is based on the EcoRI endonuclease restriction site. Diagnostic sites defined in this study are shown in bold, along with those reported previously (not bold; [30])