Table 2.
Main features of intergenotype, intersubtype and intrapatient recombination in hepatitis C virus published cases
| Strain | Genotype | Country | Recombination breakpoint(s) | Ref. |
| Intergenotype | ||||
| RF1_2k/1b | 2k/1b | Russia, Ireland, Uzbekistan, Georgia, France, Cyprus, Estonia | NS2, positions 3175-3176 | [124-129] |
| D3 | 2i/6p | Viet Nam | NS2/NS3 junction, between positions 3405 and 3464 | [130] |
| SE-03-07-1689 | RF3_2b/1b | Philippines | NS3, positions 3466-3467 | [137] |
| HC10-0804 | 2b/1b | Japan | NS2/NS3 junction, positions 3443-3444 | [135] |
| B5808, M2123, M4430, M4416, M4414, M4431, M2777, M8774 | 2b/1b | Japan | NS2, putative position 3301 | [136] |
| R1 | 2/5 | France | NS2/NS3 junction, between residues 3420 and 3440 | [132] |
| D177 | RF_2b/6w RF_3a/1b RF_2a/1a | Taiwan Taiwan, China Taiwan | NS2/NS3 junction, position 3429 Undetermined Undetermined | [131,133] |
| JF779679 | 2b/1a | United States | NS2/NS3 junction, positions 3405-3416 | [134] |
| Intersubtype | Subtypes | |||
| PE22 | RF2_1b/1a | Peru | NS5B, position 8321 | [141] |
| H23 | 1b/1a | Uruguay | Core, at position 387 | [111] |
| HC-J1 | 1a/1c | Japan | 2 sites in E1-E2, at positions 1407 and 2050 | [142] |
| Khajal | 1a/1c | India | 5 sites, from core to NS3, at positions 801 1261, 2181, 3041 and 3781 | [143] |
| R49 | 4a/4d | Portugal | Undetermined | [140] |
| EU246930 | 6a/6o | Viet Nam | NS5B, between positions 8345-9073 | [144] |
| EU246932 | 6e/6o | Viet Nam | NS5B, between positions 8358-8977 | [144] |
| EU246937 | 6n/6o | Thailand | NS5B, between positions 8372-9033 | [144] |
| EU246931 | 6e/6h | Viet Nam | NS5B, between positions 8356-9019 | [144] |
| Intrapatient | Subtype | |||
| 1b | Spain | NS5B, at residue 286 | [145] | |
| 1a, 1b, 3a | Spain | 1 or 2 sites within E1-E2 or NS5A | [146] | |
| 4a | Ireland | E2 glycoprotein, HVR1 region | [147] |
Modified from ref. [49].