Table 3. The variant phylo-groups identified from phylogenetic and identity analysis of amplicon variant sequences of the 53 Prunus necrotic ringspot virus (PNRSV) samples, the % clusters identity cut-off and the resulting minimum number of variant groups in each amplicon sample RNA.
| Variant phylo-groups | Variants % identity cut-off | Minimum number of variant groups | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Sample ID | RNA1 | RNA2 | RNA3 | RNA1 | RNA2 | RNA3 | RNA1 | RNA2 | RNA3 |
| 11TAS | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| 12TAS | II | II | I & II | 99% | 98% | 97% & 97% | 1 | 1 | 2 |
| 13TAS | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| 14TAS | I | I | II | 98% | 98% | 99% | 1 | 1 | 1 |
| 15TAS | I | I | II | 98% | 99% | 99% | 1 | 1 | 1 |
| 16TAS | I | I | II | 97% | 98% | 97% | 1 | 1 | 1 |
| 17TAS | I | I | I, II & III | 98% | 98% | 99%, 97% & 97% | 1 | 1 | 3 |
| 1SA | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| 1TAS | I | I | II | 98% | 98% | 97% | 1 | 1 | 1 |
| 2TAS | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| 2VIC | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| 3VIC | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| 4TAS | I & II | II | I | 97% & 98% | 99% | 99% | 2 | 1 | 1 |
| 5SA | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| 5TAS | I & II | I | I & II | 98% & 98% | 99% | 98% & 97% | 2 | 1 | 2 |
| 6VIC | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| Cst | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| K10 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| K16 | I | I | II | 98% | 98% | 97% | 1 | 1 | 1 |
| K17 | I & II | I | I & II | 97% & 97% | 98% | 97% & 98% | 2 | 1 | 2 |
| K56 | I | I | II | 98% | 99% | 98% | 1 | 1 | 1 |
| K57 | I | I | I & II | 98% | 98% | 99% & 98% | 1 | 1 | 2 |
| K64 | II | I & II | I & III | 98% | 97% & 98% | 97% & 98% | 1 | 2 | 2 |
| K72 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| K75 | I & II | II | I | 99% & 98% | 98% | 98% | 2 | 1 | 1 |
| K77 | II | II | I & II | 98% | 99% | 97% & 99% | 1 | 1 | 2 |
| M10 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| M12 | I | I | II & III | 98% | 98% | 97% & 97% | 1 | 1 | 2 |
| M16 | I | I | II | 98% | 98% | 97% | 1 | 1 | 1 |
| M17 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| M18 | II | II | I | 98% | 98% | 97% | 1 | 1 | 1 |
| M19 | I & II | I & II | I & II | 97% & 97% | 98% & 99% | 97% & 99% | 2 | 2 | 2 |
| M22 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| M26 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| M28 | I | I | II | 98% | 99% | 99% | 1 | 1 | 1 |
| M30 | I | I | II & III | 98% | 98% | 98% & 97% | 1 | 1 | 2 |
| M31 | I & II | I | II | 97% & 97% | 98% | 97% | 2 | 1 | 1 |
| M32 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| M33 | I | I | II | 98% | 98% | 99% | 1 | 1 | 1 |
| M5 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| M6 | I | I | II | 99% | 99% | 98% | 1 | 1 | 1 |
| M8 | I | I | II | 98% | 99% | 98% | 1 | 1 | 1 |
| M9 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| NS10 | I & II | I | I & II | 99% & 97% | 98% | 97% & 98% | 2 | 1 | 2 |
| NS1 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |
| NS2 | I | I | II | 98% | 98% | 97% | 1 | 1 | 1 |
| NS4 | I | I | I | 97% | 98% | 97% | 1 | 1 | 1 |
| NS9 | I & II | II | I | 98% & 99% | 99% | 97% | 2 | 1 | 1 |
| Q15 | I & II | II | I, II & III | 97% & 97% | 98% | 99%, 97% & 97% | 2 | 1 | 3 |
| Q16 | I | I | II | 98% | 99% | 98% | 1 | 1 | 1 |
| Q1 | I | I | II | 98% | 99% | 97% | 1 | 1 | 1 |
| Q6 | I & II | I | II | 98% & 98% | 98% | 98% | 2 | 1 | 1 |
| Q7 | I | I | II | 98% | 98% | 98% | 1 | 1 | 1 |