Table 1. Genetic make-up of recombinant clinical strains.
| PID | gag | pol | env | Nearest Strains (non-C subtype region) | Recombinant* | |||||
| RIP | REGA | RIP | REGA | RIP | REGA | |||||
| 08NIIPGI01a | B | B | Not amplified | C | C | Thailand | URF_BC | |||
| 08NIIPGI12a | B | B | Not amplified | C | C | China | URF_BC | |||
| 08NIIPGI14a | C | C | Not amplified | A1, C | C | Kenya | URF_A1C | |||
| 08NIIPGI19a | B | B | Not amplified | C | C | China | URF_BC | |||
| 09NIIPGI47a | C | C | Not amplified | A1 | NA | Uganda | URF_A1C | |||
| MNP01b | C | C | B, C | NA | C | C | Thailand | URF_BC | ||
| MNP05b | C | C | B | NA | C | C | China | URF_BC | ||
| MNP07b | C | C | B, C | NA | C | C | China | URF_BC | ||
| MNP08b | C | C | B, C | NA | C | C | China | URF_BC | ||
| MNP09b | B | B | B | B | C | C | China | URF_BC | ||
| MNP11b | C | C | B, C | NA | B | B | China | URF_BC | ||
| MNP15b | C | C | B | B | B, C | NA | China/Thailand | URF_BC | ||
| 08JNC05c | C | C | Not amplified | A1,C | NA | Kenya | URF_A1C | |||
| 09SJ08c | C | C | A1 | A1 | C | C | Cyprus | URF_A1C | ||
| 09SJ56c | Not amplified | C | C | A1, C | NA | Kenya | URF_A1C | |||
| 10SJ02c | C | C | C | C | A1 | NA | Iran | URF_A1C | ||
| 11SJ74c | C | C | Not amplified | A1 | A1 | Tanzania | URF_A1C | |||
a
Samples from northern India, bNorth-eastern India and cSouthern India. The recombinants were identified based on atleast two of the three viral genes, gag, pol and env. Recombination Identification Program ver 3.0 (RIP) and REGA subtyping tool ver 2 (REGA) were used. Recombinant strains were further confirmed by bootscan analysis in Simplot version 3.5.1 using 100 nucleotide window size and 20 nucleotide step size to map the precise breakpoint and region-specific phylogenetic analysis using ML tree in MEGA 5. NA: Not Assigned.