Table 1.
Recombination events in the S1 gene of a novel recombinant IBV variant (TH/IBV/2014/CU-179 and TH/IBV/2016/CU-92) detected by RDP4 software.
| Virus name | Breakpoints |
Major parent1 (similarity) | Minor parent2 (similarity) | Detection methods (P-value)3 | |
|---|---|---|---|---|---|
| Beginning | Ending | ||||
| TH/IBV/2014/CU-179 | 891 | 1,608 | TH/IBV/2016/CU-123 (96%) | TH/IBV/2016/CU-99 (100%) | RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, 3Seq (7.668 × 10−44, 8.756 × 10−37, 1.422 × 10−35, 2.063 × 10−23, 1.880 × 10−23, 1.216 × 10−29, 1.004 × 10−57) |
| TH/IBV/2016/CU-92 | 918 | 1,633 | TH/IBV/2016/CU-123 (96.2%) | TH/IBV/2016/CU-99 (99.9%) | RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, 3Seq (7.668 × 10−44, 8.756 × 10−37, 1.422 × 10−35, 2.063 × 10−23, 1.880 × 10−23, 1.216 × 10−29, 1.004 × 10−57) |
1
Major parent is the gene sequence of parent providing the larger part of the recombinant virus's sequence.
2
Minor parent is the gene sequence of parent providing the smaller part of the recombinant virus's sequence.
3
All recombination events were detected by all 7 detection methods and the recombination events were accepted only when they were detected by 5 or more methods implemented in the RDP4, with a P-value lower than 10−14.