Table 4.
Recombination events detected in the Kenyan isolates A374/17 and A376/17. The analysis was performed using RDP4 and involved 42 complete genome sequences from different IBV lineages (described in the text). Nucleotide identities between the transferred fragment in the recombinant and the major/minor parent sequences are indicated.
| Sequence | Breakpoint | “Major Parent” Sequence (nt) a | “Minor Parent” Sequence (nt) b | Recombination Event Confirmation | |||
|---|---|---|---|---|---|---|---|
| Start | End | Gene | Detection Algorithm | p-Value | |||
| A374/17 | 12,346 | 13,046 | nsp11/12 (RdRp) |
EU095850/TCoV/ CA/MG10 (89.4%) |
KX272465/SD/ AR251-15 (95.4%) |
RDP, GENECONV, BootScan, MaxChi, SiScan, Chimaera, 3Seq |
8.71 × 10−6 |
| A376/17 | 12,337 | 13,037 | nsp11/12 (RdRp) |
EU095850/TCoV/ CA/MG10 (89.5%) |
KX272465/SD/ AR251-15 (99.1%) |
RDP, GENECONV, BootScan, MaxChi, SiScan, Chimaera, 3Seq |
2.42 × 10−37 |
| 19,955 | 23,117 | nsp16/spike | GU213200/TX-1038/98 (93.8%) | MK142676/CN/ahysx-1/16 (85.9%) | GENECONV, BootScan, MaxChi, Chimaera, SiScan, 3Seq | 3.75 × 10−20 | |
a “major parent” indicates a sequence in another strain most closely related to the sequence surrounding the fragment transferred to the recombinant strain through recombination. b “minor parent” indicates the sequence closely related to the fragment in the recombinant strain.