Table 1. Predicted recombination events using different detection methods within the RDP4 program.
The 27 predicted recombination events and their breakpoint positions within the alignment are indicated. The size of the recombination region is determined based on the size of the recombinant sequence. RUSSIA /Saratov /2017 was either predicted as the recombinant sequence and the vaccine group as the major parent sequence or reversed for one event, while in all the events the field group of viruses were the minor parent. The number of base pair differences between the recombinant sequence and the minor parent sequence is calculated for the region mentioned and similarly the number of nucleotide differences (bps) between the recombinant sequence and the major parent. The differences in base pairs between the major and minor parents are indicated. Statistical support generated through the different detection methods are provided for each of the recombination events.
| RDP Event Number | Breakpoint Positions in Alignment | Size of predicted recombination region (bp) | Predicted recombination region | Detection Methods | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Begin | End | Nucleotide differences (recombinant to minor parent(s)) | Nucleotide differences (recombinant to major parent(s)) | Nucleotide differences (minor parent(s) to major parent(s)) | Protein(s) | RDP | GENECONV | Bootscan | Maxchi | Chimaera | SiSscan | ||
| 1 | 136364 | 138545 | 2176 | 3–7 bp | 124 bp | 124–126 bp | LSD144—LSD145 | 1,52E-48 | 8,81E-45 | 3,76E-47 | 3,52E-26 | 4,88E-26 | 2,88E-28 |
| 2 | 124188 | 131635 | 7442 | 11–16 bp | 105–106 bp | 111–118 bp | LSD134—LSD138 | 3,28E-32 | 1,37E-33 | 6,38E-31 | 8,75E-05 | 8,58E-05 | 2,15E-18 |
| 3 | 5614 | 6169 | 555 | 3 bp | 43 bp | 46 bp | LSD008—LSD009 | 9,96E-23 | 5,14E-20 | 9,51E-23 | 4,94E-13 | 4,00E-13 | NS |
| 4 | 119575 | 122787 | 3204 | 17–19 bp | 71 bp | 83–86 bp | LSD131—LSD134 | 1,65E-22 | 2,86E-16 | 1,22E-09 | 4,79E-14 | 9,83E-14 | NS |
| 5 | 78289 | 84100 | 5809 | 4–8 bp | 52 bp | 56–57 bp | LSD084—LSD089 | 9,32E-20 | 6,06E-24 | 1,71E-19 | 8,27E-11 | 5,56E-11 | 2,06E-11 |
| 6 | 149628 | 151098* | 1230 | 7–8 bp | 21–22 bp | 22 bp | LSD154—LSD156 | 1,14E-19 | 3,52E-16 | 1,66E-18 | 8,80E-06 | NS | NS |
| 7 | 43456 | 50790 | 7331 | 12–15 bp | 38 bp | 50–51 bp | LSD049—LSD057 | 1,88E-16 | 3,97E-11 | 3,00E-13 | 2,15E-11 | 4,64E-12 | 2,01E-07 |
| 8 | 29524* | 33134 | 3609 | 0–2 bp | 21–22 bp | 20 -22bp | LSD035—LSD039 | 1,64E-13 | 7,65E-13 | 1,63E-13 | 2,11E-07 | 2,08E-07 | NS |
| 9 | 53041* | 55902 | 3041 | 2–6 bp | 22 bp | 24–26 bp | LSD059—LSD063 | 1,03E-12 | 2,96E-11 | 1,42E-12 | 4,74E-07 | 4,69E-07 | 1,80E-05 |
| 10 | 98171* | 100057 | 1885 | 6–10 bp | 19 bp | 23–25 bp | LSD102—LSD106 | 3,56E-08 | 1,07E-04 | 3,16E-02 | 9,30E-03 | 9,19E-03 | NS |
| 11 | 91227 | 92254 | 1027 | No difference | 12 bp | 12 bp | LSD097—LSD098 | NS | 5,96E-07 | 5,75E-08 | 3,26E-03 | 7,22E-03 | NS |
| 12 | 132260* | 133690 | 1430 | 7–10 bp | 19 bp | 26–28 bp | LSD139—LSD141 | 2,84E-08 | 1,59E-03 | 1,73E-03 | 2,38E-04 | 2,35E-04 | 0,014247 |
| 13 | 62209* | 64726* | 2517 | 6 bp | 17 bp | 21 bp | LSD071—LSD073 | 4,40E-08 | 7,46E-06 | 8,66E-07 | 3,27E-05 | 2,82E-05 | NS |
| 14 | 140868 | 142259* | 1391 | No difference | 10 bp | 10 bp | LSD147 | NS | 1,04E-06 | 3,49E-07 | NS | NS | NS |
| 15 | 73969 | 74922* | 953 | No difference | 9 bp | 9 bp | LSD081—LSD082 | NS | 1,61E-05 | 1,95E-06 | NS | NS | NS |
| 16 | 103339* | 103572 | 233 | 0–1 bp | 7 bp | 7–8 bp | LSD110—LSD111 | NS | 1,54E-03 | 2,15E-04 | NS | NS | NS |
| 17 | 100891 | 101452* | 561 | 0–1 bp | 7 bp | 6–7 bp | LSD108 | NS | 1,10E-03 | 1,51E-04 | NS | NS | NS |
| 18 | 15713* | 15921 | 208 | No difference | 6–7 bp | 6–7 bp | LSD023 | NS | 5,08E-04 | 1,33E-02 | NS | NS | NS |
| 19 | 27981 | 28590 | 608 | 0–2 bp | 7 bp | 6–7 bp | LSD034—LSD036 (LW035a) | NS | 5,32E-04 | 1,02E-03 | NS | NS | NS |
| 20 | 12602 | 13041 | 439 | No difference | 6 bp | 6 bp | LSD019 | NS | 3,03E-03 | 5,80E-04 | NS | NS | NS |
| 21 | 66209* | 66566* | 357 | No difference | 6 bp | 6 bp | LSD075 | NS | 2,18E-03 | 4,11E-04 | NS | NS | NS |
| 22 | 85973 | 86804 | 831 | 0–1 bp | 6 bp | 6–7 bp | LSD091—LSD092 | NS | 1,75E-03 | 3,24E-04 | NS | NS | NS |
| 23 | 20245* | 20701 | 456 | 3–4 bp | 6 bp | 9–10 bp | LSD027 | NS | 2,20E-02 | 2,61E-04 | NS | NS | NS |
| 24 | 37425* | 38121 | 696 | 0–2 bp | 6 bp | 4–6 bp | LSD042 | NS | 1,08E-03 | 1,74E-04 | NS | NS | NS |
| 25 | 1223* | 1611 | 387 | 0–1 bp | 3 bp | 3–4 bp | LSD002—LSD003 | NS | NS | 3,95E-03 | NS | NS | NS |
| 26 | 14618* | 15180 | 562 | 1–2 bp | 6 bp | 7–8 bp | LSD020—LSD021 | NS | NS | 1,07E-02 | NS | NS | NS |
| 27 | 72045* | 72397* | 352 | No difference | 4 bp | 4 bp | LSD079 | NS | NS | 3,08E-02 | NS | NS | NS |
Recombination Sequence: RUSSIA /Saratov /2017
Major Parental Sequence(s): Vaccine = SIS-Lumpyvax (KX764643), Herbivac (KX764644), OBP (KX764645) vaccine and isolate Cro2016 (MG972412).
Major Parent = Parental strain contributing the larger fraction of sequence.
Minor Parental Sequence(s): Field = Kenya KSGP0240 (KX683219), Kenya NI-2490 (AF325528), RSA Warmbaths (AF409137), Greece Evros/GR15 (KY829023) and Serbia/Bukanovac/2016 (KY702007).
Minor Parent = Parental strain contributing the smaller fraction of sequence.
* = The actual breakpoint position is indeterminate (it was most likely obscured by a subsequent recombination event).
NS = No significant P-value was recorded for this recombination event using this method.