TABLE 1.
Efficiency of bootstrap phylogenetic trees constructed by different BKV regions
| Subtype or subgroup comparisona | No. of strains | WGS (1-5153)
|
VP1 (1564-2652)
|
Jin, 327 bp (1630-1956)
|
LTA gene (2722-5153)
|
LTA 2nd exon (2722-4566)
|
LTA, 325 bp (3148-3472)
|
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BS (%)b | No. (%) of strains correctly assigned/total | BS (%)b | No. (%) of strains correctly assigned/total | BS (%)b | No. (%) of strains correctly assigned/total | BS (%)b | No. (%) of strains correctly assigned/total | BS (%)b | No. (%) of strains correctly assigned/total | BS (%)b | No. (%) of strains correctly assigned/total | ||
| Subtypes | |||||||||||||
| I vs II/III/IV | 105 | 100 | 105/105 (100) | 100 | 105/105 (100) | 100 | 105/105 (100) | 100 | 105/105 (100) | 100 | 105/105 (100) | 99 | 105/105 (100) |
| II vs III | 4 | 100 | 4/4 (100) | 60 | 4/4 (100) | 39 | 4/4 (66.7) | 92 | 4/4 (100) | 85 | 4/4 (100) | 64 | 2/4 (50) |
| III vs II | 2 | 100 | 2/2 (100) | 97 | 2/2 (100) | 94 | 2/2 (100) | 100 | 2/2 (100) | 100 | 2/2 (100) | 89 | 2/2 (100) |
| IV vs II/III | 51 | 100 | 51/51 (100) | 100 | 51/51 (100) | 99 | 51/51 (100) | 100 | 51/51 (100) | 100 | 51/51 (100) | 100 | 51/51 (100) |
| Subgroups | |||||||||||||
| Ib2 vs Ib1/Ia/Ic | 42 | 100 | 42/42 (100) | 97 | 42/42 (100) | 48 | 42/42 (100) | 100 | 42/42 (100) | 99 | 42/42 (100) | 57 | 42/42 (100) |
| Ib1 vs Ib2/Ia/Ic | 28 | 100 | 28/28 (100) | 71 | 28/28 (100) | 34 | 27/28 (96.43) | 100 | 28/28 (100) | 99 | 28/28 (100) | 97 | 28/28 (100) |
| Ia vs Ib1/Ib2/Ic | 13 | 100 | 13/13 (100) | 96 | 13/13 (100) | 28 | 13/13 (100) | 100 | 13/13 (100) | 99 | 13/13 (100) | 96 | 13/13 (100) |
| Ic vs Ib1/Ib2/Ia | 22 | 100 | 22/22 (100) | 96 | 22/22 (100) | 47 | 20/22 (90.91) | 100 | 22/22 (100) | 100 | 22/22 (100) | 90 | 22/22 (100) |
| IVa vs IVb/IVc | 10 | 83 | 10/10 (100) | 34 | 10/10 (100) | NAd | 0/10 (0) | 80 | 10/10 (100) | 79 | 10/10 (100) | 39 | 10/10 (100) |
| IVb vs IVa/IVc | 11 | 87 | 11/11 (100) | NAc | 6/11 (54.55) | NAd | 0/11 (0) | 56 | 11/11 (100) | 62 | 11/11 (100) | NAe | 0/11 (0) |
| IVc vs IVa/IVb | 30 | 68 | 30/30 (100) | 21 | 30/30 (100) | NAd | 0/30 (0) | 33 | 30/30 (100) | 29 | 30/30 (100) | NAe | 0/30 (0) |
a
The subtype and subgroup assigned from all strains in different trees were compared with the WGS tree which was assumed to be 100% correct.
b
BS, bootstrap value.
c
Not applicable (NA) because although six subgroup IVb1 strains were clustered together and five subgroup IVb2 strains were also clustered together, subgroup IVb2 clustered within the IVc subgroup.
d
Not applicable because all subgroup IVa, IVb, and IVc strains can't be separated from each other.
e
Not applicable because subgroup IVb and IVc strains were clustered together and can't be separated from each other.