Table 4.
The p4c gene patristic (values without parenthesis) and pairwise genetic distance (values within parenthesis) between clusters of cowpox viruses
|
Clustersd |
|
|
|
|
|
|
|
|
|---|---|---|---|---|---|---|---|---|
| CPXV 1 | CPXV 2 | CPXV 3 | CPXV 4 | CPXV 5 | CPXV 6 | CPXV 7 | VACV | |
| CPXV 1 |
|
|
|
|
|
|
|
|
| CPXV 2 |
0.013 |
|
|
|
|
|
|
|
| (0.013) | ||||||||
| CPXV 3 |
0.012 |
0.013 |
|
|
|
|
|
|
| (0.012) |
(0.014) |
|||||||
| CPXV 4 |
0.007* |
0.009* |
0.008* |
|
|
|
|
|
| (0.008)* |
(0.011)* |
(0.007)* |
||||||
| CPXV 5 |
0.007* |
0.011 |
0.010* |
0.005* |
|
|
|
|
| (0.007)* |
(0.014) |
(0.009)* |
(0.006)* |
|||||
| CPXV 6 |
0.019 |
0.024 |
0.023 |
0.018 |
0.019 |
|
|
|
| (0.020) |
(0.024) |
(0.020) |
(0.019) |
(0.019) |
||||
| CPXV 7 |
0.014 |
0.020 |
0.019 |
0.014 |
0.014 |
0.014 |
|
|
| (0.014) |
(0.022) |
(0.020) |
(0.013) |
(0.014) |
(0.013) |
|||
| VACV | 0.023 |
0.029 |
0.028 |
0.023 |
0.024 |
0.023 |
0.013 |
|
| (0.021) | (0.029) | (0.029) | (0.023) | (0.024) | (0.025) | (0.014) |
dPatristic distance of the Maximum Likelihood (ML) tree and the genetic distance without reference to a tree were generated as described in Methods. Distances (patristic and genetic) were averaged across taxa to produce a value for each node. CPXVs belonging to the same cluster have distance values less than the TATV-CMLV threshold, while CPXVs belonging to different clusters have distance values equal or more than the TATV-CMLV threshold. TATV-CMLV patristic distance threshold is 0.011 while it’s pairwise genetic distance is 0.012. *CPXVs whose distances were less than the TATV-CMLV threshold but were still classified as belonging to different clusters because the distances between one or more individual viruses (as opposed to average distance across taxa) were equal or more than the TATV-CMLV threshold. CPXV 1 (CPXV_NOR1994_MAN, CPXV-No-H1, CPXV-No-FI, CPXV-No-F2); CPXV 2 (CPXV-BR, CPXV_UK2000_K2984); CPXV 3 (CPXV_FRA2001_NANCY, CPXV-Swe-H1, CPXV-Swe-H2), CPXV 4 (CPXV_GER2002_MKY, CPXV_GER1980_EP4); CPXV 5 (CPXV_GER1991_3, CPXV GER1998_2); CPXV 6 (CPXV_AUS1999_867); CPXV 7 (CPXV-FIN/T2000, CPXV_FIN2000_MAN, CPXV_GRI_90); VACV (VACV-WR, VACV-Lister, VACV-Acambis, VACV-CVA, HPXV-MNR76).