Table 2.
Selection pressure analyses of 186 RRV and 88 BFV strains collected in Australia and the Pacific between 1959 and 2018.
| Methodsa | |||||||
|---|---|---|---|---|---|---|---|
| Virus | Gene | Codon | Amino acid substitution | FEL | SLAC P value |
MEME | FUBAR posterior probability |
| RRV | nsP1 | 248 | T248I | 0.000 | 0.00006 | 0.000 | 1.000 |
| nsP1 | 441 | K441E/T | 0.064 | 0.102 | 0.030 | 0.986 | |
| nsP3 | 435 | A435I/G/T/Vb | 0.0498 | 0.198 | 0.000 | 0.967 | |
| BFV | nsP1 | 297 | K297E/I/N | 0.0862 | 0.233 | 0.010 | 0.980 |
| nsP1 | 447 | S447G | 0.0835 | 0.234 | 0.010 | 0.982 | |
a
The P-value thresholds used were <0.05 (FEL and MEME) and <0.1 (SLAC). The posterior probability (PP) threshold used for FUBAR was >0.900. Sites under significant positive selection by at least two methods are indicated by P-values and PPs shown in bold font.
b
RRV isolates containing nsP3 aa site 435 mutations in the intrinsically unstructured region of the hypervariable domain (HDV) included MN038278|SW72209|WA_Busselton|2003 (A435I), MN038284|SW94735|WA_Harvey|2013 (A435G), MW350155|19 502|QLD_Charleville|1976 (435 T), and MW321536|V-309|NT_ Jabiru|1983 (A435V).