Table 3.
Selection Pressure Analysis on Genome-wide Non-synonymous Substitutions Detected in Six “Established” Lineages of DENV-1
| Substitutiona | Lineage | Selection Pressure Analysisb |
||||
|---|---|---|---|---|---|---|
| SLAC | FEL | IFEL | FUBAR | MEME | ||
| E-I337F | GIII 2011; GIII 2013 | Neg (0.01) | Neg (0.004) | Neu | Neg (0.99) | Epi (0.04) |
| E-S338L | GIb | Neu | Neg (0.04) | Neg (0.05) | Neg (0.93) | Neu |
| NS1-F323Y | GIa | Neg (0.04) | Neg (0.02) | Neu | Neg (0.99) | Neu |
| NS2B-L21F | GIb | Neg (0.001) | Neg (<0.001) | Neg (0.04) | Neg (0.99) | Neu |
| NS2B-I106 | GIc | Neg (0.02) | Neg (0.03) | Neu | Neg (0.97) | Neu |
| NS4A-V68M | GIb | Neg (0.04) | Neg (0.01) | Neu | Neg (0.99) | Neu |
| NS5-V231I | GIa | Neg (0.04) | Neg (0.01) | Neu | Neg (0.99) | Neu |
| NS5-N285C | GIa | Neu | Pos (0.03) | Pos (0.01) | Neu | Epi (0.002) |
NCBI reference genome NC_001477 was used as the wild type sequence.
The data are given for the residues identified in genetic signatures of each “established” lineage (Tables 1 and 2). The table includes only the sites that were either under purifying or positive (shown in bold) by at least three methods. The neutral sites are given in Table S3. p values (SLAC, FEL, IFEL, and MEME) and posterior probability (FUBAR) are given in brackets. E, envelope protein; Epi, episodic selection; GI, genotype I; GIII, genotype III; prM, precursor membrane protein; Neg, purifying selection; Neu, neutral; NS, non-structural proteins; Pos, positive selection.