Table 3. Genome-wide selection pressure analysis of non-synonymous substitutions detected in the epidemic lineage.
| Substitution | Other reports of similar substitution | Selection pressure analysis method |
|||
|---|---|---|---|---|---|
| SLAC | FEL | IFEL | MEME | ||
| PrM-K90R | Vietnam (GQ199833), Cambodia (FJ639678) | Neutral | Negative (p = 0.04) | Neutral | Neutral (p = 0.09) |
| prM-K122R | Common mutation in isolates from Southeast Asia and the Americas | Neutral | Neutral (p = 0.07) | Neutral | Neutral (p = 0.08) |
| E-I140V | Unique | Neutral | Neutral (p = 0.79) | Neutral | Neutral (p = 0.60) |
| E-S171L | Unique | Neutral | Neutral (p = 0.51) | Neutral | Neutral (p = 0.30) |
| E-I173V | Unique | Neutral | Neutral (p = 0.79) | Neutral | Neutral (p = 0.60) |
| E-D290G | Unique | Neutral | Neutral (p = 0.38) | Neutral | Positive (p = 0.02) |
| E-S339I | China (KF864667), Angola (KF184975), India (JQ922546), India (JN903578), Singapore (EU081258), Cote D’Ivoire (AF298807) | Neutral | Neutral (p = 0.19) | Neutral | Neutral (p = 0.39) |
| E-T346A | Unique | Neutral | Neutral (p = 0.75) | Neutral | Neutral (p = 0.67) |
| E-V365I | AF226686, Solomon Islands (JQ655094), Japan (AB204803) | Neutral | Neutral (p = 0.13) | Negative (p = 0.03) | Positive (p = 0.05) |
| E-A369I | Unique | Neutral | Neutral (p = 0.15) | Neutral | Neutral (p = 0.67) |
| NS1-S94Y | Unique | Neutral | Neutral (p = 0.69) | Neutral | Neutral (p = 0.67) |
| NS2A-V39I | Unique | Neutral | Neutral (p = 0.34) | Neutral | Positive (p = 0.01) |
| NS3-A325S | Unique | Neutral | Neutral (p = 0.23) | Neutral | Positive (p = 0.04) |
| NS4B-K212R | India (JQ917404, KF289072, JQ692085) | Neutral | Neutral (p = 0.81) | Neutral | Neutral (p = 0.33) |
| NS5-L45M | Unique | Negative (p = 0.02) | Negative (p = 0.001) | Neutral | Neutral (p = 0.67) |
| NS5-V270T | Unique | Neutral | Negative (p = 0.05) | Neutral | Positive (p = 0.05) |
*Reference sequence = NCBI Accession No. NC001477. The cut-off for significance level was set at 0.05. prM = membrane protein, E = envelope protein, NS = non-structural proteins.