Background
Methods
Sample collection and virus isolation
Amplification and sequencing
Phylogenetic tree construction and recombination analyses
Molecular evolution analyses
Results
Enterovirus cell culture and molecular classification
Phylogenetic tree construction
Similarity and recombination analyses
Molecular evolution analysis
Genes | Model codea
| ℓb
| Parameter estimatesc
| Neutral sitesd
|
---|---|---|---|---|
VP4 |
M1a(nearly neutral) | −1073.6 |
p0 = 0.963, p1 = 0.037 | 18 N, 64S |
ω0 = 0.014, ω1 = 1.000 | ||||
M2a(positive selection) | −1073.6 |
p0 = 0.963, p1 = 0.037, p2 = 0.000 | ||
ω0 = 0.014, ω1 = 1.000, ω2 = 4.752 | ||||
M0(one ω) | −1076.3 |
ω = 0.021 | ||
Branch(
ω changed
)
| −1076.2 |
ω = 0.021, ω(KM branch) = 0.0001 | ||
VP3 |
M1a(nearly neutral) | −3343.7 |
p0 = 0.984, p1 = 0.016 | 35 N, 80A, 232R |
ω0 = 0.006, ω1 = 1.000 | ||||
M2a(positive selection) | −3343.7 |
p0 = 0.984, p1 = 0.016, p2 = 0.000 | ||
ω0 = 0.006, ω1 = 1.000, ω2 = 5.550 | ||||
M0(one ω) | −3353.0 |
ω = 0.010 | ||
Branch(
ω changed
)
| −3351.5 |
ω = 0.009, ω(KM branch) = 0.048 | ||
VP2 |
M1a(nearly neutral) | −3769.9 |
p0 = 0.977, p1 = 0.023 | 55Q, 137 V, 163 T, 165G |
ω0 = 0.010, ω1 = 1.000 | ||||
M2a(positive selection) | −3769.9 |
p0 = 0.977, p1 = 0.023, p2 = 0.000 | ||
ω0 = 0.010, ω1 = 1.000, ω2 = 6.220 | ||||
M0(one ω) | −3777.8 |
ω = 0.015 | ||
Branch(
ω changed
)
| −3777.2 |
ω = 0.015, ω(KM branch) = 0.0001 | ||
VP1 |
M1a(nearly neutral) | −4171.4 |
p0 = 0.991, p1 = 0.009 | 139A |
ω0 = 0.014, ω1 = 1.000 | ||||
M2a(positive selection) | −4171.4 |
p0 = 0.991, p1 = 0.009, p2 = 0.000 | ||
ω0 = 0.014, ω1 = 1.000, ω2 = 33.127 | ||||
M0(one ω) | −4177.0 |
ω = 0.016 | ||
Branch(
ω changed
)
| −4177.0 |
ω = 0.016, ω(KM branch) = 0.023 | ||
2A |
M1a(nearly neutral) | −2500.2 |
p0 = 0.962, p1 = 0.038 | 7A, 14I, 23 N, 49 T, 63 V |
ω0 = 0.020, ω1 = 1.000 | ||||
M2a(positive selection) | −2500.2 |
p0 = 0.962, p1 = 0.023, p2 = 0.015 | ||
ω0 = 0.014, ω1 = 1.000, ω2 = 1.000 | ||||
M0(one ω) | −2533.4 |
ω = 0.032 | ||
Branch(
ω changed
)
| −2532.3 |
ω = 0.031, ω(KM branch) = 0.090 | ||
2B |
M1a(nearly neutral) | −1743.4 |
p0 = 0.994, p1 = 0.006 | |
ω0 = 0.022, ω1 = 1.000 | ||||
M2a(positive selection) | −1743.4 |
p0 = 0.994, p1 = 0.006, p2 = 0.000 | ||
ω0 = 0.022, ω1 = 1.000, ω2 = 5.357 | ||||
M0(one ω) | −1743.6 |
ω = 0.023 | ||
Branch(
ω changed
)
| −1743.4 |
ω = 0.023, ω(KM branch) = 0.0001 | ||
2C |
M1a(nearly neutral) | −6875.4 |
p0 = 0.991, p1 = 0.009 | 34I, 48S |
ω0 = 0.008, ω1 = 1.000 | ||||
M2a(positive selection) | −6875.4 |
p0 = 0.991, p1 = 0.009, p2 = 0.000 | ||
ω0 = 0.008, ω1 = 1.000, ω2 = 17.307 | ||||
M0(one ω) |
−6889.1
|
ω = 0.010 | ||
Branch(
ω changed
)
|
−6882.4
|
ω = 0.009, ω(KM branch) = 0.1052 | ||
3AB |
M1a(nearly neutral) | −2355.5 |
p0 = 0.977, p1 = 0.023 | 41K, 48I |
ω0 = 0.020, ω1 = 1.000 | ||||
M2a(positive selection) | −2355.5 |
p0 = 0.977, p1 = 0.029, p2 = 0.000 | ||
ω0 = 0.020, ω1 = 1.000, ω2 = 12.815 | ||||
M0(one ω) |
−2356.4
|
ω = 0.024 | ||
Branch(
ω changed
)
|
−2348.1
|
ω = 0.021, ω(KM branch) = 0.445 | ||
3C |
M1a(nearly neutral) | −3926.0 |
p0 = 0.992, p1 = 0.008 | 57 V |
ω0 = 0.016, ω1 = 1.000 | ||||
M2a(positive selection) | −3926.0 |
p0 = 0.992, p1 = 0.008, p2 = 0.000 | ||
ω0 = 0.016, ω1 = 1.000, ω2 = 2.687 | ||||
M0(one ω) |
−3929.2
|
ω = 0.018 | ||
Branch(
ω changed
)
|
−3923.8
|
ω = 0.016, ω(KM branch) = 0.1411 | ||
3D |
M1a(nearly neutral) | −8184.6 |
p0 = 0.989, p1 = 0.011 | 32H, 75R, 259S, 435S |
ω0 = 0.014, ω1 = 1.000 | ||||
M2a(positive selection) | −8184.6 |
p0 = 0.989, p1 = 0.011, p2 = 0.000 | ||
ω0 = 0.014, ω1 = 1.000, ω2 = 33.13 | ||||
M0(one ω) | −8217.2 |
ω = 0.017 | ||
Branch(
ω changed
)
| −8217.1 |
ω = 0.017, ω(KM branch) = 0.025 |
Genes | Modela
| ℓ | Parameter estimatesb
| Sites with ω2a changed on the KM branchc
|
---|---|---|---|---|
2C |
H0
| −6933.9 |
p0 = 0.88, p1 = 0.01, p2a = 0.11, p2b = 0.00 | 260 V, 307 L, 312 T, 319I, 321R
|
Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00 | ||||
Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00 | ||||
H1
| −6933.9 |
p0 = 0.88, p1 = 0.01, p2a = 0.11, p2b = 0.00 | ||
Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00 | ||||
Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00 | ||||
3AB |
H0
| −2348.1 |
p0 = 0.52, p1 = 0.01, p2a = 0.47, p2b = 0.00 |
15D, 16 T, 29 L, 41 K, 55D
|
Background: ω0 = 0.02, ω1 = 1.00, ω2a = 0.02, ω2b = 1.00 | ||||
Foreground: ω0 = 0.02, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00 | ||||
H1
| −2348.1 |
p0 = 0.52, p1 = 0.01, p2a = 0.47, p2b = 0.00 | ||
Background: ω0 = 0.02, ω1 = 1.00, ω2a = 0.02, ω2b = 1.00 | ||||
Foreground: ω0 = 0.02, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00 | ||||
3C |
H0
| −3919.5 |
p0 = 0.85, p1 = 0.01, p2a = 0.15, p2b = 0.00 |
3P, 16G, 52H, 84 M, 98S |
Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00 | ||||
Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 1.00, ω2b = 1.00 | ||||
H1
| −3919.2 |
p0 = 0.93, p1 = 0.01, p2a = 0.06, p2b = 0.00 | ||
Background: ω0 = 0.01, ω1 = 1.00, ω2a = 0.01, ω2b = 1.00 | ||||
Foreground: ω0 = 0.01, ω1 = 1.00, ω2a = 3.31, ω2b = 3.31 |