Table 3.
Genome-wide mutation and selection pressure analysis of Pakistan DENV-3 isolates
| Polyprotein position | Gene | Gene position | Wild type | Pakistan isolates (n=6) | Other reports of similar substitutions |
Mixed effect model of evolution (MEME) analysis |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| α | β- | q- | β+ | P value | Log L | ||||||
|
951 |
NS1 |
178 |
L |
M |
India 2003–07[32,33] &China 2009§ |
1.83 |
0.36 |
0.99 |
1844.02 |
<0.01 |
−53.95 |
|
2063 |
NS3 |
590 |
K |
R |
Unique to Pakistan£ |
1.28 |
0 |
0.98 |
42.42 |
0.58 |
−17.20 |
| 2393 |
NS4B |
151 |
M |
I |
India 2003–07
[32,33] & China 2009§ |
1.35 |
0.16 |
1.00 |
0.31 |
1.00 |
−9.87 |
| 2678 |
NS5 |
188 |
T |
A |
India 2003–07
[32,33], China 2009§, Venezuela 2001-07§, Puerto Rico 2006§ |
0.85 |
0.38 |
0.99 |
707.57 |
0.21 |
−35.65 |
| 3052 |
NS5 |
562 |
Q |
L |
India 2003–07
[32,33], China 2009§, Colombia 2004§ |
1.74 |
1.00 |
0 |
2.65 |
0.64 |
−33.19 |
| 3385 | NS5 | 895 | S | L | Puerto-Rico 2002-03§, Colombia 2003§, Vietnam 2006§ | 2.00 | 0 | 0.99 | 35.8 | 0.47 | −21.96 |
§Directly obtained from the GenBank database.
£Reported in this study.
Mutations under positive selection and those that are unique to Pakistan DENV-3 isolates are shown in bold.