Table 2.
Genome-wide mutation and selection pressure analysis of Pakistan DENV-2 isolates
| Polyprotein position | Gene | Gene position | Wild type | Post-2008 Pakistan isolates (n=5) | Other reports of similar substitutions |
Mixed effect model of evolution (MEME) analysis |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| α | β- | q- | β+ | P value | Log L | ||||||
| 130 |
prM |
16 |
R |
K |
Sri Lanka2003-04§ & Pakistan
[17] |
1.87 |
0 |
0.97 |
91.05 |
0.15 |
−35.52 |
|
184 |
prM |
70 |
S |
A |
Pakistan£[17] &Malaysia (sylvatic)[24,25] |
3.61 |
0 |
1 |
134.67 |
0.05 |
−41.97 |
| 862 |
NS1 |
87 |
T |
S |
Sri Lanka2003-04§ |
1.25 |
0 |
0.97 |
6.49 |
0.74 |
−27.76 |
| 1160 |
NS2A |
33 |
I |
V |
India2001-06§ & Sri Lanka 1996-2004§ |
0 |
1 |
0.06 |
0.33 |
0.66 |
−13.61 |
| 1243 |
NS2A |
116 |
I |
T |
Thailand 1984
[26] |
0 |
0 |
0.6 |
2.7 |
0.42 |
−40.58 |
| 2891 |
NS5 |
400 |
T |
A |
Sri Lanka 2003-04§ |
0 |
0 |
0.93 |
2.85 |
0.48 |
−10.8 |
| 2953 |
NS5 |
462 |
L |
I |
India2001-06§ & Sri Lanka 1996-04§ |
1.12 |
0 |
0.99 |
513.74 |
0.20 |
−38.62 |
| 3107 |
NS5 |
616 |
E |
G |
India2001-06§ & Sri Lanka 1996-2004§ |
0 |
1 |
0.62 |
0.85 |
0.44 |
−9.39 |
| 3122 |
NS5 |
631 |
S |
G |
India2001-06§ & Sri Lanka 1996-2004§ |
0.35 |
0.45 |
0.16 |
1.44 |
0.23 |
−32.15 |
|
3352 |
NS5 |
861 |
K |
R |
Unique to Pakistan£ |
0 |
0 |
0.98 |
20.75 |
0.26 |
−11.06 |
| 3367 | NS5 | 876 | N | S | India2001-06§ & Sri Lanka 1996-04§ | 0 | 0 | 0.98 | 19.81 | 0.19 | −11.44 |
§Directly obtained from the GenBank database.
£Reported in this study.
Mutations under positive selection and those that are unique to Pakistan DENV-2 isolates are shown in bold.