Background
Methods
Case presentation
Virus isolation, identification and serotyping
Whole-genome sequencing analysis
5′ / 3′ rapid amplification of cDNA ends (RACE)
Accession number
Genomic characterization analysis
Phylogenetic analysis
Recombination analysis
Selection pressure analysis
Results
Identification and serotyping of virus
Full-length sequence and genomic characterization of YNPE2
Serial number | Accession number | NT identity (%) | AA identity (%) |
---|---|---|---|
1 | EU056811 | 89.5 | 96.7 |
2 | GQ868588 | 89.5 | 96.7 |
3 | AY702040 | 89.7 | 96.7 |
4 | HM582105 | 89.8 | 96.8 |
5 | HM582108 | 89.8 | 96.9 |
6 | HM582099 | 89.9 | 96.9 |
7 | JN851123 | 91.1 | 97.2 |
8 | HQ012538 | 92.1 | 97.1 |
9 | JX470186 | 91.2 | 97.1 |
10 | FJ898454 | 91.3 | 97.4 |
11 | FJ850088 | 91.4 | 96.7 |
12 | GQ252676 | 91.4 | 97.4 |
13 | EU179858 | 91.5 | 97.0 |
14 | EU482636 | 91.7 | 97.0 |
15 | FJ639703 | 91.8 | 97.4 |
16 | EU482788 | 91.9 | 97.4 |
17 | AY702039 | 92.0 | 97.0 |
18 | EU529695 | 92.2 | 97.1 |
19 | GQ398271 | 92.1 | 97.1 |
20 | GQ868540 | 92.2 | 97.1 |
21 | FJ898450 | 92.3 | 97.3 |
22 | GQ398264 | 92.3 | 97.3 |
23 | DQ181801 | 92.4 | 97.4 |
24 | AF119661 | 92.4 | 97.4 |
25 | GQ398269 | 92.4 | 97.3 |
26 | JF730055 | 94.4 | 98.0 |
27 | HQ891024 | 94.4 | 97.9 |
28 | AF204178 | 94.4 | 97.7 |
29 | EU854293 | 94.6 | 98.1 |
30 | AF038403 | 94.5 | 98.1 |
31 | GQ398268 | 94.6 | 98.3 |
32 | FJ196851 | 96.0 | 98.2 |
33 | FJ639705 | 98.2 | 99.5 |
34 | FJ906957 | 98.3 | 99.5 |
35 | FJ410215 | 98.4 | 99.7 |
36 | EU482445 | 98.5 | 99.7 |
37 | GQ868543 | 98.7 | 99.5 |
38 | FJ639832 | 99.0 | 99.8 |
39 | DQ181797 | 99.0 | 99.8 |
Amino acid sequence diversity
Serial number | AAa position (ORF) | AA position (Protein) | MF459663 (YNPE2) | AF038403 (New Guinea) |
---|---|---|---|---|
Capsid | ||||
1 | 9 | 9 | K | R |
2 | 101 | 101 | S | T |
prM | ||||
3 | 129 | 15 | G | S |
4 |
130
|
16
|
I
|
R
|
5 | 169 | 55 | L | F |
6 | 266 | 152 | V | A |
E | ||||
7 | 351 | 71 | E | D |
8 | 363 | 83 | K | N |
9 |
406
|
126
|
E
|
K
|
10 | 409 | 129 | I | V |
11 | 421 | 141 | V | I |
12 | 444 | 164 | V | I |
13 |
456
|
176
|
A
|
T
|
14 | 506 | 226 | K | T |
15 | 508 | 228 | E | G |
16 |
626
|
346
|
Y
|
H
|
17 | 682 | 402 | F | I |
18 | 764 | 484 | I | V |
NS1 | ||||
19 | 825 | 50 | Q | H |
20 |
855
|
80
|
A
|
S
|
21 | 880 | 105 | R | Q |
22 |
904
|
129
|
Y
|
H
|
23 | 947 | 172 | K | R |
24 | 952 | 177 | A | V |
25 | 997 | 222 | N | S |
26 | 1022 | 247 | L | F |
27 |
1036
|
261
|
Y
|
H
|
28 |
1039
|
264
|
I
|
T
|
29 | 1056 | 281 | D | E |
30 | 1061 | 286 | I | V |
NS2A | ||||
31 |
1132
|
5
|
V
|
T
|
32 | 1178 | 51 | K | R |
33 | 1184 | 57 | V | M |
34 |
1192
|
65
|
A
|
T
|
35 | 1247 | 120 | V | I |
36 | 1263 | 136 | I | M |
37 | 1266 | 139 | N | K |
38 |
1285
|
158
|
T
|
A
|
39 | 1308 | 181 | L | F |
40 |
1316
|
189
|
T
|
A
|
NS2B | ||||
41 |
1402
|
57
|
T
|
A
|
42 | 1457 | 112 | I | V |
43 | NS3 | |||
44 | 1488 | 13 | M | V |
45 |
1595
|
120
|
T
|
A
|
46 | 1662 | 187 | R | K |
47 | 1808 | 333 | I | M |
48 | 1820 | 345 | N | S |
49 | 2024 | 549 | K | R |
50 |
2081
|
606
|
A
|
T
|
NS4A | ||||
51 |
2114
|
21
|
T
|
A
|
NS4B
| ||||
52 |
2262
|
19
|
A
|
T
|
53 | 2355 | 112 | L | F |
54 | 2418 | 175 | I | V |
NS5 | ||||
55 |
2626
|
135
|
I
|
T
|
56 | 2792 | 301 | R | K |
57 | 2826 | 335 | L | V |
58 |
2828
|
337
|
T
|
M
|
59 | 2920 | 429 | G | S |
60 | 3122 | 631 | N | S |
61 | 3132 | 641 | V | I |
62 | 3167 | 676 | H | S |
63 | 3178 | 687 | I | V |
64 | 3189 | 698 | K | R |
65 | 3310 | 819 | R | Q |
66 |
3356
|
865
|
A
|
T
|
Phylogenetic analysis
Recombination analysis
Selection pressure analysis
AAa position (ORF) | MEME | SLAC | FEL | IFEL | ||||
---|---|---|---|---|---|---|---|---|
ω | p-Value | ω | p-Value | ω | p-Value | ω | p-Value | |
prM | ||||||||
248 | 55.584 | 0.062 | 4.778 | 0.445 | 1.525 | 0.277 | 1.123 | 0.278 |
253 | > 100 | 0.089 | 2.368 | 0.672 | 0.789 | 0.446 | < 0 | 1 |
Envelope | ||||||||
408 | > 100 | 0.093 | 2.309 | 0.712 | 0.824 | 0.406 | 2.171 | 0.333 |
735 | > 100 | 0.096 | 1.602 | 0.995 | 0.486 | 9.56 | < 0 | 1 |
NS1 | ||||||||
986 | > 100 | 0.054 | 2.417 | 0.68 | 0.826 | 0.322 | < 0 | 1 |
1010 | > 100 | 0.017 | 2.431 | 0.664 | 0.713 | 0.416 | 2.098 | 0.305 |
NS2A | ||||||||
1142 | > 100 | < 0.001 | 3.231 | 0.988 | 0.997 | 0.929 | < 0 | 1 |
1195 | > 100 | 0.093 | 1.685 | 0.946 | 0.576 | 0.819 | < 0 | 1 |
NS2B | ||||||||
1439 | > 100 | 0.019 | 4.765 | 0.447 | 1.485 | 0.246 | < 0 | 1 |
1459 | > 100 | 0.014 | 5146 | 0.8 | 1.81 | 0.649 | 1.044 | 0.718 |
NS3 | ||||||||
1489 | > 100 | 0.067 | 9.674 | 0.198 | 3.111 | 0.979 | < 0 | 1 |
NS4B | ||||||||
2262 | 5.444 |
0.0838
| 13.16 | 0.108 | 3.4 |
0.088
| 6.196 |
0.082
|
NS5 | ||||||||
3310 | 2.249 | 0.107 | 8.065 | 0.296 | 4.012 |
0.085
| 8.109 |
0.058
|