Background
Materials and methods
Virus
Isolate/strain | Origin | Year of isolation | District | Accession |
---|---|---|---|---|
GTPV-Thx | goat | April .2010 | Nanjiang | – |
GTPV-KS | goat | April.2011 | Nanjiang | – |
GTPV-SS | goat | July.2011 | Nanjiang | – |
SPPV-M1 | sheep | January.2011 | Nanjiang | – |
SPPV-M2 | sheep | February.2011 | Nanjiang | – |
GTPV-YM | vaccine | – | – | – |
PCR and sequencing
ORF | Primer sequence(5′-3′) | Length of amplicon (~bp) |
---|---|---|
ORF010 | F1:CGGAATTCGCAATCATCAATTACTATGG (PCR) R1:CCGCTCGAGAACTTTTTATTGTTTGCC (PCR) | 636 |
ORF138 | F1:CGGAATTCGATGATTTTGTTATACGATTAC (PCR) R1:CCGCTCGAGTTATGGCGTATACACAAC (PCR) GTTATACGATTACATCACGCTC (Seq.) ATTCGTCAGGATCCAAAGTGAATAA (Seq.) TGGGATTTGTTGCGTATT (Seq.) | 1896 |
ORF140 | F1:CGGAATTCGTCACCAAAAATGTCACTGT (PCR) R1:CCGCTCGAGTTATAAAAAGTACTTCTTTG (PCR) TTGCTACTAAAAAACGGTGC (Seq.) TATCTAAGGATTTACGTGTATATGA (Seq.) | 1497 |
ORF141.2 | F1:CGGAATTCGACCATGGAATACATTAGTG (PCR) R1:CCGCTCGAGTCATTTTATTGCCAACAAC (PCR) ACAGTTTTGGGCAACAAAAG (Seq.) | 1344 |
ORF145 | F1:CGGAATTCGTATACTTACAAAATGGAT (PCR) R1:CCGCTCGAGTAAATTTTACTTTAACGG (PCR) AATACTTACAACGAGATTCGCC (Seq.) | 1400 |
Sequence analysis of ANK 010,138,140,141.2 and 145
Isolate | Accession number | ||||
---|---|---|---|---|---|
010 | 138 | 140 | 141.2 | 145 | |
GTPV AV41 | MH381810.1 | MH381810.1 | MH381810.1 | / | MH381810.1 |
GTPV India/P100 | MF629128.1 | MF629136.1 | MF629110.1 | MF629119.1 | / |
GTPV India/P62 | MF629127.1 | MF629135.1 | MF629109.1 | MF629118.1 | MF629099.1 |
GTPV India/P6 | MF629126.1 | MF629134.1 | MF629108.1 | MF629117.1 | MF629098.1 |
GTPV India/P21 | MF629125.1 | / | / | MF629116.1 | / |
GTPV India/P19 | MF629124.1 | MF629133.1 | / | MF629115.1 | MF629097.1 |
GTPV India/P3 | MF629123.1 | MF629132.1 | / | MF629114.1 | MF629096.1 |
GTPV FZ | KC951854.1 | KC951854.1 | KC951854.1 | KC951854.1 | KC951854.1 |
GTPV Gorgan | KX576657.1 | KX576657.1 | KX576657.1 | KX576657.1 | KX576657.1 |
GTPV G20-LKV | AY077836.1 | AY077836.1 | AY077836.1 | AY077836.1 | AY077836.1 |
GTPV Pellor | AY077835.1 | AY077835.1 | AY077835.1 | AY077835.1 | AY077835.1 |
LSDV Herbivac | MK441838.1 | MK441838.1 | MK441838.1 | MK441838.1 | MK441838.1 |
LSDV Cro2016 | MG972412.1 | MG972412.1 | MG972412.1 | MG972412.1 | MG972412.1 |
LSDV LSD | KX764645.1 | KX764645.1 | KX764645.1 | KX764645.1 | KX764645.1 |
LSDV Herbivac | KX764644.1 | KX764644.1 | KX764644.1 | KX764644.1 | KX764644.1 |
LSDV Lumpyvax | KX764643.1 | KX764643.1 | KX764643.1 | / | KX764643.1 |
LSDV Vaccine | AF409138.1 | AF409138.1 | AF409138.1 | AF409138.1 | AF409138.1 |
LSDV Saratov | MH646674.1 | MH646674.1 | MH646674.1 | MH646674.1 | MH646674.1 |
SPPV India/P42 | MF629131.1 | MF629138.1 | MF629113.1 | MF629122.1 | / |
SPPV India/P4 | MF629129.1 | / | MF629111.1 | MF629120.1 | / |
SPPV Jaipur | MG000156.1 | MG000156.1 | MG000156.1 | MG000156.1 | MG000156.1 |
SPPV NISKHI | AY077834.1 | AY077834.1 | AY077834.1 | AY077834.1 | AY077834.1 |
SPPV A | AY077833.1 | AY077833.1 | AY077833.1 | AY077833.1 | AY077833.1 |
SPPV 10700–99 | AY077832.1 | AY077832.1 | AY077832.1 | AY077832.1 | AY077832.1 |
SPPV India/P7 | MF629130.1 | MF629137.1 | MF629112.1 | MF629121.1 | / |
LSDV 155920 | KX894508.1 | KX894508.1 | KX894508.1 | KX894508.1 | KX894508.1 |
LSDV Dagestan | MH893760.2 | MH893760.2 | MH893760.2 | MH893760.2 | MH893760.2 |
LSDV GR/15 | KY829023.3 | KY829023.3 | KY829023.3 | KY829023.3 | KY829023.3 |
LSDV Bujanovac | KY702007.1 | KY702007.1 | KY702007.1 | KY702007.1 | KY702007.1 |
LSDV 0240 | KX683219.1 | KX683219.1 | KX683219.1 | KX683219.1 | KX683219.1 |
LSDV 2490 | AF325528.1 | AF325528.1 | AF325528.1 | AF325528.1 | AF325528.1 |
LSDV Warmbaths | AF409137.1 | AF409137.1 | AF409137.1 | AF409137.1 | AF409137.1 |
GTPV Turkey | MN072622.1 | MN072622.1 | MN072622.1 | MN072622.1 | MN072622.1 |
GTPV India | MN072620.1 | MN072620.1 | MN072620.1 | MN072620.1 | MN072620.1 |
GTPV Vietna | MN072621.1 | MN072621.1 | MN072621.1 | MN072621.1 | MN072621.1 |
GTPV Yemen | MN072625.1 | MN072625.1 | MN072625.1 | MN072625.1 | MN072625.1 |
GTPV Sudan | MN072624.1 | MN072624.1 | MN072624.1 | MN072624.1 | MN072624.1 |
SPPV Turkey | MN072631.1 | MN072631.1 | MN072631.1 | MN072631.1 | MN072631.1 |
SPPV Saudi | MN072630.1 | MN072630.1 | MN072630.1 | MN072630.1 | MN072630.1 |
SPPV Pendik | MN072629.1 | MN072629.1 | MN072629.1 | MN072629.1 | MN072629.1 |
SPPV Saudi | MN072627.1 | MN072627.1 | MN072627.1 | MN072627.1 | MN072627.1 |
SPPV Abu | MN072626.1 | MN072626.1 | MN072626.1 | MN072626.1 | MN072626.1 |
GTPV Oman | MN072623.1 | MN072623.1 | MN072623.1 | MN072623.1 | MN072623.1 |
SPPV Nigeria | MN072628.1 | MN072628.1 | MN072628.1 | MN072628.1 | MN072628.1 |
LSDV Kenya | MN072619.1 | MN072619.1 | MN072619.1 | MN072619.1 | MN072619.1 |
SPPV Fenner | / | MG000157.1 | MG000157.1 | MG000157.1 | / |
Analysis of phylogenetic tree based ANK010,138,140,141.2 and 145
Result
Sequence analysis of ANK genes010,138,140,141.2,145
Isolate | Identity%(nucleotide/amino acid) | ||||
---|---|---|---|---|---|
GTPV India/P62 | |||||
ORF010 | ORF138 | ORF140 | ORF141.2 | ORF145 | |
KS | 100.00/100.0 | 99.74/− | 99.93/100.0 | 99.93/99.8 | 98.60/97.8 |
Thx | 99.69/99.1 | 99.79/99.8 | 99.73/99.6 | 99.93/99.8 | 99.78/99.6 |
YM | 99.53/99.5 | 99.74/− | 99.33/− | 99.33/− | 99.34/97.8 |
SS | 97.18/96.2 | 96.22/96.2 | 96.79/96.2 | 96.73/94.0 | 95.67/92.7 |
M1 | 100.00/100.0 | 96.22/96.2 | 96.79/96.2 | 96.36/− | 95.67/92.7 |
M2 | 97.80/96.2 | 96.22/96.2 | 96.33/− | 96.65/93.8 | 95.67/92.7 |
SL.No | Nucleotide position and difference | Amino acid position and difference | ||||||
---|---|---|---|---|---|---|---|---|
Position | GTPV | SPPV | LSDV | Position | GTPV | SPPV | LSDV | |
1 | 24 | A | C | T | ||||
2 | 30 | T | C | T | ||||
3 | 90 | A | G | A | ||||
4 | 102 | T | C | T/C | ||||
5 | 135 | C | T | C | ||||
6 | 309 | G | A | G | ||||
7 | 338 | T | C | C | 113 | L | S | S |
8 | 360 | A | G | A | ||||
9 | 361 | A | G | A/G | 121 | S | G | S/G |
10 | 387 | C | T | C | ||||
11 | 513 | C | T | C/T | ||||
12 | 547 | C | T | T | 183 | L | F | F |
13 | 555 | T | C | C | ||||
14 | 564 | G | A | G | ||||
15 | 567 | G | A | A/G | ||||
16 | 614 | G | A | A | 205 | S | N | N/D |
17 | 629 | C | T | C | 210 | T | I | T/S |
18 | 648 | T | C | C | ||||
19 | 651 | A | C | C | ||||
20 | 675 | C | T | C/T | ||||
21 | 699 | A | G | A | ||||
22 | 795 | A | G | A | ||||
23 | 920 | T | C | C | 307 | L | S | S |
24 | 928–929 | GT | AC | AC | 310 | V | T | T |
25 | 980 | G | A | A | 327 | R | K | K |
26 | 1016 | A | G | A | 339 | N | S | N |
27 | 1044 | T | G | G/A | ||||
28 | 1089 | G | A | G | 363 | M | I | R |
29 | 1102 | G | T | G | 368 | A | S | A |
30 | 1137 | T | C | C | ||||
31 | 1292–1293 | GT | AC | GT | 431 | S | N | S |
32 | 1308 | A | G | T/A | ||||
33 | 1425 | T | A | T | ||||
34 | 1428 | T | C | C/T | ||||
35 | 1454 | G | A | A | 485 | R | K | K |
36 | 1482 | G | A | A | ||||
37 | 1535 | C | T | C/T | 511 | S | L | S/L |
38 | 1542 | C | T | C/T | ||||
39 | 1543 | T | G | A | ||||
40 | 1545 | T | A | A | 515 | Y | E | K |
41 | 1551 | T | C | C/T | ||||
42 | 1589 | A | G | G | 530 | N | S | S |
43 | 1602 | G | A | G | ||||
44 | 1606 | G | A | G | 536 | V | I | V |
45 | 1609 | T | C | T | 537 | S | P | S |
46 | 1617 | T | C | C | ||||
47 | 1618 | G | A | G | 540 | D | N | D |
48 | 1662 | A | G | A | ||||
49 | 1671 | G | A | G | 557 | M | I | M |
50 | 1678 | A | G | A | ||||
51 | 1679 | T | G | G | 560 | I | G | R |
52 | 1692 | A | G | A | ||||
53 | 1706 | C | G | C | 569 | A | G | A |
54 | 1764 | T | C | C | ||||
55 | 1770 | C | T | C | ||||
56 | 1854 | G | A | G | ||||
57 | 1875 | C | A | C | ||||
58 | 1888 | G | T | G | 630 | V | F | V |
59 | 1896 | T | A | T | 631 | Y | – | Y |
60 | 1897–1905 | AAGCCATAA | – | AAGCCATAA | 633–634 | KP | – | KP |
SL.No | Nucleotide position and difference | Amino acid position and difference | ||||||
---|---|---|---|---|---|---|---|---|
Position | GTPV | SPPV | LSDV | Position | GTPV | SPPV | LSDV | |
1 | 21 | C | T | C | ||||
2 | 24 | T | C | C | ||||
3 | 49 | A | G | G | 17 | N | D | D |
4 | 105 | T | C | C/T | ||||
5 | 147 | G | T | G | ||||
6 | 156 | T | C | T | ||||
7 | 162 | T | G | G | ||||
8 | 164 | G | A | G | 55 | R | K | R |
9 | 175 | G | A | G | 59 | E | K | E |
10 | 186 | C | T | T | ||||
11 | 241 | T | C | T | 81 | Y | H | Y |
12 | 280 | C | T | C | ||||
13 | 300 | A | T | G | ||||
14 | 301 | A | G | G | 101 | N | D | D |
15 | 342 | T | G | G | 114 | I | M | M |
16 | 387 | G | A | G | ||||
17 | 408 | A | T | A | ||||
18 | 438 | G | A | A/G | ||||
19 | 453 | C | T | T | ||||
20 | 472 | C | T | T | 158 | L | F | F |
21 | 492 | C | T | T | ||||
22 | 501 | C | T | T | ||||
23 | 552 | G | T | G | ||||
24 | 571 | G | A | G | 191 | D | N | D |
25 | 669 | A | G | G | ||||
26 | 679 | T | C | C | ||||
27 | 690 | C | T | C | ||||
28 | 748 | A | T | T | 250 | I | L | L |
29 | 763 | G | A | G | 255 | E | K | E |
30 | 873 | T | C | T | ||||
31 | 876 | T | A | A | ||||
32 | 885 | A | C | C | ||||
33 | 931 | G | T | G | 311 | A | S | A |
34 | 937 | A | G | G | 313 | K | E | E |
35 | 942 | A | C | C | ||||
36 | 1019 | G | A | G | 340 | S | N | S |
37 | 1077 | A | G | G | ||||
38 | 1170 | G | T | G | 390 | K | N | K |
39 | 1218 | A | G | A | ||||
40 | 1309 | G | A | A | 437 | D | N | N |
41 | 1322 | G | A | G | 441 | R | K | R |
42 | 1359 | T | G | G | ||||
43 | 1366–1368 | ATA | TAT | TAT | 456 | I | Y | Y |
44 | 1417 | C | T | C | 473 | H | Y | H |
SL.No | Nucleotide position and difference | Amino acid position and difference | ||||||
---|---|---|---|---|---|---|---|---|
Position | GTPV | SPPV | LSDV | Position | GTPV | SPPV | LSDV | |
1 | 16 | G | A | G | 6 | D | N | D |
2 | 24 | A | C | A | 8 | E | D | E |
3 | 25 | G | A | G | 9 | E | K | E |
4 | 39 | G | A | G | ||||
5 | 107 | C | A | C | 36 | T | K | T |
6 | 161 | T | G | G | 54 | I | S | S |
7 | 338 | C | A | C | 113 | T | K | T |
8 | 355 | A | G | G | ||||
9 | 357 | C | T | T | 119 | N | D | D |
10 | 376 | T | C | T/C | ||||
11 | 402 | T | G | G | 134 | N | K | K |
12 | 442 | A | G | G | 148 | N | D | D |
13 | 507 | T | G | G/T | 169 | D | E | E/D |
14 | 552 | T | C | C | ||||
15 | 654 | C | T | T | ||||
16 | 684 | A | C | C | ||||
17 | 708 | A | G | A | ||||
18 | 714 | A | T | A | ||||
19 | 717 | A | G | A | ||||
20 | 756 | T | C | T | ||||
21 | 758 | G | A | G | 253 | S | N | S |
22 | 789 | T | A | T/C | ||||
23 | 827 | C | T | C | 276 | T | I | T |
24 | 870 | C | A | C | ||||
25 | 887 | G | A | G | 296 | C | Y | C |
26 | 896 | G | A | A | 299 | S | N | N/D |
27 | 899 | A | T | A | 300 | Y | F | Y |
28 | 907 | G | A | G | 303 | D | N | D |
29 | 958 | G | A | G | 320 | E | K | E |
30 | 997 | A | G | G | 333 | K | E | E |
31 | 1005 | C | T | C | ||||
32 | 1063–1064 | AA | GG | AG | 355 | N | G | S |
33 | 1078 | G | A | G | 360 | D | N | D |
34 | 1121 | G | T | G | 374 | R | M | R |
35 | 1124 | A | G | A | 375 | Y | C | Y |
36 | 1211 | A | G | G | 404 | K | R | R |
37 | 1230 | T | G | G | 410 | N | K | K |
38 | 1246 | G | A | A | 416 | D | N | N |
39 | 1252- | T | G | G/A | ||||
40 | 1253 | T | C | C | 418 | L | A | A/T |
41 | 1296 | C | A | C | ||||
42 | 1308 | A | G | G | ||||
43 | 1334 | C | T | C | 445 | A | V | A |
SL.No | Nucleotide position and difference | Amino acid position and difference | ||||||
---|---|---|---|---|---|---|---|---|
Position | GTPV | SPPV | LSDV | Position | GTPV | SPPV | LSDV | |
1 | 32 | C | T | C | 11 | A | V | A |
2 | 39 | G | T | G | 13 | R | S | R |
3 | 40 | G | A | G | 14 | G | S | G |
4 | 47 | A | C | C | 16 | H | P | P |
5 | 72 | C | T | T | ||||
6 | 73 | A | G | G | 25 | N | D | D |
7 | 96 | A | G | G | ||||
8 | 99 | C | T | T | ||||
9 | 141 | C | T | C | ||||
10 | 166 | C | T | T | ||||
11 | 204 | G | A | A | ||||
12 | 219 | A | G | A | ||||
13 | 276 | T | C | C | ||||
14 | 304 | A | G | A | 102 | N | D | N |
15 | 310 | G | A | G | 104 | D | N | D |
16 | 321 | G | A | A | ||||
17 | 325 | C | T | T | ||||
18 | 388 | C | A | C | 130 | Q | K | Q |
19 | 391 | G | A | A | 131 | V | M | M |
20 | 399 | A | C | C | ||||
21 | 400 | G | A | G | 134 | E | K | E |
22 | 412 | C | T | C | ||||
23 | 466 | G | A | A | 156 | V | I | I |
24 | 474 | C | T | C/T | ||||
25 | 570 | T | C | T | ||||
26 | 581 | G | A | G | 194 | R | K | R |
27 | 600 | G | A | G | ||||
28 | 645 | C | A | A | 215 | N | K | K |
29 | 690 | C | T | C | ||||
30 | 691 | A | G | G | 231 | N | D | D/E |
31 | 720 | T | C | C | ||||
32 | 733 | A | G | A | 245 | T | A | T |
33 | 742 | A | G | A | 248 | N | D | N |
34 | 768 | A | G | A | ||||
35 | 841 | A | G | A | 281 | N | D | N |
36 | 867 | A | C | C | ||||
37 | 868 | A | G | G | 290 | N | D | D |
38 | 898 | A | C | C | 300 | S | R | R |
39 | 902 | A | G | G | 301 | N | S | S |
40 | 917 | C | A | A | 306 | T | N | N |
41 | 960 | C | T | T | ||||
42 | 967 | T | A | T | 323 | Y | N | Y |
43 | 973 | A | C | C | 325 | I | L | L |
44 | 985 | C | A | C | ||||
45 | 999 | C | T | C | ||||
46 | 1015 | A | G | A | 339 | I | V | I |
47 | 1048 | C | T | C | 350 | H | Y | H |
48 | 1074 | C | T | C | ||||
49 | 1077 | T | C | C | ||||
50 | 1081 | C | A | C | ||||
51 | 1088 | G | T | G | 363 | R | L | R |
52 | 1194 | C | T | C/T | ||||
53 | 1224 | G | T | G | ||||
54 | 1237 | G | A | G | ||||
55 | 1281 | C | T | T | ||||
56 | 1337 | A | T | T | 446 | E | V | V |
57 | 1355 | T | A | A | 452 | I | N | N |
58 | 1362 | A | T | C/T | 454 | – | C | C |