Background
Methods
Cells and Viruses
RT-PCR amplification of the IHNV genome
IHNV primers | Sequences | Position |
---|---|---|
IHNV 1F | GTATAAGAAAAGTAACTTGAC | 1-21 |
IHNV 1R | CTTCCCTCGTATTCATCCTC | 2097-2078 |
IHNV 2F | GCAGGATCCCAAGAGGTGAAG | 2033-2053 |
IHNV 2R | GGAACGAGAGGATTTCTGATCC | 3819-3818 |
IHNV 3F | CAGTGGATACGGACAGATCTC | 3767-3787 |
IHNV 3R | CTTGGGAGCTCTCCTGACTTG | 5579-5559 |
IHNV 4F | GTACTTCACAGATCGAGGATCG | 5523-5544 |
IHNV 4R | CGGGGACTCTTGTTCTGGAATG | 7147-7128 |
IHNV 5F | CGTACCAGTGGAAATACATCGG | 7098-7119 |
IHNV 5R | CAGGTGGTGAAGTAGGTGTAG | 9018-8997 |
IHNV 6F | GAGGGAGTTCTTTGATATTCCC | 8931-8952 |
IHNV 6R | ATAAAAAAAGTAACAGAAGGGTTCTC | 11130-11105 |
IHNV NheR | CGTTTCTGCTAGCTTGTTGTTGG | 525-503 |
IHNV 1MF | ACAGAAGCTAACCAAGGCTAT | 729-749 |
IHNV 2MF | AGATCCCAATGCAGACCTACT | 2610-2630 |
IHNV 3MF | GTATCAGGGATCTCCATCAG | 4322-4341 |
IHNV 4MF | GATACATAAACGCATACCACA | 6113-6133 |
IHNV 5MF | TCAGAGATGAAGCTCAGCAA | 7546-7565 |
IHNV 6MF | AACACCATGCAGACCATACTC | 9559-9579 |
IHNV 5'End | CGATATTGAAGAGAAAGGAATAAC | 10692-10715 |
Oligo (dT) | GCGGCCGCTTTTTTTTTTTTTTTTTTTTT |
Sequence and phylogenetic tree analysis
Database accession numbers
Results
The complete nucleotide sequence of 220-90
S. No | Gene | Start | End | 5'UTR | ORF | 3'UTR | Total Lengtha | Protein Size (aa) | MWbkDa |
---|---|---|---|---|---|---|---|---|---|
1. | Leader | 1 | 60 | 60 | |||||
2. | N | 63 | 1430 | 112 | 1176 | 80 | 1638 | 391 | 42.3 |
3. | P | 1433 | 2199 | 33 | 693 | 41 | 767 | 230 | 26.0 |
4. | M | 2202 | 2945 | 53 | 588 | 103 | 744 | 195 | 22.0 |
5. | G | 2948 | 4567 | 51 | 1527 | 42 | 1620 | 508 | 56.6 |
6. | NV | 4570 | 4938 | 26 | 336 | 7 | 369 | 111 | 13.2 |
7. | L | 4941 | 11031 | 76 | 5961 | 54 | 6091 | 1986 | 225.0 |
8. | Trailer | 11032 | 11133 | 102 |
ORF 1 or Nucleocapsid (N) protein gene
IHNV Strains
|
3' Leader
¥
|
N
|
P
|
M
|
G
|
NV
| L |
5' Trailer
¥
|
193-110 | - |
98
| - | - |
97
| 96 | - | - |
332 | - | - | - | - |
97
| - | - | - |
Auke77 | - | - | - | - |
97
| - | - | - |
Carson-89 | - |
96
| - | - |
97
| - | - | - |
Col-80 | - | 95 | - | - |
96
| - | - | - |
Col-85 | - | 95 | - | - |
96
| - | - | - |
Cro/05 | - | - | - | - |
97
| 96 | - | - |
CST-82 | - |
97
| - | - |
97
| 96 | - | - |
G4 | - | - | - | - |
96
| - | - | - |
IHNV-PRT | - | 93 | 95 | 98 |
95
| 95 | - | - |
FR0031 | - | - | - | - |
96
| - | - | - |
FF030-91 | - | - | - | - |
96
| - | - | - |
Fs42/95 | - | - | - | - |
97
| 97 | - | - |
Fs62/95 | - | - | - | - |
97
| - | - | - |
FsK/88 | - | - | - | - |
97
| - | - | - |
FsVi100/96 | - | - | - | - |
97
| - | - | - |
HO-7 | - |
98
| - | - |
97
| 97 | - | - |
HV7601 | - | - | - |
98
|
97
| 97 | - | - |
J04321 | - | 95 | - | - | - | - | - | - |
LB91KI | - |
96
| - | - | - | - | - | - |
LR-73 | - | 95 | - | - |
97
| 96 | - | - |
LR-80 | - |
98
| - | - |
97
| 97 | - | - |
LWS-87 | - |
96
| - | - |
97
| - | - | - |
WRAC | 96 |
97
|
98
|
98
|
97
| 96 | 98 | 96 |
RB-76 | - |
96
| - | - |
97
| - | - | - |
RB-1 | - |
96
| - | - | 97 | 97 | - | - |
RtUi02 | - |
-
| - | - | 94 | - | - | - |
SRCV | - | 95 | - | - |
96
| - | - | - |
Strain K | - |
97
|
97
|
98
|
97
| 97 | 98 | - |
X89213 | 96 |
97
|
97
|
98
|
97
| 97 | 98 | 95 |
HIRRV
| 64 | 62 | 65 | 74 | 74 | 53 | 84 | 71 |
SHRV
| 44 | 42 | 30 | 35 | 39 | 10 | 58 | 36 |
VHSV
| 41 | 40 | 35 | 36 | 38 | 10 | 60 | 29 |
ORF 2 or Phosphoprotein (P) gene
ORF 3 or Matrix (M) gene
ORF 4 or glycoprotein (G) gene
ORF 5 or Non-virion (NV) protein gene
ORF 6 or Polymerase (L) gene
The Genomic termini and untranslated sequences
Type Species | Gene Junctions | ||
---|---|---|---|
N/P | P/M | M/G | |
IHNV
| UCU AUCUUUUUUU AC CGUGAUAUCACG | UCUGUCUUUUUUU AC CGUGCGUUCACA | UCUGUCUUUUUUU AC CGUGAAAACACG |
SHRV
| UCUAUCUUUUUUU GC CGUGCUCUCACG | UCUGUCUUUUUUU ACCGUGCUCUCACG | UCUGUCUUUUUUU AC CGUGCUCUCACG |
VHSV
| UCUAUCUUUUUUU GC CGUGCUAAUAUU | UCUAUCUUUUUUU GC CGUGCUGACAAG | UCUAUCUUUUUUU AC CGUGUAAACACA |
HIRRV
| UCUAUCUUUUUUU AC CGUGCAAACACA | UCUAUCUUUUUUU AC CGUGCAAUCACA | UCUAUCUUUUUUU AC CGUGUAAACACA |
G/NV
|
NV/L
| ||
IHNV
| UCUGUCUUUUUUU GC CGUGUAAACACG | UCUAUCUUUUUUU AC CGUGAAAACACG | |
SHRV
| UCUGUCUUUUUUU U GC CGUGAUAUCACG | UCUAUCUUUUUUU GC CGUGCAUUACACG | |
VHSV
| UCUAUCUUUUUUU AC CGUGGAAAUACU | UCUAUCUUUUUUU AC CGAGAAAACAAC | |
HIRRV
| UCUAUCUUUUUUU GC CGUGUAUACAGA | UCUAUCUUUUUUU AC CGUGAACACACG |