Background
Results
Genome sequencing of equine influenza viruses
Primer name | Primer sequence (5′-3′) | Approximate nucleotide coverage (5′-3′) | Annealing temperature used (°C) |
---|---|---|---|
PB2/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGGCAAATATATTCAATATG | 1-655 | 50 |
PB2/AR | GC AACAGCTATGACCATG CTCTTTCTAGCATGTAT | ||
PB2/BF | GC GTAAAACGACGGCCAGT CACAACTAACAATAACCAA | 569-1335 | 60 |
PB2/BR | GC AACAGCTATGACCATG CCTCAAGAGTTGATG | ||
PB2/CF | GC GTAAAACGACGGCCAGT GCAATAATTGTAGCC | 1216-1874 | 45 |
PB2/CR | GC AACAGCTATGACCATG ATTATTTGAGCAGTATC | ||
PB2/DF | GC GTAAAACGACGGCCAGT GAAGCCAATACAGCGGT | 1793-2341 | 50 |
PB2/DR | GC AACAGCTATGACCATG AGTAGAAACAAGG TCGTTTTTAAACAATTC | ||
PB1/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGG CAAACCATTTGAATGG | 1-719 | 50 |
PB1/AR | GC AACAGCTATGACCATG CAGCGTCCTTGGTCATTG | ||
PB1/BF | GC GTAAAACGACGGCCAGT CTTCCAACGAAAGAGAA | 577-1301 | 50 |
PB1/BR | GC AACAGCTATGACCATG GGTTTAATATGGATACACC | ||
PB1/CF | GC GTAAAACGACGGCCAGT GCGGCTTCACTGAGTCCTGGC | 1222-1863 | 50 |
PB1/CR | GC AACAGCTATGACCATG CATTTTAAACAAACTTC | ||
PB1/DF | GC GTAAAACGACGGCCAGT CAAAGACTGGTCTACTG | 1789-2341 | 50 |
PB1/DR | GC AACAGCTATGACCATG AGTAGAAACAAGG CATTTTTTCATGAAGATC | ||
PA/AF | GC GTAAAACGACGGCCAGT AGCAAAAGCAGG TACTGATCCAAAATGG | 1-615 | 50 |
PA/AR | GC AACAGCTATGACCATG GCCTCTCTCGGACTGAC | ||
PA/BF | GC GTAAAACGACGGCCAGT GCCAGAATCAAGACCAGG | 529-1255 | 50 |
PA/BR | GC AACAGCTATGACCATG CTCACTTGGAATCCAACTTGC | ||
PA/CF | GC GTAAAACGACGGCCAGT GAGAGAAAGTGGATTTTGAGGATTG | 1149-1785 | 50 |
PA/CR | GC AACAGCTATGACCATG CTGAAGGAGGCAGCGCC | ||
PA/DF | GC GTAAAACGACGGCCAGT GACCCATGTTTTTGTATG | 1700-2233 | 50 |
PA/DR | GC AACAGCTATGACCATG AGTAGAAACAAGG TACTTTTTTGGACAG | ||
HA/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGGGGACGATATT | 1-515 | 50 |
HA/AR | GC AACAGCTATGACCATG GATTTGTTAGCCAATTCAG | ||
HA/BF | GC GAAAACGACGGCCAGT CAGGTGTCACTCAAAAC G | 428-1032 | 50 |
HA/BR | GC AACAGCTATGACCATG GGATTTGCTTTTCTGGTAC | ||
HA/CF | GC GTAAAACGACGGCCAGT GGTTACATATGGAAAATGCC | 939-1336 | 50 |
HA/CR | GC AACAGCTATGACCATG GAGCCACCAGCAATTCT | ||
HA/DF | GC GTAAAACGACGGCCAGT GAAGGAAGAATTCAGGA | 1251-1733 | 50 |
HA/DR | GC AACAGCTATGACCATG GAGTAGAAACAAGGGTGTTTTTAAC | ||
NP/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGGGTAGATAATC | 1-570 | 50 |
NP/AR | GC AACAGCTATGACCATG CCGTGGGAGGGTTGAGCC | ||
NP/BF | GC GTAAAACGACGGCCAGT GACACCACATACCAAAC | 480-1075 | 45 |
NP/BR | GC AACAGCTATGACCATG CTCTCAGGTCCTCAAAT | ||
NP/CF | GC GTAAAACGACGGCCAGT CCAGCACACAAGAGCCAG | 1012-1569 | 55 |
NP/CR | GC AACAGCTATGACCATG AGTAGAAACAAGGGTATTTTTC | ||
NA/AF | GC GTAAAACGACGGCCAGT AGCAAAAGCAGGAGTTT | 1-508 | 45 |
NA/AR | GC AACAGCTATGACCATG GCCCTATTTTGACACTC | ||
NA/BF | GC GTAAAACGACGGCCAGT CACACAGGGCTCATTAC | 417-1049 | 45 |
NA/BR | GC AACAGCTATGACCATG CCGAAACCTTTTACACCG | ||
NA/CF | GC GTAAAACGACGGCCAGT CACAGTTGGATATTTGTG | 951-1461 | 50 |
NA/CR | GC AACAGCTATGACCATG AGTAGAAACAAGGAGTT | ||
M/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGGTAGATATTTAAAG | 1-654 | 50 |
M/AR | GC AACAGCTATGACCATG CTAGCCTTACTAGCAAC | ||
M/BF | GC GTAAAACGACGGCCAGT CAGTACCACGGCTAAAG | 571-1027 | 50 |
M/BR | GC AACAGCTATGACCATG AGTAGAAACAAGGTAGTTTTTTAC | ||
NS/AF | GC GTAAAACGACGGCCAGT AGCGAAAGCAGGGTGACAAAAAC | 1-492 | 50 |
NS/AR | GC AACAGCTATGACCATG CTGCTCCTTCTTCGGTG | ||
NS/BF | GC GTAAAACGACGGCCAGT CATCATACTTAAAGCAAAC | 407-890 | 50 |
NS/BR | GC AACAGCTATGACCATG AGTAGAAACAAGGTAGTGTTTTTTAT |
Segment | Nucleotide changes | Protein | Amino acid changes | Amino acid changes from Richmond/1/07 to Lincolnshire/1/07 |
---|---|---|---|---|
1 | 35 | PB2 | 4 | A105T, K251R, I398V, K660R |
2 | 48 | PB1 | 8 | F94L, M119V, V149I, M179I, R329Q, E377D,D618E, K621R |
3 | 47 | PA | 13 | D64E, I86M, M210A, K237E, G240E, P259S, N321S, L348I, S409N, I465V, T476A, I500V, R626K |
4 | 47a | HA1† | 11b | K-14T, F-11L, I-9a1, F-9b1, N7G, R62K, V78A, D104N, A138S, N159S, E291D |
HA2 | 3 | T43A, E50G, I198V | ||
5 | 30 | NP | 4 | I131M, T257I, A359T, S450N |
6 | 37 | NA‡ | 12 | T9A, S12F, V35A, E40K, G42D, H66Y, P78S, I191V, N235D, S337N, I410V, G416E |
7 | 24 | M1 | 3 | I15V, I80V, K95R |
M2 | 2 | S86D, 290G | ||
8 | 11 | NS1 | 4 | I48S, I84V, Y207H, G210R |
NS2/NEP | 1 | M52I |
Sequencing of the non-coding regions of equine influenza viruses
Primer | Primer sequence† |
---|---|
Universal 3′ | 5′-CCTTGTTTCTACTAGC-3′ |
Universal 5′ | 5′-CCTGCTTTTGCTAGT-3′ |
PB2 3′ | 5′-GG G TATTTCATTGCCATCATCC-3′ |
PB2 5′ | 5′-GACTCTAGCATACTTACTGACAG-3′ |
PB1 3′ | 5′-GAC A GT A TCCATGGTGTATCCTGT-3′ |
PB1 5′ | 5′-G T ATGGT T GAGGCCATGGTGTC C-3′ |
PA 3′ | 5′-A T C CCTGTGATTTCAAATCTTTCTTC-3′ |
PA 5′ | 5′-GA A TGCCTGATTAATGATCCCTG-3′ |
HA 3′ | 5′-A AT GTTCC A TTTG CT ACTGCATG-3′ |
HA 5′ | 5′-GGATTTC A TT C GCCATATCATG-3′ |
NP 3′ | 5′-TCAAA T GC C GA A AG T-3′ |
NP 5′ | 5′-CCGATCGTGCC T TC C TTTGACA T-3′ |
NA 3′ | 5′-GTGGAGTAGATCATAAAATTGCC-3′ |
NA 5′ | 5′-CAGACCTGTTTCATTGTTATTGAG-3′ |
M 3′ | 5′-A T AAAGCGTCTACGCTGCAGTCC-3′ |
M 5′ | 5′-AAAGAGGGCCTTCTACGGAAGG-3′ |
NS 3′ | 5′-C C GT A TTATCATTCCATT T AAG-3′ |
NS 5′ | 5′-TGATAA T ACG GTTA GAA TCTCT-3′ |