Background
Methods
Case history
Sample number | Region of Morocco | Month of sample collection | Type of birds | Age | AIV detection RT-PCR Ct Value | Virus isolation | Full genome sequencing |
---|---|---|---|---|---|---|---|
1 | Kenitra | January | Broiler | 31 days | 18,9 | yes | yes |
2 | Fes | January | Breeders | 43 weeks | 20,6 | yes | yes |
3 | Oujda | February | Broiler | 27 days | 23,2 | yes | yes |
4 | Temara | January | Broiler | 22 days | 37,2 | - | - |
5 | Tiznit | February | Broiler | 33 days | 29,5 | - | - |
6 | Meknes | January | Broiler | 30 days | 33,1 | - | - |
7 | Casablanca | February | Broiler | 47 days | 17,5 | yes | yes |
8 | Sefrou | January | Broiler | 32 days | negative | - | - |
9 | Meknes | January | Broiler | 39 days | 32,4 | - | - |
10 | Oujda | January | Broilers | 36 days | 29,6 | - | - |
11 | EL Hajeb | January | Broiler | 19 days | 23,1 | yes | yes |
Virus isolation
Full genome amplification and sequencing of H9N2 Moroccan isolates
Sequences and phylogenetic analyses
Results
Epidemiology of H9N2 outbreaks in Morocco
Post-mortem examinations
Real time RT-PCR
Phylogenetic analyses
Molecular characterization
Hemagglutinin cleavage site and receptor binding domains
Protein | Molecular determinants of virulence | Molecular determinants of host specificity (adaptation to mammals) | Molecular determinants of drug resistance | Miscellaneous |
---|---|---|---|---|
PB2 | 147 V, 504 V | 318R, 590S, 661 T | ||
PB1 | 13P | |||
PB1-F2 | 66 N | 82 L | Truncated protein of 52 aa | |
PA | 127 V, L550, 672 L | I100, R312, 409 N | ||
PA-X | Full length 252 amino acids | |||
HAa
| 158 N, 183H, 226 L, 391 K | Cleavage site: RSSRGL*F Glycosylation sites: 29NSTE, 82NPSC, 105NGTC, 141NVTY, 298 NSTM, 305NISK, 492NGTY | ||
NP | 372D | |||
NA | None | No stalk deletion | ||
M1 | 15I | |||
M2 | D16 | 31 N (amantadane resistance) | ||
NS1 | 42S, 189D | No 80–84 deletion and GSEV PL motif | ||
NS2 | 31 M, 56H |