Background
Materials and methods
Case history
Sampling
RNA extraction
AIV detection and sub-typing
Virus isolation and characterization
Full genome amplification
Sequencing and phylogenetic analyses
Genes | Strains | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
6BBD | 8BBD | 9BBD | 10BBD | 12BBD | 13BBD | 15BBD | 17BBD | 18BBD | 19BBD | |
PB2 | MK796878 | MK796879 | MK796880 | MK796881 | MK796882 | MK796883 | MK796884 | MK796885 | MK796886 | MK796887 |
PB1 | MK796868 | MK796869 | MK796870 | MK796871 | MK796872 | MK796873 | MK796874 | MK796875 | MK796876 | MK796877 |
PA | MK796835 | MK796836 | MK796837 | MK796838 | MK796839 | MK796840 | MK796841 | MK796842 | MK796843 | MK796844 |
HA | MK788274 | MK788275 | MK788276 | MK788277 | MK788278 | MK788279 | MK788280 | MK788281 | MK788282 | MK788283 |
NP | MK796798 | MK796799 | MK796800 | MK796801 | MK796802 | MK796803 | MK796804 | MK796805 | MK796806 | MK796807 |
NA | MK796787 | MK796788 | MK796789 | MK796790 | MK796791 | MK796792 | MK796793 | MK796794 | MK796795 | MK796796 |
M | MK803312 | MK803313 | MK803314 | MK803315 | MK803316 | MK803317 | MK803318 | MK803319 | MK803320 | MK803321 |
NS | MK796816 | MK796817 | MK796818 | MK796819 | MK796820 | MK796821 | MK796822 | MK796823 | MK796824 | MK796825 |
Results
AIV detection
Phylogenetic analysis of the surface genes
Phylogenetic analysis of internal genes
Algerian strains | Genes | References strains | Contemporary Algerian’s strains | Strains from neighboring country | UAE | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HK-G1 | HK-Y280 | HK-Y439 | CK-Bei | HK-G9 | Alg-216 | Alg-225 | Morocco-SF1 | Morocco-SF5 | Tun-12 | Tin-51 | Dubai-D2506.A | ||
19BDD | PB2 | 86.77 | 84.75 | 85.79 | 84.89 | 88.18 | 98.90 | 98.95 | 99.12 | 99.08 | 93.16 | 93.16 | 98.59 |
PB1 | 88.13 | 87.06 | 88.54 | 88.60 | 88.10 | 99.08 | 99.08 | 99.47 | 99.52 | 94.17 | 94.17 | 98.33 | |
PA | 88.76 | 87.14 | 91.80 | 87.65 | 86.81 | 99.30 | 99.35 | 99.35 | 99.44 | 94.61 | 94.61 | 98.74 | |
HA | 89.14 | 86.64 | 81.75 | 87.57 | 87.35 | 98.92 | 98.80 | 99.16 | 98.92 | 92.53 | 92.53 | 98.62 | |
NP | 94.33 | 87.50 | 91.10 | 87.81 | 88.43 | 99.13 | 99.27 | 99.20 | 99.13 | 95.32 | 95.32 | 97.86 | |
NA | 89.68 | 87.49 | 84.08 | 89.05 | 87.46 | 98.37 | 98.37 | 99.22 | 99.36 | 92.20 | 92.35 | 98.44 | |
M | 94.16 | 92.86 | 89.50 | 93.02 | 93.24 | 98.79 | 98.79 | 99.39 | 99.28 | 96.23 | 96.23 | 98.35 | |
NS | 88.70 | 88.94 | 91.47 | 89.54 | 89.23 | 99.41 | 99.41 | 99.05 | 99.28 | 95.15 | 95.15 | 98.58 | |
9BDD | PB2 | 86.82 | 84.75 | 85.79 | 84.89 | 87.37 | 98.95 | 98.99 | 99.16 | 99.12 | 93.20 | 93.20 | 98.63 |
PB 1 | 88.04 | 87.97 | 88.45 | 88.51 | 88.10 | 99.08 | 99.08 | 99.47 | 99.52 | 94.17 | 94.17 | 98.33 | |
PA | 88.76 | 87.14 | 91.80 | 87.65 | 86.81 | 99.30 | 99.35 | 99.35 | 99.44 | 94.61 | 94.61 | 98.74 | |
HA | 89.14 | 86.64 | 81.75 | 87.57 | 87.35 | 98.92 | 98.80 | 99.16 | 98.92 | 92.53 | 92.53 | 98.62 | |
NP | 94.33 | 87.50 | 91.10 | 87.81 | 88.43 | 99.13 | 99.27 | 99.20 | 99.13 | 95.32 | 95.32 | 97.86 | |
NA | 89.68 | 87.49 | 84.08 | 89.05 | 87.46 | 98.37 | 98.37 | 99.22 | 99.36 | 92.20 | 92.35 | 98.44 | |
M | 94.16 | 92.87 | 89.51 | 93.02 | 93.35 | 98.89 | 98.89 | 99.39 | 99.28 | 96.23 | 96.23 | 98.35 | |
NS | 88.70 | 88.94 | 91.47 | 89.54 | 89.23 | 99.41 | 99.41 | 99.05 | 99.28 | 95.15 | 95.15 | 98.58 | |
6BDD | PB2 | 87.04 | 85.06 | 86.10 | 85.20 | 87.59 | 99.04 | 99.08 | 99.25 | 99.21 | 93.29 | 93.29 | 98.68 |
PB 1 | 88.13 | 88.06 | 88.54 | 88.60 | 88.18 | 98.81 | 98.81 | 99.21 | 99.25 | 93.94 | 93.94 | 98.07 | |
PA | 88.39 | 86.82 | 91.52 | 87.32 | 86.49 | 98.88 | 98.93 | 98.93 | 99.02 | 94.19 | 94.19 | 98.33 | |
HA | 89.15 | 86.71 | 82.07 | 87.70 | 87.40 | 98.50 | 98.38 | 98.86 | 98.62 | 92.30 | 92.29 | 98.32 | |
NP | 94.19 | 87.50 | 90.98 | 87.74 | 88.31 | 99.13 | 99.26 | 99.20 | 99.13 | 95.12 | 95.12 | 97.86 | |
NA | 89.46 | 87.14 | 83.94 | 88.77 | 87.31 | 98.23 | 98.23 | 99.08 | 99.22 | 92.06 | 92.20 | 98.30 | |
M | 94.16 | 92.67 | 89.61 | 92.81 | 93.25 | 98.99 | 98.99 | 99.59 | 99.49 | 96.44 | 96.44 | 98.55 | |
NS | 88.46 | 88.70 | 91.47 | 89.30 | 88.99 | 99.17 | 99.17 | 98.81 | 99.04 | 94.91 | 94.91 | 98.34 |
Molecular characterization
Avian influenza viruses | Receptor binding Site (RBS) | Right-edge of binding pocket | Left-edge of binding pocket | Connecting peptide aa sequence | Potentials glycosylation sites (PGS) | |||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
106 | 110 | 161 | 163 | 166 | 191 | 198 | 202 | 203 | 234 | 235 | 148–152 a142–146 | 232–236 b233–237 | 333–338 c366–441 | |||||||||||||||
A/Quail/Hong_Kong/G1/97 | V | P | W | T | S | H | E | L | Y | L | Q | S | R | A | C | S | N | D | L | Q | G | P | A | R | S | S | R | 8 |
A/Turkey/Wisconsin/1/1966 | – | – | – | – | – | – | – | – | – | Q | – | – | – | – | – | – | G | Q | – | – | V | – | – | 7 | ||||
A/Duck/Hong_Kong/Y280/97 | – | – | – | – | N | N | T | – | – | – | – | – | K | – | – | – | – | G | – | – | – | – | – | – | – | – | – | 6 |
A/Duck/Hong_Kong/Y439/97 | – | – | – | – | – | – | – | – | – | Q | – | – | – | – | – | – | Q | – | – | A | – | N | – | 6 | ||||
A/Guangdong/MZ058/2016 * | – | – | – | – | D | N | T | – | – | – | M | – | T | – | – | – | – | G | – | M | – | – | S | – | – | – | – | 7 |
A/Lebanon/11 L046/2012 (H3N2) | – | – | – | – | N | – | D | – | – | I | P | – | – | R | S | N | R | N | I | P | S | – | E | K | Q | T | – | 12 |
A/Minnesota/19/2011(H1N2) | – | – | – | – | N | – | N | – | – | Q | E | – | A | S | – | – | R | – | Q | E | – | – | S | I | Q | – | – | 9 |
A/Paris/650/2004 (H1N1) | – | – | – | – | N | – | D | – | – | Q | E | – | A | S | – | – | R | – | Q | E | – | – | S | I | Q | – | – | 10 |
A/Egypt/N02752/2009(H5N1) | – | – | – | – | D | – | – | – | – | Q | S | – | S | – | – | P | – | G | Q | S | – | – | Q | G | E | R | R | 7 |
A/Shanghai/02/2013(H7N9) | I | – | – | – | L | – | – | – | – | L | S | T | S | – | – | R | – | G | – | S | – | – | I | P | K | G | – | 5 |
A/Chicken/Karachi/NARC100/2004 (H7N3) | I | K | C | R | G | S | G | I | I | Q | Q | aG | A | T | S | S | bN | G | Q | S | G | cP | k | R | R | K | R | 2 |
A/Chicken/Morocco/SF1/2016 | – | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Tunisia/12/2010 | – | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | – | – | – | – | – | – | 7 |
A/Chicken/Egypt/F12168B/2016 | – | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | – | – | – | – | – | – | 7 |
A/Chicken/Dubai/D2506.A/2015 | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 | |
A/Chicken/Pakistan/10A/2015 | – | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | – | – | K | – | – | – | 7 |
A/Chicken/B Faso/17RS93–9/2017 | – | – | – | – | N | – | A | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 8 |
A/Chicken/Algeria/6BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/8BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/9BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/10BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/12BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria13BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 8 |
A/Chicken/Algeria/15BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/17BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 8 |
A/Chicken/Algeria/18BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
A/Chicken/Algeria/19BBD/2017 | – | – | – | – | N | – | T | – | – | – | I | – | K | S | – | – | – | G | – | I | – | H | – | – | – | – | – | 7 |
Avian influenza viruses | Hemadsorbing site (HB) | Potentials glycosylation sites (PGS) | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1st loop 366–373 | 2nd loop 399–404 | 3rd loop 431–433 | ||||||||||||||||
A/Quail/Hong_Kong/G1/97 | I | K | K | D | S | R | S | G | D | S | D | I | R | S | P | Q | E | 6 |
A/Turkey/Wisconsin/1/1966 | – | S | – | – | – | – | – | – | – | – | N | N | W | – | – | – | – | 7 |
A/Duck/Hong_Kong/Y280/97 | – | – | E | – | – | – | – | – | – | – | – | N | W | – | – | – | – | 7 |
A/Duck/Hong_Kong/Y439/97 | – | S | – | – | – | – | – | – | – | N | N | N | W | – | – | – | – | 10 |
A/Guangdong/MZ058/2016a | – | – | N | G | – | – | – | – | – | – | – | D | W | – | – | – | – | 8 |
A/Lebanon/11 L046/2012 (H3N2) | – | N | E | T | – | – | L | – | – | R | G | D | – | – | K | E | – | 8 |
A/Minnesota/19/2011(H1N2) | – | N | E | T | L | – | L | – | E | K | G | D | – | – | K | E | – | 9 |
A/Paris/650/2004 (H1N1) | K | S | N | R | L | K | – | I | T | – | D | W | – | – | R | – | 9 | |
A/Egypt/N02752/2009 (H5N1) | K | S | T | N | – | – | – | – | I | T | – | D | W | – | – | K | – | 3 |
A/Shanghai/02/2013 (H7N9) | – | S | T | A | – | – | – | – | L | N | A | D | W | – | – | K | – | 7 |
A/Chicken/Karachi/NARC-100/2004 (H7N3) | S | N | S | G | R | S | G | F | N | N | D | W | S | G | N | K | N | 6 |
A/Chicken/Morocco/SF1/2016 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Tunisia/12/2010 | – | – | – | – | L | – | A | – | – | – | – | N | W | – | – | – | – | 7 |
A/Chicken/Egypt/F12168B/2016 | – | – | – | – | – | – | A | – | – | – | – | S | W | – | – | – | – | 7 |
A/Chicken/Dubai/D2506.A/2015 | – | – | – | – | L | – | A | – | – | – | – | N | W | – | – | R | – | 8 |
A/Chicken/Pakistan/10A/2015 | – | E | – | – | – | – | T | – | – | – | G | N | – | – | – | – | – | 7 |
A/Chicken/B Faso/17RS93–19/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/6BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | – | – | 8 |
A/Chicken/Algeria/8BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/9BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/10BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 9 |
A/Chicken/Algeria/12BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/13BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/15BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/17BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/18BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
A/Chicken/Algeria/19BBD/2017 | – | – | – | – | L | – | A | – | – | N | – | N | W | – | – | R | – | 8 |
Genes | Molecular determinants of virulence | Molecular determinants of host specificity and host pathogenicity | Molecular determinants of drug resistance | Miscellaneous | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sites | ALG | HK-G1 | Virulent | Sites | ALG | HK-G1 | Mammalian preference | sites | ALG | HK-G1 | ||
PB2 | 89 | V | V | L | 44 | A | A | S | ||||
147 | V | M | L | 64 | M | M | T | |||||
250 | V | V | G | 81 | T | T | M | |||||
253 | D | D | N | 158 | E | E | G | |||||
404 | F | F | L | 190 | K | R | K | |||||
504 | V | V | V | 199 | A | A | S | |||||
271 | T | T | A | |||||||||
318 | R | K | R | |||||||||
339 | K | K | T | |||||||||
526 | K | K | R | |||||||||
543 | E | E | D | |||||||||
588 | A | A | V | |||||||||
590 | S | S | ||||||||||
591 | Q | Q | K | |||||||||
627 | E | E | K | |||||||||
643 | S | S | T | |||||||||
655 | V | A | V | |||||||||
661 | T | T | A | |||||||||
666 | T | T | I | |||||||||
701 | D | D | N | |||||||||
702 | Q | K | R | |||||||||
714 | S | S | R | |||||||||
PB1 | 105 | N | N | S | 13 | P | P | P | ||||
317 | M | I | I | 207 | K | K | R | |||||
577 | K | K | E | 336 | V | V | I | |||||
622 | G | G | G | 375 | N | N | S | |||||
436 | Y | Y | H | |||||||||
578 | K | K | Q | |||||||||
677 | T | T | M | |||||||||
PB1-F2 | Truncated protein of 52 aa | |||||||||||
PA | 127 | V | V | V | 28 | P | P | L | ||||
550 | L | L | L | 44 | V | V | I | |||||
672 | L | L | L | 55 | D | D | N | |||||
57 | R | R | Q | |||||||||
63 | V | V | I | |||||||||
97 | T | T | I | |||||||||
100 | I | V | A | |||||||||
133 | E | E | G | |||||||||
142 | K | K | N/E | |||||||||
225 | S | S | C | |||||||||
241 | C | C | Y | |||||||||
268 | L | L | I | |||||||||
312 | R | K | R | |||||||||
343 | A | A | S | |||||||||
347 | D | D | E | |||||||||
356 | K | K | R | |||||||||
382 | E | E | D | |||||||||
383 | D | D | D | |||||||||
400 | T | L | L | |||||||||
404 | A | A | S | |||||||||
409 | N | S | N | |||||||||
515 | T | T | T | |||||||||
552 | T | T | S | |||||||||
556 | Q | Q | R | |||||||||
573 | I | I | V | |||||||||
615 | K | R | N | |||||||||
PA-X | Full length 252 aa | |||||||||||
NP | 210 | D | D | D | 31 | R | R | K | ||||
33 | V | V | I | |||||||||
34 | G | G | N | |||||||||
61 | I | I | L | |||||||||
100 | R | R | V | |||||||||
109 | I | I | V | |||||||||
127 | E | E | D | |||||||||
136 | M | M | M | |||||||||
214 | R | R | K | |||||||||
283 | L | L | P | |||||||||
293 | R | R | K | |||||||||
305 | R | R | K | |||||||||
313 | F | F | Y | |||||||||
357 | Q | Q | K | |||||||||
372 | D | E | D | |||||||||
375 | D | D | G/E | |||||||||
398 | Q | Q | Q | |||||||||
422 | R | R | K | |||||||||
430 | K | K | ||||||||||
442 | T | T | A | |||||||||
455 | D | D | E | |||||||||
480 | D | D | ||||||||||
M1 | 30 | D | D | D | 15 | I | I | I | ||||
43 | M | M | M | 115 | V | R | I | |||||
215 | A | A | A | 121 | T | T | A | |||||
137 | T | T | A | |||||||||
M2 | 64 | S | S | S/A/F | 11 | T | T | I | 26 | L | L | |
69 | P | P | P | 16 | D | G | G/D | 27 | V | V | ||
28 | V | V | I/V | 31 | N | S | ||||||
55 | F | F | F | 34 | G | G | ||||||
57 | Y | Y | H | 38 | L | L | ||||||
86 | V | V | A | |||||||||
NS1 | 42 | S | S | S | 227 | G | E | K/R | Non 80TIASV84 deletion GSEV PL motif | |||
92 | D | E | E | |||||||||
103 | L | L | F | |||||||||
106 | M | I | M | |||||||||
149 | A | A | A | |||||||||
189 | D | D | N | |||||||||
NS2 | 31 | M | M | I | ||||||||
56 | H | H | Y |