Table 3.
HA protein sequence diversity of H5N1 viruses associated with HPAI outbreaks in eight smallholder duck farms with multiple isolates
| Farm No (Farm ID) | Virus namea | Statusb | Date | HA 1 | HA 2 | |||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -11 | -9 | -4 | 66 | 72 | 86 | 95 | 120 | 121 | 140 | 163 | 183 | 210 | 217 | 234 | 236 | 263 | 285 | 328 | 329 | 18 | 62 | 72 | 82 | 143 | 158 | 164 | 183 | 203 | ||||
| 9 | Ck/BT/446-24454/07 | Dead | 6-Jul-07 | A | L | S | M | N | I | F | S | S | S | S | N | V | S | K | D | A | I | K | K | V | Q | N | K | K | N | E | T | I |
| (BCAT01) | Ck/BT/446-24452/07 | Dead | 12-Jul-07 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Ck/BT/446-24456/07 | Dead | 12-Jul-07 | - | - | - | - | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | - | - | - | - | - | - | - | - | - | - | |
| Ck/BT/446-24453/07 | Dead | 12-Jul-07 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
| Dk/BT/1005-24442/07 | Live | 17-Dec-07 | V | - | - | - | - | T | L | - | - | - | G | D | A | - | - | N | T | - | - | - | - | - | - | - | R | - | D | - | - | |
| 34 | Dk/BT/678-2D403/07 | Live | 21-Sep-07 | - | - | - | T | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | R | - | - | - | - | - | - | - | - | - |
| (BCAT03) | Dk/BT/678-24404/07 | Live | 21-Sep-07 | - | - | - | T | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | R | - | - | - | - | - | - | - | - | - |
| Ck/BT/678-441/07 | Live | 21-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | S | D | - | - | |
| Ck/BT/678-443/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| 30 | Ck/KP/610-11019/07 | Dead | 19-Aug-07 | - | - | - | - | - | T | - | - | - | R | - | D | - | - | - | N | - | - | - | - | - | - | D | - | - | - | - | - | - |
| (KWAH45) | Ck/KP/610-11020/07 | Dead | 19-Aug-07 | - | - | - | - | - | T | - | - | - | R | - | D | - | - | - | N | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Dk/KP/618-11001/07 | Live | 19-Aug-07 | - | - | - | - | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | R | - | N | - | - | - | - | - | |
| Dk/KP/618-11003/07 | Live | 19-Aug-07 | - | - | - | - | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | R | - | N | - | - | - | - | - | |
| Dk/KP/618-11009/07 | Live | 19-Aug-07 | - | - | - | - | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | R | - | N | - | - | - | - | - | |
| 11 | Ck/KP/667-601/07 | Dead | 19-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - |
| (KBUG35) | Ck/KP/677-602/07 | Dead | 19-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - |
| Ck/KP/677-603/07 | Dead | 19-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - | |
| Ck/KP/677-60X/07 | Dead | 19-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - | |
| Ck/KP/667-604/07 | Dead | 22-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - | |
| Ck/KP/667-605/07 | Dead | 22-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | P | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - | |
| 32 | Ck/MG/662-762/07 | Dead | 14-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - |
| (MBUM74) | Ck/MG/662-762A/07 | Dead | 14-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Ck/MG/662-763/07 | Dead | 14-Sep-07 | - | - | - | - | - | T | - | - | - | - | - | D | - | - | - | N | - | V | R | - | - | - | - | - | - | - | - | - | - | |
| Ck/MG/662-764/07 | Dead | 14-Sep-07 | V | - | - | - | - | T | - | - | - | - | - | D | - | - | N | N | - | - | - | - | - | - | - | - | - | - | - | - | M | |
| 13 | Ck/MG/680-74X/07 | Dead | 21-Sep-07 | - | - | - | - | - | T | - | - | - | - | - | D | - | - | - | N | - | V | R | - | - | - | - | - | - | - | - | - | - |
| (MBUM75) | Ck/MG/680-744/07 | Dead | 21-Sep-07 | - | - | - | T | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | R | - | - | - | - | - | - | - | - | - |
| Dk/MG/680-41042/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Dk/MG/680-41043/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Dk/MG/680-41047/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Dk/MG/680-41050/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Dk/MG/680-41052/07 | Live | 21-Sep-07 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Dk/MG/680-41041/07 | Live | 21-Sep-07 | - | - | - | T | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | R | - | - | - | - | - | - | - | - | - | |
| Dk/MG/680-41044/07 | Live | 21-Sep-07 | - | - | - | T | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | R | - | - | - | - | - | - | - | - | - | |
| Dk/MG/680-41051/07 | Live | 21-Sep-07 | - | - | G | - | - | T | - | N | F | - | - | D | - | - | - | N | - | - | - | - | - | - | - | R | - | - | - | - | - | |
| 10 | Dk/SM/379-34423/07 | Dead | 24-Jul-07 | - | - | - | - | - | T | - | - | - | - | - | D | - | - | - | N | - | V | - | - | - | - | - | - | - | - | - | A | - |
| (SSDG62) | Ck/SM/493-214/07 | Dead | 24-Jul-07 | - | - | - | - | - | T | - | - | - | - | - | D | - | - | - | N | - | - | - | - | I | - | - | - | - | - | - | - | - |
| 4 | Ck/SM/626-233/07 | Dead | 31-Jul-07 | - | - | - | - | - | T | - | - | - | R | - | D | - | - | - | N | - | - | - | - | - | - | - | - | - | - | - | - | - |
| (SSDG65) | Ck/SM/626-234/07 | Dead | 31-Jul-07 | - | - | - | - | - | T | - | - | - | R | - | D | - | - | - | N | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Ck/SM/71-231/07 | Dead | 27-Jan-08 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
| Ck/SM/71-236/07 | Dead | 27-Jan-08 | V | I | - | - | - | T | - | - | - | - | - | D | A | - | - | N | - | - | - | - | - | - | - | - | - | S | D | - | - | |
The HA signal peptide that contains 16 amino acids is counted from -15 to 0, using the H5 numbering [26]. Amino acid variations were detected at the HA cleavage site (HA 1, position 328 and 329). Abbreviation: chicken (Ck), duck (Dk), Bantul (BT), Kulon Progo (KP), Sleman (SM), Magelang (MG).
a The letters 'BBVW' have been removed from the virus names.
b Status indicates the clinical presentation of birds when samples were collected.