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. 2011 Sep 7;8:425. doi: 10.1186/1743-422X-8-425

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.