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Table 3 HA protein sequence diversity of H5N1 viruses associated with HPAI outbreaks in eight smallholder duck farms with multiple isolates

From: A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008

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

-

-

  1. 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).
  2. a The letters 'BBVW' have been removed from the virus names.
  3. b Status indicates the clinical presentation of birds when samples were collected.