Phylogenetic Tree of Nucleotide Sequence of Gen M of CC Strain IA/h5N1 Clade 7 (Established by Neighbo-Joining Analysis Using Mega 5 Software, Gi T


67 A/CHICKEN/VIETNAM/NCVD-04/2008

52

94

94

83

91

A/CHICKEN/VIETNAM/NCVD-05/2008 A/CHICKEN/VIETNAM/NCVD-093/2008 A/CHICKEN/VIETNAM/NCVD-03/2008

A/CHICKEN/VIETNAM/NCVD-016/2008

Clade 7

83

35

A/chicken/Shanxi/10/2006 2006

A/chicken/Shandong/A-10/2006 2006

A/chicken/Shanxi/2/2006

Clade 7

33

33

A/Beijing/01/2003

A/chicken/Korea/es/2003

99

A/black-headed goose/Qinghai/January 2005

A/chicken/Bhutan/248006/2010 A/duck/India/TR-NIV4396/2008

A/duck/Hunan/1386/2003

99

14

59

55

58

27

A/Indonesia/239H/2005 A/Indonesia/CDC1046/2007 A/Indonesia/535H/2006

A/Ck/Indonesia/2A/2003 2003 A/chicken/East Java/UT6045/2007

A/duck/Guangxi/351/2004

96

28 80 A/chicken/Thailand/ICRC-7356/2010

68

53

34

51


53


66


74

31

A/Thailand/Kan353/2004 2004

A/duck/Vietnam/48/2004 2004 A/Cambodia/P0322095/2005

A/Vietnam/CL100/2004 A/duck/Vietnam/286/2005

A/Muscovy duck/Ca Mau/April 7, 2007 A/chicken/Lang Son/200/2005 2005

A/duck/Guiyang/3834/2005 2005

A/Anhui/T2/2006 2006

46

77 A/Anhui/2/2005 2005

25

68

A/Shanghai/1/2006 2006

A/crested myna/Hong Kong/540/2006

41

99

97

33

A/Hong Kong/6841/2010 A/mallard/Korea/1195/2010

A/Hunan/1/2006

83

77 A/duck/Guangxi/150/2006

A/duck/Laos/P0117/2007

A/duck/Zhejiang/52/2000

A/goose/Fujian/bb/2003

100

A/goose/Vietnam/3/05 2005

99 A/Duck/Hong Kong/y283/1997 A/Hong Kong/156/1997

94

93

A/duck/Shantou/195/2001 A/Chicken/Hong Kong/SF219/2001

A/Goose/Guangdong/1/96


0.002


Figure 3.5. Phylogenetic tree of M gene nucleotide sequence of A/H5N1 clade 7 strains (Established by neighbor-joining analysis using MEGA 5 software, boostrap value 1000)

Table 3.7. Identification of A/H5N1 strains used in the establishment of the M-genotype


STT


International trade

Species

battery

Capacity

set up

Place of isolation

S bank registration

gene

1

A/Goose/Guangdong/1/96

Goose

1996

China

AF144306

2

A/Hong Kong/156/1997

People

1997

Hong Kong

AF036358

3

A/Duck/Hong Kong/y283/1997

Duck

1997

Hong Kong

AF098567

4

A/duck/Zhejiang/52/2000

Duck

2000

China

AY585397

5

A/duck/Shantou/195/2001

Duck

2001

Hong Kong

CY029002

6

A/Chicken/Hong Kong/SF219/2001

Chicken

2001

China

AF509048,

7

A/chicken/Korea/es/2003

Chicken

2003

Korea

EF541460

8

A/Ck/Indonesia/2A/2003

Chicken

2003

Indonesia

AY651377

9

A/goose/Fujian/bb/2003

Goose

2003

China

DQ997402

10

A/Beijing/01/2003

People

2003

China

EF587280

11

A/duck/Hunan/1386/2003

Duck

2003

China

CY029310

12

A/Thailand/Kan353/2004 2004

People

2004

Thailand

EF541446

13

A/duck/Guangxi/351/2004

Duck

2004

China

DQ320943

14

A/Vietnam/CL100/2004

People

2004

Vietnam

DQ492986

15

A/duck/Vietnam/48/2004 2004

Duck

2004

Vietnam

DQ492944

16

A/Cambodia/P0322095/2005

People

2005

cambodia

divide

HQ200461

17

A/Indonesia/239H/2005

People

2005

Indonesia

EU146665

18

A/black-headed

goose/Qinghai/1/2005

Goose

2005

China

DQ100567

19

A/Anhui/2/2005

People

2005

China

CY060147

20

A/duck/Guiyang/3834/2005

Duck

2005

China

EF124151

21

A/chicken/Lang Son/200/2005

Chicken

2005

Vietnam

GU186717

22

A/goose/Vietnam/3/05 2005

Goose

2005

Vietnam

DQ366317

23

A/duck/Vietnam/286/2005

Duck

2005

Vietnam

DQ492958

24

A/crested myna/Hong

Kong/540/2006

Bird

2006

Hong Kong

EF12405

25

A/Indonesia/535H/2006

People

2006

Indonesia

EU146756

26

A/chicken/Shandong/A-10/2006

Chicken

2006

China

HM172139

27

A/chicken/shanxi/10/2006

Chicken

2006

China

HM172135.1

28

A/chicken/shanxi/2/2006

Chicken

2006

China

DQ914817

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Phylogenetic Tree of Nucleotide Sequence of Gen M of CC Strain IA/h5N1 Clade 7 (Established by Neighbo-Joining Analysis Using Mega 5 Software, Gi T



STT


International trade

Species

battery

Capacity

set up

Place of isolation

S bank registration

gene

29

A/Anhui/T2/2006 2006

People

2006

China

EU008577

30

A/Hunan/1/2006

People

2006

China

CY060173

31

A/Shanghai/1/2006

People

2006

China

AB462298

32

A/duck/Guangxi/150/2006

Duck

2006

China

EF124078

33

A/chicken/East Java/UT6045/2007

Chicken

2007

Indonesia

GQ122542

34

A/Indonesia/CDC1046/2007

People

2007

Indonesia

CY019411

35

A/duck/Laos/P0117/2007

Duck

2007

Laos

CY040921

36

A/Muscovy duck/Ca Mau/07-

April 2007

Goose

2007

Vietnam

GU186746

37

A/duck/India/Tr-NIV4396/2008

Duck

2008

India

CY046105

38

A/chicken/Bhutan/248006/2010

Chicken

2010

Bhutan

CY066007

39

A/mallard/Korea/1195/2010

Duck

God

2010

Korea

HQ695916

40

A/Hong Kong/6841/2010

People

2010

Hong Kong

HQ636463

41

A/chicken/Thailand/ICRC-

7356/2010

Chicken

2010

Thailand

HM590792

Based on the analysis of the gene family tree, we can conclude that the avian influenza A/H5N1 virus strains of clade 7 in Vietnam have high similarity and are arranged in a group with each other, and in a group with the influenza A/H5N1 virus strains of China. This analysis results in the M gene of the influenza A/H5N1 virus of clade 7 in Vietnam and China having the same origin. To see more clearly the genetic differences at the nucleotide and amino acid levels, we compared the genes of the influenza A/H5N1 virus strains of Vietnam with some influenza A/H5N1 viruses of China. The results are shown in Fig.

Table 3.8.

The level of genetic difference in M ​​gene between Vietnamese A/H5N1 clade 7 influenza virus strains is almost negligible, with the maximum difference in nucleotide level being 1% and amino acid level being 0.6%.

The level of difference between the Vietnamese A/H5N1 influenza virus strains belonging to clade 7 and the strains belonging to clade 7 in China is also very low. The minimum difference

The genetic diversity at the nucleotide and amino acid levels between the viruses of these two groups was 3.0±0.1% and 3.3±0.2%, respectively (virus A chicken/Shanxi/2/2006).

Comparing the genetic differences between the influenza virus strains of the clade we isolated with those of other clade viruses on the basis of genes, we found that the differences in nucleotides and amino acids were not much, only about 3.6% in nucleotides and 2-4% in amino acids. Only the two strains A goose Vietnam 3 0 and A HongKong 1 6 9 belonging to clade 0 had quite large differences: the difference in nucleotide levels was up to 10% and the difference in amino acids was up to 7%. Another AH N1 virus strain also belonging to clade 0, the A Goose Guangdong 1 96 strain, considered the ancestor of highly pathogenic AH N1 influenza virus strains, had genetic differences with the virus strains belonging to clade 0.

In Vietnam, the nucleotide level was .3±0.2% (.2-.6%) and the amino acid level was 4.2±0.2% (4.1-4.4%).

In summary, the results of phylogenetic analysis and genetic differences analysis based on the H, N1 genes of the A/H5N1 clade 7 influenza virus strains in Vietnam show that the virus strains belonging to clade 7 in Vietnam have high similarity with each other, proving that they have the same origin, and are similar to the AH N1 virus strains also belonging to the clade isolated in China.

From the above results, it can be concluded that the AH N1 influenza virus strains belonging to clade 7 in Vietnam have the same origin as the viruses belonging to clade 7 in China, and have entered Vietnam, not viruses that have evolved from highly pathogenic AH N1 influenza virus strains that previously caused disease in poultry (2003-2008) in Vietnam. The phenomenon of virus strains belonging to the clade discovered in the border area in 2008, along with the appearance of many other clades in Vietnam such as clade 2.3.4 and 2.3.2 in Vietnam, which are very similar to the AH N1 influenza virus strains circulating and causing disease in Chinese poultry, shows that the risk of infiltration and emergence of A/H5N1 influenza virus strains from outside into Vietnam is very high, so it is necessary to strengthen surveillance to detect early AH N1 influenza viruses that may invade or are circulating in Vietnamese poultry.


Table 3.8. Comparison of genetic differences in the M gene of 5 A/H5N1 virus strains belonging to clade 7

remember some reference strains


Species symbol

Strain name i 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15


Amino acids (%)

1

A/Chicken/Vietnam/NCVD-016/2008


0.6

0.3

0.3

0.3

1.6

1.3

3.5

1.9

7.4

1.9

2.1

3.8

4.4

7.4

2

A/chicken/Vietnam/NCVD-093/2008

1.0


0.3

0.3

0.3

1.6

1.3

3.5

1.9

7.4

1.9

1.8

3.8

4.4

7.4

3

A/chicken/Vietnam/NCVD-03/2008

0.9

0.3


0.0

0.0

1.3

0.9

3.2

1.6

7.1

1.6

1.8

3.5

4.1

7.1

4

A/chicken/Vietnam/NCVD-04/2008

0.9

0.3

0.2


0.0

1.3

0.9

3.2

1.6

7.1

1.6

1.8

3.5

4.1

7.1

5

A/chicken/Vietnam/NCVD-05/2008

0.9

0.3

0.2

0.0


1.3

0.9

3.2

1.6

7.1

1.6

1.8

3.5

4.1

7.1

6

A/chicken/Shandong/A-10/2006

1.3

1.3

1.2

1.2

1.2


0.9

3.8

1.6

7.4

1.6

1.8

3.5

4.4

7.4

7

A/chicken/Shanxi/10/2006

0.8

0.9

0.8

0.8

0.8

0.8


4.1

1.6

7.4

1.6

1.8

3.5

4.4

7.4

8

A/chicken/Shanxi/2/2006

3.1

3.1

2.8

2.9

2.9

2.8

3.0


3.2

7.4

3.2

3.5

5.1

5.8

7.4

9

A/Beijing/01/2003_2003

2.4

2.4

2.3

2.3

2.3

1.7

2.1

3.5


5.8

0.0

0.7

1.9

2.8

5.8

10

A/goose/Vietnam/3/05

10.0

10.1

9.7

9.7

9.7

10.0

10.4

9.3

8.7


5.8

5.7

5.8

3.8

0.0

11

A/Anhui/2/2005

3.0

3.1

3.0

3.0

3.0

2.4

2.7

4.0

0.9

8.1


0.7

1.9

2.8

5.8

12

A/blackheadedgoose/Qinghai/January 2005

3.2

3.2

3.2

3.2

3.2

2.6

2.7

4.0

1.4

9.3

1.3


2.1

3.2

5.7

13

A/goose/Fujian/bb/2003

4.0

4.1

3.8

3.8

3.8

3.4

3.7

4.4

2.1

8.1

2.0

2.3


2.8

5.8

14

A/Goose/Guangdong/1/96

5.5

5.6

5.2

5.2

5.2

5.0

5.3

5.7

3.5

6.0

3.4

3.8

3.2


3.8

15

A/Hong_Kong/156/97

10.7

10.8

10.5

10.5

10.5

10.7

11.1

9.3

9.4

1.3

8.8

9.8

8.8

7.5


Nucleotides (%)


83

3.3. Determination of biological characteristics of A/H5N1 clade 7 virus isolated in Vietnam (A/chicken/Vietnam/NCVD-016/2008)

3.3.1. Chicken breed adaptation (EID 50 specification )

Influenza viruses in general and highly pathogenic avian influenza A/H N1 viruses have the ability to grow well on chicken embryos, so 9-10 day old chicken embryos are often used to isolate highly pathogenic avian influenza viruses in diagnostic work as well as to maintain virus strains. However, avian influenza virus strains have different characteristics when multiplying on egg embryos, as shown by embryo infectivity, embryo lethality and optimal titer of virus when multiplying on egg embryos. The differences in embryo lethality time and optimal titer of different virus strains are different. Low pathogenic viruses usually kill egg embryos more slowly and can obtain higher virus concentrations than highly pathogenic influenza viruses and vice versa.

To determine the adaptability of H5N1 clade avian influenza virus strains

isolated, we chose strain A/Chicken/Vietnam/NCVD-016/2008 as the representative strain because this strain can be considered close to the original strain of the clade from China.

Embryos were obtained from healthy chicken flocks that had not been vaccinated against H N1 avian influenza, and were not naturally infected with avian influenza virus to avoid the impact (if any) of antibodies from vaccinated hens (in the yolk of the embryos). Eggs were purchased at 8 days of age and incubated for 1 day to stabilize in the laboratory before being used for the experiment to determine the adaptation of the influenza virus strain A/Chicken/Vietnam/NCVD-016 2008 on chicken embryos.

The influenza virus strain A/Chicken/Vietnam/NCVD-016/2008 was divided into many small tubes after isolation and kept at -86 0 C. Before conducting the experiment, the virus suspension was checked for sterility according to the routine and was mixed into many concentrations from 10 -1 to 10 -8 with PBS buffer solution at pH 7.2. Egg embryos were infected with 6 dilutions from 10 -3 to 10 -8 into the allantoic cavity of the egg embryo, each concentration infected

embryos with a dose of 100µl embryos, continue incubation at 37 0 C, monitor twice a day

about 8 hours within 4 days, embryos that died before 24 hours. In this experiment, 3 embryos injected with PBS solution were used as negative controls and incubated under the same conditions.

The embryos that died during the monitoring period were cooled at 2-8 0 C for 24 hours to restore blood vessels and the eggs were dissected to harvest the tissue fluid. The embryos that survived after the monitoring period (including negative controls) were all collected for tissue fluid and tested by HA reaction to determine the virus infection of the embryos and determine the EID 50 index according to the Reed-Muench formula.

Before infection, we tested the sterility of the virus tubes on the following media: meat broth, BHI, regular agar, blood agar, Sabauraud and anaerobic liver broth, with the aim of determining for sure that the death of the embryos was caused by the influenza virus. We checked the embryos twice a day, 8 hours apart, to record the details of the time of death of the embryos. The results of the time of death of the embryos are presented in Table 3.9.

The results of determining the infectivity of chicken embryos and the EID 50 index of the virus strain A/Chicken/Vietnam/NCVD-016/2008 are presented in Table 3.10.

Table 3.9. Time to lethality monitoring


TN batch

Number of infected embryos

Tracking dead embryos

Total number of dead embryos

Rate (%)

0-24 h

25-48 h

49-72 hours

73-96h

1

30

0

10

5

5

20

67

2

30

0

10

5

4

19

63

3

30

0

10

5

4

19

63

The results showed that: no embryos died before 24 hours, the virus started killing embryos within 2 days after infection. This is also consistent with our daily observations when isolating samples containing avian influenza H N1 virus on egg embryos, and also consistent with previous studies (Easterday

et al., 199; Wanasawaeng et al., 2009) observed that highly pathogenic influenza viruses usually kill embryonated eggs within 48 hours post-infection (hpi) of the urothelial sinus.

Table 3.10. Results of monitoring the survival/death ratio of eggs when infected with virus A/Chicken/Vietnam/NCVD-016/2008



Experimental times


Dilution titer

Number of infected embryos


Number of infected embryos

Number of uninfected embryos

Accumulated number

Virus infection rate (%)

A (A+B) × 100

Viral infection (A)

Not infected

(B)

Total (A+B)


First time

10 -3

5

5

0

20

0

20

100

10 -4

5

5

0

15

0

15

100

10 -5

5

5

0

10

0

10

100

10 -6

5

4

1

5

1

6

83.3

10 -7

5

1

4

1

5

6

16.7

10 -8

5

0

5

0

10

10

0

DC (-)

3

0

3





EID 50 /0.1ml

10 7 (according to the eed-Muench formula)


2nd time

10 -3

5

5

0

19

0

19

100

10 -4

5

5

0

14

0

14

100

10 -5

5

5

0

9

0

9

100

10 -6

5

3

2

4

1

5

80.0

10 -7

5

1

4

1

5

6

16.7

10 -8

5

0

5

0

10

10

0

DC (-)

3

0

3





EID 50 /0.1 ml

10 6.9 (according to the eed-Muench formula)


3rd time

10 -3

5

5

0

19

0

19

100

10 -4

5

5

0

14

0

14

100

10 -5

5

5

0

9

0

9

100

10 -6

5

3

2

4

1

5

80.0

10 -7

5

1

4

1

5

6

16.7

10 -8

5

0

5

0

10

10

0

DC (-)

3

0

3




0

EID 50 /0.1 ml

10 6.9 (according to the eed-Muench formula)

- At a dilution concentration of 10-3 , all embryos died within 40 hours after infection.

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