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The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2005)
Board on Global Health (BGH)

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The Threat of Pandemic Influenza: Are We Ready? - Workshop Summary

TABLE 2-1 Analysis of H5N1 Influenza viruses isolated from poultry in Hong Kong and mainland China during 2000–04

 

2000

2001

Aquatic

Terrestrial

Aquatic

Terrestrial

Sampling

Hong Kong

H5N1-Positive/ total tested

33/533

0/8,256

37/606

36/16,116

Non-H5N1 isolates

16

715

11

983

Mainland China

H5N1-Positive/ total tested

0/445

0/1,891

38/2,579

10/3,197

Non-H5N1 isolates

122

143

468

290

Total number sampled

11,125

22,498

Genetic Analysis

Hong Kong

Number of viruses analysed (genotypes detected)

11 (9Gs/Gd; 2C)

13 (4B, 9C)

24 (13A, 4B, 4C, 1D, 2E)

Mainland China

Number of viruses analysed (genotypes detected)

7 (2B, 5X0)

1 (1X0)

Number of Genotypes

2

6

Faecal droppings from apparently healthy poultry in live poultry markets in Hong Kong (2000–04), Guangdong (2000–04) and Hunan and Yunnan (2002–04) provinces were sampled monthly for influenza virus isolation. For each month that H5N1 virus was identified, one isolate was selected from each type of infected poultry for sequencing. During H5N1 disease outbreaks, additional isolates were sequenced. Of a total of 96,235 samples, 253 H5N1 virus isolates were genetically sequenced and analysed.

rise to new H9N2 reassortants (Li et al., 2003), and a similar mechanism may generate novel H5N1 reassortants.

It is notable that in the short time since its emergence in 2002, genotype Z has replaced genotypes AE, X, and Y to become dominant in both aquatic and terrestrial poultry in this region (Table 2-1). To define the genetic stability of this new gene constellation, we analysed the rates of non-synonymous (Ka) and synonymous (Ks) nucleotide substitutions in six internal gene segments of genotype Z viruses isolated in 2002–04. A Ka/Ks ratio >1 suggests evidence of positive natural selection (Presgraves et al., 2003). Of these internal genes, the M2 gene was under positive selection pressure in late 2002 to early 2003, but under less selection pressure in late 2003 to early 2004. The NS1 and NS2 genes, acquired in late 2000, were also under positive selection pressure (Supplementary Table 1).12 These

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