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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 A–E, 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