Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures
Table 3
Amino acid comparison with various H5 clades and maximum likelihood analysis of natural selection.
H5 virus clade
HA amino acid position1
47 (56)2
56 (65)2
177 (181)2
293 (296)2
Clade 0 ()
V
S
G
N
Clade 1 ()
V
S
G
N
Clade 2.1 ()
V
S
G
N
Clade 2.2 ()
V
S
G
N
Clade 2.3.2 ()
V
S
G
N
Clade 2.3.4 ()
V
S
G
N
Clade 2.3.4.4 ()
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)-Lung
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)-Trachea
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)-Fecal specimen
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)-Colon
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)–L3
G
R
W
H
A/Thailand/NBL1/2006 (H5N1)–T4
V
S
G
N
A/Thailand/NBL1/2006 (H5N1)–F5
V
S
G
N
dN-dS
-3.5
-2.0
-4.5
-5.7
dN/dS
0.125
0.186
0.100
0.073
value
0.995
0.980
0.998
0.999
Note: 1numbering based on A/Thailand/1(KAN-1)/2004 (H5N1). 2Numbering of the HA is based on H3 numbering. 3Virus isolate from lung. 4Virus isolate from trachea. 5Virus isolate from fecal specimen.
