﻿Full Genome Sequence of a Recombinant H5N1 Influenza Virus from
a Condor in Southern China
Peirong Jiao, Runyu Yuan, Yafen Song, Liangmeng Wei, Tao Ren, Ming Liao, and Kaijian Luo
MOA Key Laboratory for Animal Vaccine Development, Key Laboratory of Zoonoses Control and Prevention of Guangdong, College of Veterinary Medicine, South China
Agricultural University, Guangzhou, China
In this study, we report the first genomic information on an H5N1 avian influenza virus (AIV) isolated from a condor in Guang-
dong Province in southern China in 2003. Full genome sequencing and phylogenetic analyses show that it is a recombinant virus
containing genome segments derived from the Eurasia and North America gene pools. This will be useful for analyses of the evo-
lution of H5N1 AIV in southern China.
H5N1 highly pathogenic avian influenza (HPAI) is caused by
H5N1 influenza A virus, which can result in serious systemic
or respiratory diseases in birds. H5N1 avian influenza viruses
(AIV) have been reported to be transmitted from wild birds to
domestic poultry and various mammalian species (1). In 1996, the
H5N1 HPAI virus (A/Goose/Guangdong/1/1996) was first iso-
lated from a sick goose in southern China (2, 9). In 1997, the
transmission of H5N1 viruses to humans had caused the deaths of
6 of 18 infected persons in southern China (3, 8). Since 2003,
H5N1 HPAI viruses which had developed a high degree antigenic
variation began to spread and caused serious outbreaks in more
than 60 countries of Asia, Europe, and Africa, not only resulting in
the destruction of hundreds of millions of poultry but also causing
serious infection and death of humans. Therefore, H5N1 AIVs are
zoonotic agents recognized as a continuing threat to both the
poultry industry and human public health.
Here, a H5N1 influenza virus (A/Condor/Guangdong/139/
2003 [GD139]) was isolated from a sick condor in southern
China in 2003. To investigate more information about this
recombinant virus, we determined the complete genomic se-
quence with an ABI 3730 genetic analyzer using the Sanger
method, which is based on DNA fragments amplified by PCR
with a previous primer (5). Sequence fragments were assem-
bled using Sequencher 5.0. The 8 genome segments of the virus
encode 10 proteins (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1,
and NS2) with lengths of 759, 757, 716, 568, 498, 449, 252, 97,
225, and 121 amino acids, respectively. There are 20- and
5-amino-acid deletions in NA and NS1, respectively. The
GD139 virus has a series of basic amino acids at the cleavage site
of the HA (RRKKR) that is characteristic of HPAI viruses. The
receptor-binding pocket of HA1 retains the amino acid residues
Q226 and G228 (H3 numbering), which preferentially bind to the
avian influenza virus receptor (4). The PB2 protein has E and D at
positions 627 and 701, which are characteristic of the avian influ-
enza virus (6, 7).
Phylogenetic analysis of GD139 revealed that the HA and NA
genes belong to the Eurasia gene pool (A/Hong Kong/213/2003
[H5N1]-like virus) and share 99% and 94.7% nucleotide identity
with HK213-like virus, respectively. The internal genes showed
that PB1, PA, NP, M, and NS genes also belong to the Eurasia gene
pool and exhibit more than 99%, 96%, 99% and 99% sequence
identity to HK213-like virus, respectively. However, the PB2 gene
belongs to the North America gene pool and has 94% sequence
identity with the A/Pheasant/NJ/9804570/1998(H5N2) virus.
Thus, GD139 virus is a recombinant virus between the Eurasia
gene pool and the North America gene pool which has rarely been
reported in southern China.
The genomic information on this H5N1 natural recombinant
virus from a condor will be helpful for analyses of the evolution of
H5N1 AIV in southern China.
Nucleotide sequence accession numbers. The genome se-
quences of A/Condor/Guangdong/139/2003 (H5N1) have been
deposited in GenBank under accession numbers JQ966928 to
JQ966935.
ACKNOWLEDGMENTS
This work was supported by grants from the Agriculture Science and
Technology Projects of China (no. 2011GB2E000005), the Natural
Science Foundation of Guangdong Province (no. 10251064201000004
and 10151064201000021), the National Natural Science Foundation of
China (no. 31172343), the Science and Technology Projects of Guang-
dong Province (no. 2010B020307005), the Earmarked Fund for Mod-
ern Agro-Industry Technology Research System (nycytx-42-G3-03),
and the High-level Talents in University Project of Guangdong Prov-
ince.
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Received 26 April 2012 Accepted 30 April 2012
Address correspondence to Kaijian Luo, kjluo@scau.edu.cn.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
doi:10.1128/JVI.01043-12
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