﻿Genome Sequence of a Novel Reassortant H3N6 Avian Influenza
Virus from Domestic Mallard Ducks in Eastern China
Qunhui Li,a Lei Zhong,a Qingqing Zhao,a Liang He,a Zhiqiang Duan,a Chaoyang Chen,a Yuxin Chen,a Min Gu,a,b Xiaoquan Wang,a,b
Xiaowen Liu,a,b Xiufan Liua,b
Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, Chinaa; Ministry of Education Key Lab for Avian Preventive
Medicine, Yangzhou University, Yangzhou, Jiangsu, Chinab
Here, we report the complete genome sequence of an H3N6 avian influenza virus (AIV) isolated from domestic ducks in Jiangsu
province of eastern China in 2010. Phylogenetic analysis showed that the H3N6 virus is a natural recombinant virus whose genes
were derived from H3N8, H4N6, H6N6, H7N7, and H11N2 AIVs. This analysis will help to understand the molecular character-
istics and evolution of the H3N6 influenza virus in eastern China.
Received 18 December 2012 Accepted 14 February 2013 Published 11 April 2013
Citation Li Q, Zhong L, Zhao Q, He L, Duan Z, Chen C, Chen Y, Gu M, Wang X, Liu X, Liu X. 2013. Genome sequence of a novel reassortant H3N6 avian influenza virus from
domestic mallard ducks in eastern China. Genome Announc. 1(2):e00223-12. doi:10.1128/genomeA.00223-12.
Copyright © 2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Xiufan Liu, xfliu@yzu.edu.cn.
Avian influenza viruses (AIV) are members of the family Or-
thomyxoviridae and have been shown to have 17 hemaggluti-
nin (HA) and 10 neuraminidase (NA) subtypes (1, 2). Some of
these subtypes have been transmitted to domestic poultry, causing
severe or mild diseases, and domestic ducks play an important role
in the transmission of influenza virus from wild aquatic birds
to terrestrial poultry (3). However, H3 avian influenza viruses
are one of the most frequently isolated subtypes from feral
ducks and also the major subtype that causes human disease (4,
5). In addition, previous studies demonstrated that some novel
H3N6 subtype viruses were reassortants between highly patho-
genic H7 and H5 viruses isolated in Eurasia (6). Therefore, it is
important to enhance the surveillance of H3 AIVs for under-
standing the genesis and emergence of novel reassortants with
pandemic potential.
In this study, strain A/duck/Jiangsu/4/2010 (H3N6) was iso-
lated from apparently healthy domestic mallard ducks in the
Jiangsu province of eastern China. The complete genomic se-
quence was determined by reverse transcription-PCR (RT-
PCR) using a universal primer set (7). The amplification prod-
ucts were purified and sequenced on an ABI 3730 capillary
DNA-sequencing instrument. MEGA5.0 software was used to
analyze the genomic sequences.
The complete genomic segments include polymerase basic 2
(PB2), PB1, polymerase acidic (PA), HA, nucleoprotein (NP),
NA, matrix (M), and nonstructural (NS) genes, with full lengths of
2,341, 2,341, 2,233, 1,765, 1,565, 1,464, 1,027, and 890 nucleo-
tides, respectively. The amino acid sequence at the cleavage site in
the HA molecule is PEKQTR2G, which is characteristic of low-
pathogenic AIV. Analysis of potential glycosylation sites of the
isolate revealed that there were 6 potential N-linked glycosylation
sites in HA (positions 8, 22, 38, 165, 285, and 483), while there
were 9 in NA (positions 51, 54, 62, 67, 70, 86, 146, 201, and 402).
Furthermore, there were no changes in the length of the NA stalk
region and the NS1 protein.
Phylogenetic analysis showed that the nucleotide sequence
identity of the HA gene with that of the H3N8 isolate A/duck/
Beijing/40/04 was 99%. The nucleotide sequence identities of the
PB2, PB1, PA, and M genes with those of the H6N6 isolate A/duck/
Jiangsu/022/2009 (H6N6) were all 99%. The nucleotide sequence
identity of the NS gene with that of the isolate A/mallard/Korea/
GH171/2007 (H7N7) was 98%. The nucleotide sequence identity of
the NA gene with that of the isolate A/chicken/India/WB-
NIV101006/2009 (H4N6) was 99%. In addition, the NP gene was
mostcloselyrelatedtothatoftheisolateA/spotbillduck/Xuyi/6/2005
(H11N2), with which it shares 99% nucleotide homology. Thus, the
H3N6 virus proved to be a novel multiple-gene reassortant AIV
whose genes were derived from H3N8, H4N6, H6N6, H7N7, and
H11N2.
Therefore, the genome information of A/duck/Jiangsu/4/2010
(H3N6) will help in analyses of the epidemiology and evolution-
ary characteristics of AIV in domestic ducks in China.
Nucleotide sequence accession numbers. The complete
genomic sequence of A/duck/Jiangsu/4/2010 (H3N6) was depos-
ited in GenBank under the accession no. KC261674 to KC261681.
ACKNOWLEDGMENTS
This work was supported by the Major State Basic Research Development
Program of China (973 Program) (grant no. 2011CB505003), the ear-
marked fund for Modern Agro-Industry Technology Research System
(grant no. nycytx-41-G07), the National Key Technologies R&D Program
of China (grant no. 2010BAD04B01), the Priority Academic Program
Development of Jiangsu Higher Education Institutions (PAPD), and the
Program for Changjiang Scholars and Innovative Research Team in Uni-
versity (PCSIRT) (grant no. IRT0978).
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