Abstract
For the first time we report the complete genomic sequence of an H11N3 influenza virus from domestic ducks in China. Phylogenetic analysis showed that the H11N3 virus was a novel reassortant with its genes from different subtypes of domestic duck-origin avian influenza viruses, which further underlined that domestic ducks play a key role in the genetic reassortment and evolution of influenza viruses in China.
GENOME ANNOUNCEMENT
Avian influenza viruses (AIV) are members of the family Orthomyxoviridae. According to the antigenicity of hemagglutinin (HA) and neuraminidase (NA), 17 HA subtypes and 10 NA subtypes are defined (8, 9). In the last 10 years, H11 viruses, which are usually mix infected with other subtypes, have been continuously detected in domestic ducks in eastern China (13). Although H11 viruses generally produce asymptomatic infections in domestic ducks, it is evidenced that they do have the potential of interspecies transmission to mammals, including human beings (1, 2, 7). Therefore, surveillance of the H11 virus in poultry could help us better understand the ecology and epidemiology of AIV.
During our routine surveillance of AIV in Jiangsu Province of eastern China in 2011, an H11N3 virus (A/duck/Jiangsu/10-d4/2011) was isolated from apparently healthy domestic ducks. The complete genomic sequence was determined by reverse transcription (RT)-PCR using the universal primer set (6) and direct sequencing for investigating genetic characteristics in detail. Based on the records in GenBank, this is the first report of the complete genomic sequence of an H11N3 virus in China.
The eight genomic segments include PB2, PB1, PA, HA, NP, NA, M, and NS genes, with the entire lengths of 2,341, 2,341, 2,233, 1,754, 1,565, 1,453, 1,027, and 890 nucleotides, respectively. The HA gene possessed Q226 and G228 (H3 numbering), showing a preferential binding of the avian influenza virus receptor. The residues of the HA cleavage site were AIASR↓G, a hallmark of low-pathogenic AIV. Seven potential N-linked glycosylation sites in HA (26, 27, 39, 181, 304, 469, and 556) and five in NA (14, 57, 66, 72, and 146) were detected. There were no changes in the length of the NA stalk region and NS1 protein. In addition, amino acids, including E-627 and D-701 of PB2 protein, K-198 and M-317 of PB1 protein, together with D-92 of NS1 protein, were shown to be conservative.
Phylogenetic analysis demonstrated that the HA gene belonged to the Eurasian H11 lineage and were closely related with A/duck/Hokkaido/W245/2004(H11N9). The remaining seven genes all had the greatest sequence identities (over 99.0%) with the low-pathogenic H1N3 and H7N3 viruses isolated from domestic ducks in Zhejiang Province in 2011 (10, 12). In addition, the PB2 and NP genes had highly similar nucleotide sequence identities of 96.3% and 96.1%, respectively, to the previously reported reassortant pathogenic virus A/duck/Zhejiang/2245/2011(H5N1) (11). Therefore, the H11N3 virus may be a novel reassortant with its genes from different subtypes of domestic duck-origin AIV, and the rapid emergence of the new H11N3 virus and the related H1N3 and H7N3 viruses highlights that domestic ducks as reassortant vessels prompt the genetic reassortment and evolution of AIV in China.
In conclusion, the genome sequence of the H11N3 virus is helpful for the analyses of ecological and epidemiological characteristics of AIV in domestic ducks in China.
Nucleotide sequence accession numbers.
The complete genomic sequence of A/duck/Jiangsu/10-d4/2011(H11N3) was deposited in GenBank under the accession numbers CY125004 to CY125011.
ACKNOWLEDGMENTS
This work was supported by the Major State Basic Research Development Program of China (973 Program) (grant 2011CB505003), the Earmarked Fund for Modern Agro-Industry Technology Research System (grant nycytx-41-G07), the National Key Technologies R&D Program of China (grant 2010BAD04B01), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT; grant IRT0978).
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