Abstract
A/duck/Shanghai/28-1/2009(H4N2) (DK28) was isolated from a live poultry market in Shanghai, China. Using PCR and sequencing analysis, we obtained the complete genome sequences of the DK28 virus. The sequence analysis demonstrated that this H4N2 virus was a novel multiple-gene reassortant avian influenza virus (AIV) whose genes originated from H1N1, H1N3, H3N3, H4N2, and H4N6. Knowledge regarding the complete genome sequences of the DK28 virus will be useful for epidemiological surveillance.
GENOME ANNOUNCEMENT
Avian influenza (AI) originates from birds, particularly wild waterfowl, and has been demonstrated to have 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes (1, 3). In the early 1970s, live poultry markets (LPM) had been considered to be a prolific source of avian influenza virus (AIV) (5). The H3, H4, H9, and H10 subtype AIVs have been circulating and evolving in LPM in China (4). The H4N2 subtype avian influenza virus has infected migratory water birds (1) and domestic ducks (6). In addition, the H4 avian influenza virus has infected pigs (3) and poses a threat to mammals. Thus, it is important to enhance the surveillance of H4 AIVs.
In this study, A/duck/Shanghai/28-1/2009(H4N2) (DK28) was isolated from LPM in Shanghai, China. The PCR was performed using universal primers for influenza A virus (2). The amplification products were directly sequenced, and SeqMan (DNASTAR, Madison, WI) was used to analyze the sequences.
The genome of the DK28 virus consisted of 8 segments of single-stranded RNA and was 13,602 nucleotides in length: the polymerase genes PB1 and PB2 each consisted of 2,341 nucleotides, polymerase acidic protein (PA) consisted of 2,233 nucleotides, the HA gene consisted of 1,738 nucleotides, the nucleoprotein (NP) gene consisted of 1,565 nucleotides, the NA gene consisted of 1,467 nucleotides, the matrix (M) gene consisted of 1,027 nucleotides, and the nonstructural (NS) gene consisted of 890 nucleotides.
Sequence analysis revealed that the nucleotide sequences of the HA gene of the DK28 virus were most closely related to that of the H4N6 isolate A/avian/Japan/8KI0185/2008(H4N6), with which it shared 97% nucleotide homology. The nucleotide sequences of the NA gene were most closely related to that of the H4N2 isolate A/duck/Guangxi/912/2008(H4N2), with which it shared 100% nucleotide homology. The nucleotide sequences of the PB1 and PB2 genes were most closely related to those of the H10N6 isolate A/canvasback/Mongolia/2-69/2007(H10N6) and the H3N3 isolate A/duck/Zhejiang/5/2011(H3N3), with which they shared 98% and 97% nucleotide homology, respectively. The nucleotide sequences of the PA gene were most closely related to that of the H1N2 isolate A/duck/Zhejiang/0607-13/2011(H1N2), with which it shared 98% nucleotide homology. The nucleotide sequences of the NP and M genes were most closely related to those of the H1N3 isolate A/duck/Zhejiang/0611-8/2011(H1N3) and the H1N1 isolate A/wild duck/Korea/SH13/2006(H1N1), with which they shared 98% and 99% nucleotide homology, respectively. The nucleotide sequences of the NS gene were most closely related to that of the H6N5 isolate A/aquatic bird/Korea/W69/2005(H6N5), with which it shared 98% nucleotide homology.
In conclusion, the DK28 virus isolate proved to be a novel multiple-gene reassortant AIV whose genes were derived from H1N1, H1N3, H3N3, H4N2, and H4N6.
Nucleotide sequence accession numbers.
The genome sequences of A/duck/Shanghai/28-1/2009(H4N2) have been deposited in GenBank under the accession numbers JX485426 to JX485433.
ACKNOWLEDGMENTS
This study was supported by the National Natural Science Foundation of China (grant 31172332), the Special Fund for Agro-Scientific Research in the Public Interest, China (grant 201003012), the Special Fund for International Communication and Cooperation (grant S2011ZR0429), and the National High Technology Research and Development Program of China (863 Program) (grant 2011AA10A200).
REFERENCES
- 1. Bui VN, et al. 2011. Surveillance of avian influenza virus in migratory water birds in eastern Hokkaido, Japan. J. Vet. Med. Sci. 73:209–215 [DOI] [PubMed] [Google Scholar]
- 2. Hoffmann E, Stech J, Guan Y, Webster RG, Perez DR. 2001. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146:2275–2289 [DOI] [PubMed] [Google Scholar]
- 3. Karasin AI, Brown IH, Carman S, Olsen CW. 2000. Isolation and characterization of H4N6 avian influenza viruses from pigs with pneumonia in Canada. J. Virol. 74:9322–9327 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Liu M, et al. 2003. The influenza virus gene pool in a poultry market in South Central China. Virology 305:267–275 [DOI] [PubMed] [Google Scholar]
- 5. Shortridge KF. 1992. Pandemic influenza: a zoonosis? Semin. Respir. Infect. 7:11–25 [PubMed] [Google Scholar]
- 6. Zhang H, Chen Q, Chen Z. 2012. Characterization of an H4N2 avian influenza virus isolated from domestic duck in Dongting Lake wetland in 2009. Virus Genes 44:24–31 [DOI] [PubMed] [Google Scholar]