Abstract
A total of 100 H1N1 flu real-time-PCR positive throat swabs collected from fever patients in Zhejiang, Hubei and Guangdong between June and November 2009, were provided by local CDC laboratories. After MDCK cell culture, 57 Influenza A Pandemic (H1N1) viruses were isolated and submitted for whole genome sequencing. A total of 39 HA sequences, 52 NA sequences, 36 PB2 sequences, 31 PB1 sequences, 40 PA sequences, 48 NP sequences, 51 MP sequences and 36 NS sequences were obtained, including 20 whole genome sequences. Sequence comparison revealed they shared a high degree of homology (96%∼99%) with known epidemic strains (A/California/04/2009(H1N1). Phylogenetic analysis showed that although the sequences were highly conserved, they clustered into a small number of groups with only a few distinct strains. Site analysis revealed three substitutions at loop 220 (221–228) of the HA receptor binding site in the 39 HA sequences: A/Hubei/86/2009 PKVRDQEG→PKVRDQEA, A/Zhejiang/08/2009 PKVRDQEG→PKVRDQER, A/Hubei/75/2009 PKVRDQEG→PKVRDQGG, the A/Hubei/75/2009 was isolated from an acute case, while the other two were from patients with mild symptoms. Other key sites such as 119, 274, 292 and 294 amino acids of NA protein, 627 of PB2 protein were conserved. Meanwhile, all the M2 protein sequences possessed the Ser32Asn mutation, suggesting that these viruses were resistant to adamantanes. Comparison of these sequences with other H1N1 viruses collected from the NCBI database provides insight into H1N1 transmission and circulation patterns.
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References
Belshe, Robert. 2009. Implications of the emergence of a novel H1 influenza virus. N Engl J Med. 360:2667–2668.
Bragstad K, Nielsen L P, Fomsgaard A. 2008.The evolution of human influenza A viruses from 1999 to 2006: A complete genome study. Virol J, 5(40):1–19.
CDC. 2009. Realtime RTPCR (rRTPCR) Protocol for Detection and Characterization of Swine Influenza (version2009). http://www.who.int/csr/restheces/publications/swineflu/realtimeptpcr/en/index.html.
Cinatl J Jr, Michaelis M, Doerr H W, et al. 2007. The threat of avian influenza A (H5N1). Part I: Epidemiologic concerns and virulence determinants._Med Microbiol Immunol, 196:181–190.
Deyde V M, Sheu T G, Trujillo A A, et al. 2010. Detection of Molecular Markers of Drug Resistance in 2009 Pandemic Influenza A (H1N1) Viruses by Pyrosequencing. Antimicrob Agents Ch, 54(3): 1102–1110.
Dunham E J, Dugan V G, Kaser E K, et al. 2009. Different Evolutionary Trajectories of European Avian-Like and Classical Swine H1N1 Influenza A Viruses. J Virol, 83(11): 5485–5494.
European Centre for Disease Prevention and Control special report. The 2009 A(H1N1) pandemic in Europe. http://www.ecdc.europa.eu/en/publications/Publications/101108_SPR_pandemic_experience.pdf.
Galwankar S, Clem A. 2009. Swine influenza A (H1N1) strikes a potential for global disaster. J Emerg Trauma Shock, 99–105.
Mould J A, Drury J E, Frings S M, et al. 2000. Permeation and activation of the M2 ion channel of influenza A virus. J Biol Chem, 275: 31038–31050.
Nelson M, Spiro D, Wentworth D, et al. 2009. The early diversification of influenza A/H1N1pdm. PLoS Curr, RRN1126.
Puzelli S, Facchini M, Di Martino A, et al. 2011. Evaluation of the antiviral drug susceptibility of influenza viruses in Italy from 2004/05 to 2009/10 epidemics and from the recent 2009 pandemic. Antiviral Res. 90: 205–212.
Shinde V, Bridges C B, Uyeki T M, et al. 2009. Triple-reassortant swine influenza A (H1) in humans in the United States, 2005–2009. N Engl J Med. 360:2616–2625.
Subbarao E K, London W, Murphy B R, et al. 1993. A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. J Virol, 67:1761–1764.
Wetherall N T, Trivedi T, Zeller J, et al. 2003. Evaluation of neuraminidase enzyme assays using different substrates to measure susceptibility of influenza virus clinical isolates to neuraminidase inhibitors: report of the neuraminidase inhibitor susceptibility network. J Clin Microbiol, 742–750.
World Health Organization (WHO). 2010. Update on oseltamivir-resistant pandemic A (H1N1) 2009 influenza virus. Wkly Epidemiol, 85:37–48.
Yang J R, Lin Y C, Huang Y P, et al. 2011. Reassortment and Mutations Associated with Emergence and Spread of Oseltamivir-Resistant Seasonal Influenza A/H1N1 Viruses in 2005–2009. PLoS ONE. 6(3): e18177.
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Foundation items: The Ministry of Science and Technology of China (2010CB534005, 2007FY210700, 2009ZX10004-109); the National Natural Science Foundation of China (30970024, 30900060); The National R&D Infrastructure and Facility Development Program of China under Grant No. BSDN2009-10 &18; The Chinese Academy of Sciences (KSCX2-YW-N-065, KSCX2-YW-R-157, 158 and 159; INFO-115-C01-SDB3-01, INFO-115-C01-SDB4-21, IN-FO-115-D02, IN-FO-115-C01-SDB2-02).
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Zhao, Jr., Li, Yd., Pan, Lm. et al. Genetic characteristics of 2009 pandemic H1N1 influenza a viruses isolated from Mainland China. Virol. Sin. 26, 418–427 (2011). https://doi.org/10.1007/s12250-011-3228-3
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DOI: https://doi.org/10.1007/s12250-011-3228-3